JAligner-1.0/000077500000000000000000000000001216526722600130565ustar00rootroot00000000000000JAligner-1.0/LICENSE000066400000000000000000000352021216526722600140650ustar00rootroot00000000000000GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. JAligner-1.0/README000066400000000000000000000002651216526722600137410ustar00rootroot00000000000000JAligner is an open-source Java implementation of the Needleman–Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model. JAligner-1.0/README.md000066400000000000000000000005411216526722600143350ustar00rootroot00000000000000**JAligner** is an open-source Java implementation of the [Needleman–Wunsch](http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm) and [Smith-Waterman](http://en.wikipedia.org/wiki/Smith-Waterman_algorithm) algorithms for biological pairwise [sequence alignment](http://en.wikipedia.org/wiki/Sequence_alignment) with the affine gap penalty model. JAligner-1.0/build.properties000066400000000000000000000017331216526722600162770ustar00rootroot00000000000000# The project name will be the name of the jar file. project.name = jaligner # Where source files are found src.dir = ./src # Classpath class.path = ${classpath}:${java.home}/lib/javaws.jar # Intermediate directory for building class files. build.dir = ./bin # Compiler options. debug = on optimize = on deprecation = off packagename = jaligner # Javadoc options. javadoc.dir = ./api javadoc.style = jaligner.css javadoc.author = true javadoc.private = false javadoc.use = true javadoc.version = true javadoc.window.title = JAligner javadoc.doc.title = JAligner: Java implementation of Smith-Waterman for biological sequence alignment javadoc.header = JAligner javadoc.footer = javadoc.bottom = By: Ahmed Moustafa | JAligner is licensed under The GNU General Public License (GPL) JAligner-1.0/build.xml000066400000000000000000000044551216526722600147070ustar00rootroot00000000000000 JAVA_HOME: ${java.home} JAligner-1.0/src/000077500000000000000000000000001216526722600136455ustar00rootroot00000000000000JAligner-1.0/src/jaligner/000077500000000000000000000000001216526722600154405ustar00rootroot00000000000000JAligner-1.0/src/jaligner/Alignment.java000066400000000000000000000336231216526722600202300ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; import jaligner.matrix.Matrix; import jaligner.util.Commons; import java.text.DecimalFormat; /** * Holds the output of a pairwise sequences alignment. * * @author Ahmed Moustafa */ public final class Alignment { /** * Gap character */ public static final char GAP = '-'; /** * Default name for sequence #1 */ private static final String SEQUENCE1 = "jaligner_1"; /** * Default name for sequence #2 */ private static final String SEQUENCE2 = "jaligner_2"; /** * Scoring matrix */ private Matrix matrix; /** * Gap open cost */ private float open; /** * Gap extend cost */ private float extend; /** * Alignment score */ private float score; /** * Aligned sequence #1 */ private char[] sequence1; /** * Name of sequence #1 */ private String name1; /** * Alignment start location in sequence #1 */ private int start1; /** * Aligned sequence #2 */ private char[] sequence2; /** * Name of sequence #2 */ private String name2; /** * Alignment start location in sequence #2 */ private int start2; /** * Markup line */ private char[] markupLine; /** * Count of identical locations */ private int identity; /** * Count of similar locations */ private int similarity; /** * Count of gap locations */ private int gaps; private Sequence originalSequence1; private Sequence originalSequence2; /** * Constructor for Alignment */ public Alignment() { super(); } /** * @return Returns the extend. */ public float getExtend() { return extend; } /** * @param extend * The extend to set. */ public void setExtend(float extend) { this.extend = extend; } /** * @return Returns the matrix. */ public Matrix getMatrix() { return matrix; } /** * @param matrix * The matrix to set. */ public void setMatrix(Matrix matrix) { this.matrix = matrix; } /** * @return Returns the name1. */ public String getName1() { return name1 == null || name1.trim().length() == 0 ? SEQUENCE1 : name1; } /** * @param name1 * The name1 to set. */ public void setName1(String name1) { this.name1 = name1; } /** * @return Returns the name2. */ public String getName2() { return name2 == null || name2.trim().length() == 0 ? SEQUENCE2 : name2; } /** * @param name2 * The name2 to set. */ public void setName2(String name2) { this.name2 = name2; } /** * @return Returns the open. */ public float getOpen() { return open; } /** * @param open * The open to set. */ public void setOpen(float open) { this.open = open; } /** * @return Returns the score. */ public float getScore() { return score; } /** * @param score * The score to set. */ public void setScore(float score) { this.score = score; } /** * Returns the length of the alignment * * @return Alignment length */ public int getLength() { return this.sequence1.length; } /** * @return Returns the sequence1. */ public char[] getSequence1() { return sequence1; } /** * @param sequence1 * The sequence1 to set. */ public void setSequence1(char[] sequence1) { this.sequence1 = sequence1; } /** * @return Returns the sequence2. */ public char[] getSequence2() { return sequence2; } /** * @param sequence2 * The sequence2 to set. */ public void setSequence2(char[] sequence2) { this.sequence2 = sequence2; } /** * @return Returns the start1. */ public int getStart1() { return start1; } /** * @param start1 * The start1 to set. */ public void setStart1(int start1) { this.start1 = start1; } /** * @return Returns the start2. */ public int getStart2() { return start2; } /** * @param start2 * The start2 to set. */ public void setStart2(int start2) { this.start2 = start2; } /** * @return Returns the gaps. */ public int getGaps() { return gaps; } /** * @param gaps * The gaps to set. */ public void setGaps(int gaps) { this.gaps = gaps; } /** * @return Returns the identity. */ public int getIdentity() { return identity; } /** * @param identity * The identity to set. */ public void setIdentity(int identity) { this.identity = identity; } /** * @return Returns the markupLine. */ public char[] getMarkupLine() { return markupLine; } /** * @param markupLine * The markupLine to set. */ public void setMarkupLine(char[] markupLine) { this.markupLine = markupLine; } /** * @return Returns the similarity. */ public int getSimilarity() { return similarity; } /** * @param similarity * The similarity to set. */ public void setSimilarity(int similarity) { this.similarity = similarity; } /** * Returns a summary for alignment * * @return {@link String} alignment summary */ public String getSummary() { StringBuffer buffer = new StringBuffer(); DecimalFormat f1 = new DecimalFormat("0.00"); DecimalFormat f2 = new DecimalFormat("0.00%"); int length = getSequence1().length; buffer.append("Sequence #1: " + getName1()); buffer.append(Commons.getLineSeparator()); buffer.append("Sequence #2: " + getName2()); buffer.append(Commons.getLineSeparator()); buffer.append("Length #1: " + getOriginalSequence1().length()); buffer.append(Commons.getLineSeparator()); buffer.append("Length #2: " + getOriginalSequence2().length()); buffer.append(Commons.getLineSeparator()); buffer.append("Matrix: " + (matrix.getId() == null ? "" : matrix.getId())); buffer.append(Commons.getLineSeparator()); buffer.append("Gap open: " + open); buffer.append(Commons.getLineSeparator()); buffer.append("Gap extend: " + extend); buffer.append(Commons.getLineSeparator()); buffer.append("Length: " + length); buffer.append(Commons.getLineSeparator()); buffer.append("Identity: " + identity + "/" + length + " (" + f2.format(identity / (float) length) + ")"); buffer.append(Commons.getLineSeparator()); buffer.append("Similarity: " + similarity + "/" + length + " (" + f2.format(similarity / (float) length) + ")"); buffer.append(Commons.getLineSeparator()); buffer.append("Gaps: " + gaps + "/" + length + " (" + f2.format(gaps / (float) length) + ")"); buffer.append(Commons.getLineSeparator()); buffer.append("Score: " + f1.format(score)); buffer.append(Commons.getLineSeparator()); return buffer.toString(); } /** * Calculate the score of the alignment, not using the score field (the * function only uses sequence1, sequence2, matrix and gap penalties). * * @return the calculated score (By: Bram Minnaert) */ public float calculateScore() { // The calculated score float calcScore = 0; // In the previous step there was a gap in the first sequence boolean previous1wasGap = false; // In the previous step there was a gap in the second sequence boolean previous2wasGap = false; int start = 0; int end = sequence1.length - 1; char c1, c2; // the next character for (int i = start; i <= end; i++) { c1 = sequence1[i]; c2 = sequence2[i]; // the next character in the first sequence is a gap if (c1 == GAP) { if (previous1wasGap) { calcScore -= extend; } else { calcScore -= open; } previous1wasGap = true; previous2wasGap = false; } // the next character in the second sequence is a gap else if (c2 == GAP) { if (previous2wasGap) { calcScore -= extend; } else { calcScore -= open; } previous1wasGap = false; previous2wasGap = true; } // the next characters in boths sequences are not gaps else { calcScore += matrix.getScore(c1, c2); previous1wasGap = false; previous2wasGap = false; } } return calcScore; } /** * Calculate the score of the alignment without the terminal gaps. * */ public float getScoreWithNoTerminalGaps() { // The calculated score float calcScore = 0; // In the previous step there was a gap in the first sequence boolean previous1wasGap = false; // In the previous step there was a gap in the second sequence boolean previous2wasGap = false; int start = 0; int end = sequence1.length - 1; if (sequence1[start] == GAP) { while (sequence1[start] == GAP) { start++; } } else if (sequence2[start] == GAP) { while (sequence2[start] == GAP) { start++; } } if (sequence1[end] == GAP) { while (sequence1[end] == GAP) { end--; } } else if (sequence2[end] == GAP) { while (sequence2[end] == GAP) { end--; } } char c1, c2; // the next character for (int i = start; i <= end; i++) { c1 = sequence1[i]; c2 = sequence2[i]; // the next character in the first sequence is a gap if (c1 == GAP) { if (previous1wasGap) { calcScore -= extend; } else { calcScore -= open; } previous1wasGap = true; previous2wasGap = false; } // the next character in the second sequence is a gap else if (c2 == GAP) { if (previous2wasGap) { calcScore -= extend; } else { calcScore -= open; } previous1wasGap = false; previous2wasGap = true; } // the next characters in boths sequences are not gaps else { calcScore += matrix.getScore(c1, c2); previous1wasGap = false; previous2wasGap = false; } } return calcScore; } /** * Check if the calculated score matches the field score. * * @return true if equal, else false. (By: Bram Minnaert) */ public boolean checkScore() { if (calculateScore() == score) { return true; } else { return false; } } /** * Returns original {@link Sequence} #1 * * @return original {@link Sequence} #1 */ public Sequence getOriginalSequence1() { return originalSequence1; } /** * * @param originalSequence1 */ public void setOriginalSequence1(Sequence originalSequence1) { this.originalSequence1 = originalSequence1; } /** * Returns original {@link Sequence} #2 * * @return original {@link Sequence} #2 */ public Sequence getOriginalSequence2() { return originalSequence2; } /** * * @param originalSequence2 */ public void setOriginalSequence2(Sequence originalSequence2) { this.originalSequence2 = originalSequence2; } /** * Returns the number of gaps of the aligned sequence #1 * * @return the number of gaps of the aligned sequence #1 */ public int getGaps1() { int count = 0; for (int i = 0, n = sequence1.length; i < n; i++) { if (sequence1[i] == Alignment.GAP) { count++; } } return count; } /** * Returns the number of gaps of the aligned sequence #2 * * @return the number of gaps of the aligned sequence #2 */ public int getGaps2() { int count = 0; for (int i = 0, n = sequence2.length; i < n; i++) { if (sequence2[i] == Alignment.GAP) { count++; } } return count; } /** * Adds this alignment to another alignment, the order is important. * * @param a1 * The 1st alignment * @param a2 * The 2nd alignment * @return the sum of two alignment */ public static Alignment add(Alignment a1, Alignment a2) { if (a1 == null) { if (a2 == null) { return null; } else { return copy(a2); } } else { if (a2 == null) { return copy(a1); } else { Alignment sum = new Alignment(); StringBuffer buffer = new StringBuffer(); buffer.append(a1.getOriginalSequence1()); buffer.append(a2.getOriginalSequence1()); sum.setOriginalSequence1(new Sequence(buffer.toString())); buffer = new StringBuffer(); buffer.append(a1.getOriginalSequence2()); buffer.append(a2.getOriginalSequence2()); sum.setOriginalSequence2(new Sequence(buffer.toString())); buffer = new StringBuffer(); buffer.append(a1.getSequence1()); buffer.append(a2.getSequence1()); sum.setSequence1(buffer.toString().toCharArray()); buffer = new StringBuffer(); buffer.append(a1.getSequence2()); buffer.append(a2.getSequence2()); sum.setSequence2(buffer.toString().toCharArray()); buffer = new StringBuffer(); buffer.append(a1.getMarkupLine()); buffer.append(a2.getMarkupLine()); sum.setMarkupLine(buffer.toString().toCharArray()); sum.setScore(a1.getScore() + a2.getScore()); sum.setGaps(a1.getGaps() + a2.getGaps()); sum.setStart1(a1.getStart1()); sum.setStart2(a1.getStart2()); sum.setExtend(a1.getExtend()); sum.setOpen(a1.getOpen()); sum.setMatrix(a1.getMatrix()); return sum; } } } /** * Copies an alignment to another alignment. * * @param alignment * Alignment */ public static Alignment copy(Alignment alignment) { Alignment copy = new Alignment(); copy.setSequence1(alignment.getSequence1()); copy.setSequence2(alignment.getSequence2()); copy.setMarkupLine(alignment.getMarkupLine()); copy.setScore(alignment.getScore()); copy.setGaps(alignment.getGaps()); copy.setStart1(alignment.getStart1()); copy.setStart2(alignment.getStart2()); copy.setExtend(alignment.getExtend()); copy.setOpen(alignment.getOpen()); copy.setMatrix(alignment.getMatrix()); copy.setOriginalSequence1(alignment.getOriginalSequence1()); copy.setOriginalSequence2(alignment.getOriginalSequence2()); return copy; } }JAligner-1.0/src/jaligner/Cell.java000066400000000000000000000036771216526722600171770ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; /** * A cell in a similarity matrix, to hold row, column and score. * * @author Ahmed Moustafa */ public class Cell { /** * Row of the cell */ private int row; /** * Column of the cell */ private int col; /** * Alignment score at this cell */ private float score; /** * Constructor */ public Cell() { super(); this.row = 0; this.col = 0; this.score = Float.NEGATIVE_INFINITY; } /** * @return Returns the col. */ public int getCol() { return this.col; } /** * @param col The col to set. */ public void setCol(int col) { this.col = col; } /** * @return Returns the row. */ public int getRow() { return this.row; } /** * @param row The row to set. */ public void setRow(int row) { this.row = row; } /** * @return Returns the score. */ public float getScore() { return this.score; } /** * @param score The score to set. */ public void setScore(float score) { this.score = score; } /** * Sets the row, column and score of the cell. * @param row The row to set. * @param col The col to set. * @param score The score to set. */ public void set(int row, int col, float score) { this.row = row; this.col = col; this.score = score; } }JAligner-1.0/src/jaligner/Directions.java000066400000000000000000000021751216526722600204130ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; /** * Traceback directions. * * @author Ahmed Moustafa */ public abstract class Directions { /** * Traceback direction stop */ public static final byte STOP = 0; /** * Traceback direction left */ public static final byte LEFT = 1; /** * Traceback direction diagonal */ public static final byte DIAGONAL = 2; /** * Traceback direction up */ public static final byte UP = 3; }JAligner-1.0/src/jaligner/Markups.java000066400000000000000000000022501216526722600177240ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; /** * Markups line characters. * * @author Ahmed Moustafa */ public abstract class Markups { /** * Markup line identity character */ public static final char IDENTITY = '|'; /** * Markup line similarity character */ public static final char SIMILARITY = ':'; /** * Markup line gap character */ public static final char GAP = ' '; /** * Markup line mismatch character */ public static final char MISMATCH = '.'; } JAligner-1.0/src/jaligner/NeedlemanWunsch.java000066400000000000000000000216371216526722600213740ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; import jaligner.matrix.Matrix; /** * An implementation of the Needleman-Wunsch algorithm for biological global * pairwise sequence alignment. * *
* Reference: Advanced * Dynamic Programming Tutorial. * * * @author Ahmed Moustafa */ public final class NeedlemanWunsch { /** * Hidden constructor */ private NeedlemanWunsch() { super(); } /** * Aligns two sequences by Needleman-Wunsch (global) * * @param s1 * sequene #1 ({@link Sequence}) * @param s2 * sequene #2 ({@link Sequence}) * @param matrix * scoring matrix ({@link Matrix}) * @param gap * open gap penalty * @return alignment object contains the two aligned sequences, the * alignment score and alignment statistics * @see Sequence * @see Matrix */ public static Alignment align(Sequence s1, Sequence s2, Matrix matrix, float gap) { float[][] scores = matrix.getScores(); int m = s1.length() + 1; int n = s2.length() + 1; byte[][] pointers = new byte[m][n]; // Initializes the element (0,0) of the traceback matrix to STOP. pointers[0][0] = Directions.STOP; // Initializes the boundaries of the traceback matrix. for (int i = 1; i < m; i++) { pointers[i][0] = Directions.UP; } for (int j = 1; j < n; j++) { pointers[0][j] = Directions.LEFT; } Cell cell = construct(s1, s2, scores, gap, pointers); Alignment alignment = traceback(s1, s2, matrix, pointers, cell); alignment.setOriginalSequence1(s1); alignment.setOriginalSequence2(s2); alignment.setMatrix(matrix); alignment.setOpen(gap); alignment.setExtend(gap); if (s1.getId() != null) { alignment.setName1(s1.getId()); } if (s2.getId() != null) { alignment.setName2(s2.getId()); } return alignment; } /** * Constructs directions matrix for the traceback. * * @param s1 * sequence #1 * @param s2 * sequence #2 * @param matrix * scoring matrix * @param gap * gap penalty * @param pointers * traceback matrix * * @return The cell where the traceback starts. */ private static Cell construct(Sequence s1, Sequence s2, float[][] matrix, float gap, byte[][] pointers) { Cell cell = new Cell(); char[] a1 = s1.toArray(); char[] a2 = s2.toArray(); int m = s1.length() + 1; // number of rows in similarity matrix int n = s2.length() + 1; // number of columns in similarity matrix // float[] v = new float[n]; // optimal alignment float[] v = new float[n]; // Initialization of v for (int j = 1; j < n; j++) { v[j] = j * -gap; } v[0] = 0; float x, y, z; float vOld = 0; // Fill the matrices for (int i = 1; i < m; i++) { // for all rows v[0] = i * -gap; for (int j = 1; j < n; j++) { // for all columns x = v[j] - gap; y = v[j - 1] - gap; z = vOld + matrix[a1[i - 1]][a2[j - 1]]; vOld = v[j]; v[j] = maximum(x, y, z); // Determine the traceback direction if (v[j] == x) { pointers[i][j] = Directions.UP; } else if (v[j] == y) { pointers[i][j] = Directions.LEFT; } else { pointers[i][j] = Directions.DIAGONAL; } } // loop columns vOld = i * -gap; } // loop rows // cell contains the row number, the column number // and the score of the cell with the maximum score // Set the traceback start at the last cell m, n // because we are doing global alignment cell.set(m - 1, n - 1, v[n - 1]); return cell; } /** * Returns the alignment of two sequences based on the passed array of * pointers * * @param s1 * sequence #1 * @param s2 * sequence #2 * @param m * scoring matrix * @param pointers * traceback matrix * @param cell * The cell where the traceback starts. * @return {@link Alignment} with the two aligned sequences and alignment * score. * @see Cell * @see Alignment */ private static Alignment traceback(Sequence s1, Sequence s2, Matrix m, byte[][] pointers, Cell cell) { char[] array1 = s1.toArray(); char[] array2 = s2.toArray(); float[][] scores = m.getScores(); Alignment alignment = new Alignment(); alignment.setScore(cell.getScore()); // maximum length after the aligned sequences int maxlen = s1.length() + s2.length(); char[] reversed1 = new char[maxlen]; // reversed sequence #1 char[] reversed2 = new char[maxlen]; // reversed sequence #2 char[] reversed3 = new char[maxlen]; // reversed markup int len1 = 0; // length of sequence #1 after alignment int len2 = 0; // length of sequence #2 after alignment int len3 = 0; // length of the markup line int identity = 0; // count of identitcal pairs int similarity = 0; // count of similar pairs int gaps = 0; // count of gaps char c1, c2; int i = cell.getRow(); // traceback start row int j = cell.getCol(); // traceback start col // Traceback flag, where true => continue and false => stop boolean stillGoing = true; while (stillGoing) { switch (pointers[i][j]) { case Directions.UP: reversed1[len1++] = array1[--i]; reversed2[len2++] = Alignment.GAP; reversed3[len3++] = Markups.GAP; gaps++; break; case Directions.DIAGONAL: c1 = array1[--i]; c2 = array2[--j]; reversed1[len1++] = c1; reversed2[len2++] = c2; if (c1 == c2) { reversed3[len3++] = Markups.IDENTITY; identity++; similarity++; } else if (scores[c1][c2] > 0) { reversed3[len3++] = Markups.SIMILARITY; similarity++; } else { reversed3[len3++] = Markups.MISMATCH; } break; case Directions.LEFT: reversed1[len1++] = Alignment.GAP; reversed2[len2++] = array2[--j]; reversed3[len3++] = Markups.GAP; gaps++; break; case Directions.STOP: stillGoing = false; } } alignment.setSequence1(reverse(reversed1, len1)); alignment.setStart1(i); alignment.setSequence2(reverse(reversed2, len2)); alignment.setStart2(j); alignment.setMarkupLine(reverse(reversed3, len3)); alignment.setIdentity(identity); alignment.setGaps(gaps); alignment.setSimilarity(similarity); return alignment; } /** * Returns the maximum of two float numbers. * * @param a * float #1 * @param b * float #2 * @param c * float #3 * @return the maximum of a and b */ private static float maximum(float a, float b, float c) { if (a > b) { return a > c ? a : c; } else { return b > c ? b : c; } } /** * Reverses an array of chars * * @param a * @param len * @return the input array of char reserved */ private static char[] reverse(char[] a, int len) { char[] b = new char[len]; for (int i = len - 1, j = 0; i >= 0; i--, j++) { b[j] = a[i]; } return b; } }JAligner-1.0/src/jaligner/NeedlemanWunschGotoh.java000066400000000000000000000245361216526722600223760ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; import jaligner.matrix.Matrix; import java.util.logging.Logger; /** * An implementation of the Needleman-Wunsch algorithm with Gotoh's improvement * for biological global pairwise sequence alignment. * * @author Ahmed Moustafa * @author Bram Minnaert */ public final class NeedlemanWunschGotoh { /** * Logger */ private static final Logger logger = Logger .getLogger(NeedlemanWunschGotoh.class.getSimpleName()); /** * Hidden constructor */ private NeedlemanWunschGotoh() { super(); } /** * Aligns two sequences by Needleman-Wunsch (global) * * @param s1 * sequene #1 ({@link Read}) * @param s2 * sequene #2 ({@link Read}) * @param matrix * scoring matrix ({@link Matrix}) * @param o * open gap penalty * @param e * extend gap penalty * @return alignment object contains the two aligned sequences, the * alignment score and alignment statistics * @see Read * @see Matrix */ public static Alignment align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) { float[][] scores = matrix.getScores(); Sequence _s1; Sequence _s2; if (s1.length() < s2.length()) { _s1 = s2; _s2 = s1; } else { _s1 = s1; _s2 = s2; } int m = _s1.length() + 1; int n = _s2.length() + 1; byte[] pointers = new byte[m * n]; int[] lengths = new int[m * n]; // Initializes the element (0,0) of the traceback matrix to STOP. pointers[0] = Directions.STOP; // Initializes the boundaries of the traceback matrix. for (int i = 1, k = n; i < m; i++, k += n) { pointers[k] = Directions.UP; lengths[k] = i; } for (int j = 1; j < n; j++) { pointers[j] = Directions.LEFT; lengths[j] = j; } Cell cell = construct(_s1, _s2, scores, o, e, pointers, lengths); Alignment alignment = traceback(_s1, _s2, matrix, pointers, cell, lengths); alignment.setMatrix(matrix); alignment.setOpen(o); alignment.setExtend(e); alignment.setName1(_s1.getId()); alignment.setName2(_s2.getId()); alignment.setOriginalSequence1(_s1); alignment.setOriginalSequence2(_s2); return alignment; } /** * Constructs directions matrix for the traceback. * * @param s1 * sequence #1 * @param s2 * sequence #2 * @param matrix * scoring matrix * @param o * open gap penalty * @param e * extend gap penalty * @param pointers * traceback matrix * * @return The cell where the traceback starts. */ private static Cell construct(Sequence s1, Sequence s2, float[][] matrix, float o, float e, byte[] pointers, int[] lengths) { logger.info("Started..."); char[] a1 = s1.toArray(); char[] a2 = s2.toArray(); int m = s1.length() + 1; // number of rows in similarity matrix int n = s2.length() + 1; // number of columns in similarity matrix float[] v = new float[n]; float vDiagonal = 0;// Float.NEGATIVE_INFINITY; // best score in cell float f = Float.NEGATIVE_INFINITY; // score from diagonal float h = Float.NEGATIVE_INFINITY; // best score ending with gap from // left float[] g = new float[n]; // best score ending with gap from above // Initialization of v and g g[0] = Float.NEGATIVE_INFINITY; for (int j = 1; j < n; j++) { v[j] = 0;// -o - (j - 1) * e; g[j] = Float.NEGATIVE_INFINITY; } int lengthOfHorizontalGap = 0; int[] lengthOfVerticalGap = new int[n]; float similarityScore; float maximumScore = Float.NEGATIVE_INFINITY; int maxi = 0; int maxj = 0; // Fill the matrices for (int i = 1, k = n; i < m; i++, k += n) { // for all rows v[0] = -o - (i - 1) * e; for (int j = 1, l = k + 1; j < n; j++, l++) { // for all columns similarityScore = matrix[a1[i - 1]][a2[j - 1]]; f = vDiagonal + similarityScore;// from diagonal // Which cell from the left? if (h - e >= v[j - 1] - o) { h -= e; lengthOfHorizontalGap++; } else { h = v[j - 1] - o; lengthOfHorizontalGap = 1; } // Which cell from above? if (g[j] - e >= v[j] - o) { g[j] = g[j] - e; lengthOfVerticalGap[j] = lengthOfVerticalGap[j] + 1; } else { g[j] = v[j] - o; lengthOfVerticalGap[j] = 1; } vDiagonal = v[j]; v[j] = maximum(f, g[j], h); // best one if (v[j] > maximumScore) { maximumScore = v[j]; maxi = i; maxj = j; } // Determine the traceback direction if (v[j] == f) { pointers[l] = Directions.DIAGONAL; } else if (v[j] == g[j]) { pointers[l] = Directions.UP; lengths[l] = lengthOfVerticalGap[j]; } else if (v[j] == h) { pointers[l] = Directions.LEFT; lengths[l] = lengthOfHorizontalGap; } } // loop columns // Reset h = Float.NEGATIVE_INFINITY; vDiagonal = 0;// -o - (i - 1) * e; lengthOfHorizontalGap = 0; } // loop rows Cell cell = new Cell(); cell.set(maxi, maxj, v[n - 1]); logger.info("Finished."); return cell; } /** * Returns the alignment of two sequences based on the passed array of * pointers * * @param s1 * sequence #1 * @param s2 * sequence #2 * @param m * scoring matrix * @param pointers * traceback matrix * @param cell * The cell where the traceback starts. * @return {@link Alignment} with the two aligned sequences and alignment * score. * @see Cell * @see Alignment */ private static Alignment traceback(Sequence s1, Sequence s2, Matrix m, byte[] pointers, Cell cell, int[] lengths) { logger.info("Started..."); char[] array1 = s1.toArray(); char[] array2 = s2.toArray(); float[][] scores = m.getScores(); Alignment alignment = new Alignment(); alignment.setScore(cell.getScore()); // maximum length after the aligned sequences int maxlen = s1.length() + s2.length(); char[] reversed1 = new char[maxlen]; // reversed sequence #1 char[] reversed2 = new char[maxlen]; // reversed sequence #2 char[] reversed3 = new char[maxlen]; // reversed markup int len1 = 0; // length of sequence #1 after alignment int len2 = 0; // length of sequence #2 after alignment int len3 = 0; // length of the markup line int identity = 0; // count of identitcal pairs int similarity = 0; // count of similar pairs int gaps = 0; // count of gaps char c1, c2; int i = cell.getRow(); // traceback start row int j = cell.getCol(); // traceback start col int n = s2.length() + 1; int row = i * n; int a = s1.length() - 1; int b = s2.length() - 1; if (a - i > b - j) { for (; a - i > b - j; a--) { reversed1[len1++] = array1[a]; reversed2[len2++] = Alignment.GAP; reversed3[len3++] = Markups.GAP; gaps++; } for (; b > j - 1; a--, b--) { c1 = array1[a]; c2 = array2[b]; reversed1[len1++] = c1; reversed2[len2++] = c2; if (c1 == c2) { reversed3[len3++] = Markups.IDENTITY; identity++; similarity++; } else if (scores[c1][c2] > 0) { reversed3[len3++] = Markups.SIMILARITY; similarity++; } else { reversed3[len3++] = Markups.MISMATCH; } } } else { for (; b - j > a - i; b--) { reversed1[len1++] = Alignment.GAP; reversed2[len2++] = array2[b]; reversed3[len3++] = Markups.GAP; gaps++; } for (; a > i - 1; a--, b--) { c1 = array1[a]; c2 = array2[b]; reversed1[len1++] = c1; reversed2[len2++] = c2; if (c1 == c2) { reversed3[len3++] = Markups.IDENTITY; identity++; similarity++; } else if (scores[c1][c2] > 0) { reversed3[len3++] = Markups.SIMILARITY; similarity++; } else { reversed3[len3++] = Markups.MISMATCH; } } } // Traceback flag, where true => continue and false => stop boolean stillGoing = true; while (stillGoing) { int l = row + j; switch (pointers[l]) { case Directions.UP: for (int k = 0, len = lengths[l]; k < len; k++) { reversed1[len1++] = array1[--i]; reversed2[len2++] = Alignment.GAP; reversed3[len3++] = Markups.GAP; row -= n; gaps++; } break; case Directions.DIAGONAL: c1 = array1[--i]; c2 = array2[--j]; reversed1[len1++] = c1; reversed2[len2++] = c2; row -= n; if (c1 == c2) { reversed3[len3++] = Markups.IDENTITY; identity++; similarity++; } else if (scores[c1][c2] > 0) { reversed3[len3++] = Markups.SIMILARITY; similarity++; } else { reversed3[len3++] = Markups.MISMATCH; } break; case Directions.LEFT: for (int k = 0, len = lengths[l]; k < len; k++) { reversed1[len1++] = Alignment.GAP; reversed2[len2++] = array2[--j]; reversed3[len3++] = Markups.GAP; gaps++; } break; case Directions.STOP: stillGoing = false; } } alignment.setSequence1(reverse(reversed1, len1)); alignment.setStart1(i); alignment.setSequence2(reverse(reversed2, len2)); alignment.setStart2(j); alignment.setMarkupLine(reverse(reversed3, len3)); alignment.setIdentity(identity); alignment.setGaps(gaps); alignment.setSimilarity(similarity); logger.info("Finished."); return alignment; } /** * Returns the maximum of two float numbers. * * @param a * float #1 * @param b * float #2 * @param c * float #3 * @return the maximum of a and b */ private static float maximum(float a, float b, float c) { if (a > b) { return a > c ? a : c; } else { return b > c ? b : c; } } /** * Reverses an array of chars * * @param a * @param len * @return the input array of char reserved */ private static char[] reverse(char[] a, int len) { char[] b = new char[len]; for (int i = len - 1, j = 0; i >= 0; i--, j++) { b[j] = a[i]; } return b; } }JAligner-1.0/src/jaligner/Sequence.java000066400000000000000000000106501216526722600200550ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; import jaligner.util.Commons; import java.io.Serializable; /** * A basic (nucleic or protein) sequence. It's a wrapper to * {@link java.lang.String}. * * @author Ahmed Moustafa */ public class Sequence implements Serializable { /** * */ private static final long serialVersionUID = 3256721801357898297L; /** * Sequence type nucleic. */ public static final int NUCLEIC = 0; /** * Sequence type protein. */ public static final int PROTEIN = 1; /** * Sequence */ private String sequence; /** * Sequence id. */ private String id = null; /** * Sequence description. */ private String description = null; /** * Sequence type. */ private int type = PROTEIN; /** * Constructor */ public Sequence() { super(); } /** * Constructor * * @param sequence */ public Sequence(String sequence) { super(); this.sequence = sequence; } /** * Constructor * * @param name * @param sequence */ public Sequence(String name, char[] sequence) { super(); this.id = name; this.sequence = new String(sequence); } /** * Constructor * * @param name * @param sequence */ public Sequence(String name, String sequence) { super(); this.id = name; this.sequence = sequence; } /** * Constructor * * @param sequence * @param id * @param description * @param type */ public Sequence(String sequence, String id, String description, int type) { super(); this.sequence = sequence; this.id = id; this.description = description; this.type = type; } /** * Returns the sequence string * * @return Returns the sequence */ public String getSequence() { return sequence; } /** * Sets the sequence string * * @param sequence * The sequence to set */ public void setSequence(String sequence) { this.sequence = sequence; } /** * Returns the sequence id * * @return Returns the id */ public String getId() { return id; } /** * Sets the sequence id * * @param id * The id to set */ public void setId(String id) { this.id = id; } /** * Returns the sequence description * * @return Returns the description */ public String getDescription() { return description; } /** * Sets the sequence description * * @param description * The description to set */ public void setDescription(String description) { this.description = description; } /** * Returns the sequence type (nucleic or protein) * * @return Returns the type */ public int getType() { return type; } /** * Sets the sequence type (nucleic or protein) * * @param type * The type to set */ public void setType(int type) { this.type = type; } /** * Returns the length of the sequence * * @return sequence length */ public int length() { return this.sequence.length(); } /** * Returns a subsequence * * @param index * start index * @param length * length of subsequence * @return subsequence */ public String subsequence(int index, int length) { return this.sequence.substring(index, index + length); } /** * Returns the acid at specific location in the sequence * * @param index * @return acid at index */ public char acidAt(int index) { return this.sequence.charAt(index); } /** * Returns the sequence as an array of characters. * * @return array of chars. */ public char[] toArray() { return this.sequence.toCharArray(); } /** * Returns the sequence id and the sequence string * * @return sequence id and the sequence string */ @Override public String toString() { return id + Commons.TAB + sequence; } }JAligner-1.0/src/jaligner/SmithWatermanGotoh.java000066400000000000000000000241631216526722600220750ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; import jaligner.matrix.Matrix; import java.util.logging.Logger; /** * An implementation of the Smith-Waterman algorithm with Gotoh's improvement * for biological local pairwise sequence alignment. * * Recursive definition: * * * @author Ahmed Moustafa */ public final class SmithWatermanGotoh { /** * Hidden constructor */ private SmithWatermanGotoh() { super(); } /** * Logger */ private static final Logger logger = Logger .getLogger(SmithWatermanGotoh.class.getName()); /** * Aligns two sequences by Smith-Waterman (local) * * @param s1 * sequene #1 ({@link Sequence}) * @param s2 * sequene #2 ({@link Sequence}) * @param matrix * scoring matrix ({@link Matrix}) * @param o * open gap penalty * @param e * extend gap penalty * @return alignment object contains the two aligned sequences, the * alignment score and alignment statistics * @see Sequence * @see Matrix */ public static Alignment align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) { logger.info("Started..."); long start = System.currentTimeMillis(); float[][] scores = matrix.getScores(); int m = s1.length() + 1; int n = s2.length() + 1; byte[] pointers = new byte[m * n]; // Initializes the boundaries of the traceback matrix to STOP. for (int i = 0, k = 0; i < m; i++, k += n) { pointers[k] = Directions.STOP; } for (int j = 1; j < n; j++) { pointers[j] = Directions.STOP; } short[] sizesOfVerticalGaps = new short[m * n]; short[] sizesOfHorizontalGaps = new short[m * n]; for (int i = 0, k = 0; i < m; i++, k += n) { for (int j = 0; j < n; j++) { sizesOfVerticalGaps[k + j] = sizesOfHorizontalGaps[k + j] = 1; } } Cell cell = SmithWatermanGotoh.construct(s1, s2, scores, o, e, pointers, sizesOfVerticalGaps, sizesOfHorizontalGaps); Alignment alignment = SmithWatermanGotoh.traceback(s1, s2, matrix, pointers, cell, sizesOfVerticalGaps, sizesOfHorizontalGaps); alignment.setOriginalSequence1(s1); alignment.setOriginalSequence2(s2); alignment.setMatrix(matrix); alignment.setOpen(o); alignment.setExtend(e); if (s1.getId() != null) { alignment.setName1(s1.getId()); } if (s2.getId() != null) { alignment.setName2(s2.getId()); } String msg = "Finished in " + (System.currentTimeMillis() - start) + " milliseconds"; logger.info(msg); return alignment; } /** * Constructs directions matrix for the traceback * * @param s1 * sequence #1 * @param s2 * sequence #2 * @param matrix * scoring matrix * @param o * open gap penalty * @param e * extend gap penalty * @return The cell where the traceback starts. */ private static Cell construct(Sequence s1, Sequence s2, float[][] matrix, float o, float e, byte[] pointers, short[] sizesOfVerticalGaps, short[] sizesOfHorizontalGaps) { logger.info("Started..."); long start = System.currentTimeMillis(); char[] a1 = s1.toArray(); char[] a2 = s2.toArray(); int m = s1.length() + 1; int n = s2.length() + 1; float f; // score of alignment x1...xi to y1...yi if xi aligns to yi float[] g = new float[n]; // score if xi aligns to a gap after yi float h; // score if yi aligns to a gap after xi float[] v = new float[n]; // best score of alignment x1...xi to // y1...yi float vDiagonal; g[0] = Float.NEGATIVE_INFINITY; h = Float.NEGATIVE_INFINITY; v[0] = 0; for (int j = 1; j < n; j++) { g[j] = Float.NEGATIVE_INFINITY; v[j] = 0; } float similarityScore, g1, g2, h1, h2; Cell cell = new Cell(); for (int i = 1, k = n; i < m; i++, k += n) { h = Float.NEGATIVE_INFINITY; vDiagonal = v[0]; for (int j = 1, l = k + 1; j < n; j++, l++) { similarityScore = matrix[a1[i - 1]][a2[j - 1]]; // Fill the matrices f = vDiagonal + similarityScore; g1 = g[j] - e; g2 = v[j] - o; if (g1 > g2) { g[j] = g1; sizesOfVerticalGaps[l] = (short) (sizesOfVerticalGaps[l - n] + 1); } else { g[j] = g2; } h1 = h - e; h2 = v[j - 1] - o; if (h1 > h2) { h = h1; sizesOfHorizontalGaps[l] = (short) (sizesOfHorizontalGaps[l - 1] + 1); } else { h = h2; } vDiagonal = v[j]; v[j] = maximum(f, g[j], h, 0); // Determine the traceback direction if (v[j] == 0) { pointers[l] = Directions.STOP; } else if (v[j] == f) { pointers[l] = Directions.DIAGONAL; } else if (v[j] == g[j]) { pointers[l] = Directions.UP; } else { pointers[l] = Directions.LEFT; } // Set the traceback start at the current cell i, j and score if (v[j] > cell.getScore()) { cell.set(i, j, v[j]); } } } String msg = "Finished in " + (System.currentTimeMillis() - start) + " milliseconds"; logger.info(msg); return cell; } /** * Returns the alignment of two sequences based on the passed array of * pointers * * @param s1 * sequence #1 * @param s2 * sequence #2 * @param m * scoring matrix * @param cell * The cell where the traceback starts. * @return {@link Alignment}with the two aligned sequences and alignment * score. * @see Cell * @see Alignment */ private static Alignment traceback(Sequence s1, Sequence s2, Matrix m, byte[] pointers, Cell cell, short[] sizesOfVerticalGaps, short[] sizesOfHorizontalGaps) { logger.info("Started..."); long start = System.currentTimeMillis(); char[] a1 = s1.toArray(); char[] a2 = s2.toArray(); float[][] scores = m.getScores(); int n = s2.length() + 1; Alignment alignment = new Alignment(); alignment.setScore(cell.getScore()); int maxlen = s1.length() + s2.length(); // maximum length after the // aligned sequences char[] reversed1 = new char[maxlen]; // reversed sequence #1 char[] reversed2 = new char[maxlen]; // reversed sequence #2 char[] reversed3 = new char[maxlen]; // reversed markup int len1 = 0; // length of sequence #1 after alignment int len2 = 0; // length of sequence #2 after alignment int len3 = 0; // length of the markup line int identity = 0; // count of identitcal pairs int similarity = 0; // count of similar pairs int gaps = 0; // count of gaps char c1, c2; int i = cell.getRow(); // traceback start row int j = cell.getCol(); // traceback start col int k = i * n; boolean stillGoing = true; // traceback flag: true -> continue & false // -> stop while (stillGoing) { switch (pointers[k + j]) { case Directions.UP: for (int l = 0, len = sizesOfVerticalGaps[k + j]; l < len; l++) { reversed1[len1++] = a1[--i]; reversed2[len2++] = Alignment.GAP; reversed3[len3++] = Markups.GAP; k -= n; gaps++; } break; case Directions.DIAGONAL: c1 = a1[--i]; c2 = a2[--j]; k -= n; reversed1[len1++] = c1; reversed2[len2++] = c2; if (c1 == c2) { reversed3[len3++] = Markups.IDENTITY; identity++; similarity++; } else if (scores[c1][c2] > 0) { reversed3[len3++] = Markups.SIMILARITY; similarity++; } else { reversed3[len3++] = Markups.MISMATCH; } break; case Directions.LEFT: for (int l = 0, len = sizesOfHorizontalGaps[k + j]; l < len; l++) { reversed1[len1++] = Alignment.GAP; reversed2[len2++] = a2[--j]; reversed3[len3++] = Markups.GAP; gaps++; } break; case Directions.STOP: stillGoing = false; } } alignment.setSequence1(reverse(reversed1, len1)); alignment.setStart1(i); alignment.setSequence2(reverse(reversed2, len2)); alignment.setStart2(j); alignment.setMarkupLine(reverse(reversed3, len3)); alignment.setIdentity(identity); alignment.setGaps(gaps); alignment.setSimilarity(similarity); String msg = "Finished in " + (System.currentTimeMillis() - start) + " milliseconds"; logger.info(msg); return alignment; } /** * Returns the maximum of 4 float numbers. * * @param a * float #1 * @param b * float #2 * @param c * float #3 * @param d * float #4 * @return The maximum of a, b, c and d. */ private static float maximum(float a, float b, float c, float d) { if (a > b) { if (a > c) { return a > d ? a : d; } else { return c > d ? c : d; } } else if (b > c) { return b > d ? b : d; } else { return c > d ? c : d; } } /** * Reverses an array of chars * * @param a * @param len * @return the input array of char reserved */ private static char[] reverse(char[] a, int len) { char[] b = new char[len]; for (int i = len - 1, j = 0; i >= 0; i--, j++) { b[j] = a[i]; } return b; } }JAligner-1.0/src/jaligner/TracebackNode.java000066400000000000000000000035031216526722600207710ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner; /** * Traceback node * * @author Bram Minnaert * @author Ahmed Moustafa */ public final class TracebackNode { /** * Direction */ private byte direction; /** * Length of gap (for up and left directions) */ private int length; /** * Constructor */ public TracebackNode() { super(); } /** * Sets the direction to diagonal * */ public void setDiagonal() { direction = Directions.DIAGONAL; length = 0; } /** * Sets the direction to up * * @param length * length of gap */ public void setUp(int length) { direction = Directions.UP; this.length = length; } /** * Sets the direction to left * * @param length * length of gap */ public void setLeft(int length) { direction = Directions.LEFT; this.length = length; } /** * Sets the direction to stop */ public void setStop() { direction = Directions.STOP; length = 0; } /** * @return Returns the direction. */ public byte getDirection() { return direction; } /** * @return Returns the length. */ public int getLength() { return length; } }JAligner-1.0/src/jaligner/example/000077500000000000000000000000001216526722600170735ustar00rootroot00000000000000JAligner-1.0/src/jaligner/example/NeedlemanWunschExample.java000066400000000000000000000043121216526722600243320ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.example; import jaligner.Alignment; import jaligner.NeedlemanWunsch; import jaligner.Sequence; import jaligner.formats.Pair; import jaligner.matrix.Matrix; import jaligner.matrix.MatrixGenerator; import jaligner.util.SequenceParser; import java.util.logging.Level; import java.util.logging.Logger; /** * Example of using JAligner API to perform global pairwise sequence alignment * with Needleman-Wunsch algorithm {@link jaligner.NeedlemanWunsch}. * * @author Ahmed Moustafa */ public class NeedlemanWunschExample { /** * Logger */ private static final Logger logger = Logger .getLogger(NeedlemanWunschExample.class.getName()); /** * * @param args */ public static void main(String[] args) { try { logger.info("Running example..."); Sequence s1 = SequenceParser.parse("GAATTCAGTTA"); Sequence s2 = SequenceParser.parse("GGATCGA"); float match = 2; float mismatch = -1; Matrix matrix = MatrixGenerator.generate(match, mismatch); float gap = 2; Alignment alignment = NeedlemanWunsch.align(s1, s2, matrix, gap); System.out.println(alignment.getSummary()); System.out.println(new Pair().format(alignment)); logger.info("Finished running example"); } catch (Exception e) { logger.log(Level.SEVERE, "Failed running example: " + e.getMessage(), e); } } }JAligner-1.0/src/jaligner/example/NeedlemanWunschGotohExample.java000066400000000000000000000060501216526722600253340ustar00rootroot00000000000000/* * $Id: NeedlemanWunschGotohExample.java,v 1.1 2006/02/03 05:00:23 ahmed Exp $ * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.example; /* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ import jaligner.Alignment; import jaligner.NeedlemanWunschGotoh; import jaligner.Sequence; import jaligner.formats.Pair; import jaligner.matrix.Matrix; import jaligner.matrix.MatrixGenerator; import jaligner.util.SequenceParser; import java.util.logging.Level; import java.util.logging.Logger; /** * Example of using JAligner API to perform global pairwise sequence alignment * with {@link jaligner.NeedlemanWunschGotoh}. * * @author Ahmed Moustafa */ public class NeedlemanWunschGotohExample { /** * Logger */ private static final Logger logger = Logger .getLogger(NeedlemanWunschGotohExample.class.getName()); /** * * @param args */ public static void main(String[] args) { try { logger.info("Running example..."); Sequence s1 = SequenceParser.parse("GAATTCAGTTA"); Sequence s2 = SequenceParser.parse("GGATCGA"); float match = 2; float mismatch = -1; Matrix matrix = MatrixGenerator.generate(match, mismatch); float open = 2; float extend = 2; Alignment alignment = NeedlemanWunschGotoh.align(s1, s2, matrix, open, extend); System.out.println(alignment.getSummary()); System.out.println(new Pair().format(alignment)); logger.info("Finished running example"); } catch (Exception e) { logger.log(Level.SEVERE, "Failed running example: " + e.getMessage(), e); } } }JAligner-1.0/src/jaligner/example/SmithWatermanGotohExample.java000066400000000000000000000061421216526722600250410ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.example; import jaligner.Alignment; import jaligner.Sequence; import jaligner.SmithWatermanGotoh; import jaligner.formats.Pair; import jaligner.matrix.MatrixLoader; import jaligner.util.SequenceParser; import java.io.IOException; import java.io.InputStream; import java.util.logging.Level; import java.util.logging.Logger; /** * Example of using JAligner API to align P53 human aganist * P53 mouse using Smith-Waterman-Gotoh algorithm. * * @author Ahmed Moustafa */ public class SmithWatermanGotohExample { /** * */ private static final String SAMPLE_SEQUENCE_P35_HUMAN = "jaligner/example/sequences/p53_human.fasta"; /** * */ private static final String SAMPLE_SEQUENCE_P35_MOUSE = "jaligner/example/sequences/p53_mouse.fasta"; /** * Logger */ private static final Logger logger = Logger.getLogger(SmithWatermanGotohExample.class.getName()); /** * * @param args */ public static void main(String[] args) { try { logger.info("Running example..."); Sequence s1 = SequenceParser.parse(loadP53Human()); Sequence s2 = SequenceParser.parse(loadP53Mouse()); Alignment alignment = SmithWatermanGotoh.align(s1, s2, MatrixLoader.load("BLOSUM62"), 10f, 0.5f); System.out.println ( alignment.getSummary() ); System.out.println ( new Pair().format(alignment) ); logger.info("Finished running example"); } catch (Exception e) { logger.log(Level.SEVERE, "Failed running example: " + e.getMessage(), e); } } /** * * @param path location of the sequence * @return sequence string * @throws IOException */ private static String loadSampleSequence(String path) throws IOException { InputStream inputStream = NeedlemanWunschExample.class.getClassLoader().getResourceAsStream(path); StringBuffer buffer = new StringBuffer(); int ch; while ((ch = inputStream.read()) != -1) { buffer.append((char)ch); } return buffer.toString(); } /** * * @return sequence string * @throws IOException */ public static String loadP53Human( ) throws IOException { return loadSampleSequence(SAMPLE_SEQUENCE_P35_HUMAN); } /** * * @return sequence string * @throws IOException */ public static String loadP53Mouse( ) throws IOException { return loadSampleSequence(SAMPLE_SEQUENCE_P35_MOUSE); } }JAligner-1.0/src/jaligner/example/package.html000066400000000000000000000003241216526722600213530ustar00rootroot00000000000000 Example for using API of JAligner to perform pairwise sequence alignment. @author Ahmed Moustafa JAligner-1.0/src/jaligner/example/sequences/000077500000000000000000000000001216526722600210665ustar00rootroot00000000000000JAligner-1.0/src/jaligner/example/sequences/p53_human.fasta000066400000000000000000000006311216526722600237050ustar00rootroot00000000000000>p53_human MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACAGR DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSDJAligner-1.0/src/jaligner/example/sequences/p53_mouse.fasta000066400000000000000000000006271216526722600237320ustar00rootroot00000000000000>p53_mouse MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEA LRVSGAPAAQDPVTETPGPAAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVM CTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCS DGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCM GGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELPPGS AKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSR AHSSYLKTKKGQSTSRHKKTMVKKVGPDSDJAligner-1.0/src/jaligner/formats/000077500000000000000000000000001216526722600171135ustar00rootroot00000000000000JAligner-1.0/src/jaligner/formats/CLUSTAL.java000066400000000000000000000066671216526722600211040ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.formats; import jaligner.Alignment; /** * CLUSTAL format. * Example: * 
 * 
 * CLUSTAL_FORMAT W(1.60) multiple sequence alignment
 *
 *
 * JC2395          NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
 * KPEL_DROME      MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
 * FASA_MOUSE      NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
 *
 *
 * JC2395          -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
 * KPEL_DROME      -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
 * FASA_MOUSE      -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
 *
 *
 * JC2395          IAEEIQAM
 * KPEL_DROME      AMRLIKDY
 * FASA_MOUSE      TLDKFQDM
 * 
 *
* * @author Ahmed Moustafa */ public class CLUSTAL extends Format { /** * Name width */ private static final int NAME_WIDTH = 36; /** * Sequence width */ private static final int SEQUENCE_WIDTH = 50; /** * CLUSTAL header */ private static final String HEADER = "CLUSTAL_FORMAT W(1.60) multiple sequence alignment\n\n"; /** * Constructor */ public CLUSTAL() { super( ); setId("CLUSTAL"); } /** * Returns CLUSTAL format * @param names array of the names of the sequences. * @param sequences array of the sequences */ public String format(String[] names, String[] sequences) { StringBuffer buffer = new StringBuffer (HEADER); int maxSequenceLength = 0; for (int i = 0; i < sequences.length; i++) { if (sequences[i].length() > maxSequenceLength) { maxSequenceLength = sequences[i].length(); } } for (int i = 0; i * SEQUENCE_WIDTH < maxSequenceLength; i++) { for (int j = 0; j < sequences.length; j++) { buffer.append( NAME_WIDTH <= names[j].length() ? names[j].substring(0, NAME_WIDTH - 1) : names[j] ); for (int k = names[j].length(); k < NAME_WIDTH; k++) { buffer.append(" "); } if (names[j].length() >= NAME_WIDTH) { buffer.append(" "); } buffer.append(sequences[j].substring(i * SEQUENCE_WIDTH, ((i + 1) * SEQUENCE_WIDTH) < sequences[j].length() ? (i + 1) * SEQUENCE_WIDTH: sequences[j].length())); if (j < sequences.length) { buffer.append("\n"); } } if ((i + 1) * SEQUENCE_WIDTH < maxSequenceLength) { buffer.append("\n\n"); } } return buffer.toString(); } /** * Returns CLUSTAL format of the alignment * @param alignment ({@link Alignment}) * @return CLUSTAL format of the alignment */ public String format (Alignment alignment) { String[] sequences = {new String(alignment.getSequence1()), new String(alignment.getSequence2())}; String[] names = {alignment.getName1(), alignment.getName2()}; return format (names, sequences); } }JAligner-1.0/src/jaligner/formats/FASTA.java000066400000000000000000000045051216526722600206200ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.formats; import jaligner.Alignment; import jaligner.Sequence; /** * FASTA format. * * @author Ahmed Moustafa */ public class FASTA extends Format { /** * Number of characters per line */ private static final int LINE_WIDTH = 60; /** * Constructor for FASTA. */ public FASTA() { super( ); setId("FASTA"); } /** * Returns the name, description and sequence combined in one string. * The length of each line in the sequence is FASTA.LINE_LENGTH * * @return String */ public String format (Sequence sequence) { StringBuffer buffer = new StringBuffer (">"); buffer.append(sequence.getId() == null ? "" : sequence.getId()); buffer.append("\n"); for (int i = 0, n = sequence.length(); i * LINE_WIDTH < n; i++) { for (int j = i * LINE_WIDTH, m = (i + 1) * LINE_WIDTH < n ? (i + 1) * LINE_WIDTH: n; j < m; j++) { buffer.append(sequence.subsequence(j, 1)); } buffer.append("\n"); } return buffer.toString( ); } /** * * @param alignment * @return FASTA format of the input alignment */ public String format (Alignment alignment) { StringBuffer buffer = new StringBuffer(); StringBuffer s1 = new StringBuffer(); StringBuffer s2 = new StringBuffer(); s1.append(alignment.getSequence1()); s2.append(alignment.getSequence2()); buffer.append(format(new Sequence(s1.toString(), alignment.getName1(), "", Sequence.PROTEIN))); buffer.append(format(new Sequence(s2.toString(), alignment.getName2(), "", Sequence.PROTEIN))); return buffer.toString(); } }JAligner-1.0/src/jaligner/formats/Format.java000066400000000000000000000024601216526722600212100ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.formats; import jaligner.Alignment; /** * Abstract format * * @author Ahmed Moustafa */ public abstract class Format { /** * Format id */ private String id = null; /** * Formats alignment * @param alignment * @return formatted alignment * @see Alignment */ public abstract String format(Alignment alignment); /** * Sets format id * @param id to set */ public void setId (String id) { this.id = id; } /** * Returns format id * @return id */ public String getId ( ) { return this.id == null ? this.getClass().getName() : this.id; } }JAligner-1.0/src/jaligner/formats/FormatFactory.java000066400000000000000000000040251216526722600225370ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.formats; import java.util.Collection; import java.util.HashMap; /** * Formats factory. * * @author Ahmed Moustafa */ public class FormatFactory { /** * Instance of {@link FormatFactory} */ private static FormatFactory instance = null; /** * {@link HashMap} of {@link Format} */ private HashMap formats = new HashMap(); /** * Hidden constructor * */ private FormatFactory ( ) { super(); } /** * Returns an instance for {@link FormatFactory}. * @return {@link FormatFactory} */ public static FormatFactory getInstance() { if (instance == null) { instance = new FormatFactory(); } return instance; } /** * Registers format. * @param format instance of format */ public void registerFormat(Format format) { formats.put(format.getId(), format); } /** * Returns an instance of {@link Format}. * @param id format id * @return {@link Format} or null if id not found */ public Format getFormat(String id) { return (Format) formats.get(id); } /** * Returns a list of registered formats * @return {@link Collection} */ public Collection getFormats( ) { return formats.keySet(); } }JAligner-1.0/src/jaligner/formats/Pair.java000066400000000000000000000116311216526722600206530ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.formats; import jaligner.Alignment; import jaligner.util.Commons; /** * Alignment Formats. * * @author Ahmed Moustafa */ public class Pair extends Format { /** * Name width */ private static final int NAME_WIDTH = 13; /** * Position width */ private static final int POSITION_WIDTH = 6; /** * Sequence width */ private static final int SEQUENCE_WIDTH = 50; /** * Space */ private static final String BLANK = " "; /** * Constructor * */ public Pair( ) { super(); setId("Pair"); } /** * Formats an alignment object to the Pair_FORMAT format * @param alignment alignment object to be formated * @return string of the alignment pair-formatted */ public String format(Alignment alignment) { char[] sequence1 = alignment.getSequence1(); char[] sequence2 = alignment.getSequence2(); char[] markup = alignment.getMarkupLine(); int length = sequence1.length > sequence2.length ? sequence2.length : sequence1.length; String name1 = adjustName(alignment.getName1()); String name2 = adjustName(alignment.getName2()); StringBuffer buffer = new StringBuffer ( ); StringBuffer preMarkup = new StringBuffer ( ); for (int j = 0; j < NAME_WIDTH + 1 + POSITION_WIDTH + 1; j++) { preMarkup.append(BLANK); } int oldPosition1, position1 = 1 + alignment.getStart1(); int oldPosition2, position2 = 1 + alignment.getStart2(); char[] subsequence1; char[] subsequence2; char[] submarkup; int line; char c1, c2; for (int i = 0; i * SEQUENCE_WIDTH < length; i++) { oldPosition1 = position1; oldPosition2 = position2; line = ((i + 1) * SEQUENCE_WIDTH) < length ? (i + 1) * SEQUENCE_WIDTH: length; subsequence1 = new char[line - i * SEQUENCE_WIDTH]; subsequence2 = new char[line - i * SEQUENCE_WIDTH]; submarkup = new char[line - i * SEQUENCE_WIDTH]; for (int j = i * SEQUENCE_WIDTH, k = 0; j < line; j++, k++) { subsequence1[k] = sequence1[j]; subsequence2[k] = sequence2[j]; submarkup[k] = markup[j]; c1 = subsequence1[k]; c2 = subsequence2[k]; if (c1 == c2) { position1++; position2++; } else if (c1 == Alignment.GAP) { position2++; } else if (c2 == Alignment.GAP) { position1++; } else { position1++; position2++; } } buffer.append(name1); buffer.append(BLANK); buffer.append(adjustPosition(new Integer(oldPosition1).toString())); buffer.append(BLANK); buffer.append(subsequence1); buffer.append(BLANK); buffer.append(adjustPosition(new Integer(position1 - 1).toString())); buffer.append(Commons.getLineSeparator()); buffer.append(preMarkup); buffer.append(submarkup); buffer.append(Commons.getLineSeparator()); buffer.append(name2); buffer.append(BLANK); buffer.append(adjustPosition(new Integer(oldPosition2).toString())); buffer.append(BLANK); buffer.append(subsequence2); buffer.append(BLANK); buffer.append(adjustPosition(new Integer(position2 - 1).toString())); buffer.append(Commons.getLineSeparator()); buffer.append(Commons.getLineSeparator()); } return buffer.toString(); } /** * * @param name name to adjusted * @return adjusted name */ private String adjustName(String name) { StringBuffer buffer = new StringBuffer ( ); if (name.length() > NAME_WIDTH) { buffer.append(name.substring(0, NAME_WIDTH)); } else { buffer.append(name); for (int j = buffer.length(); j < NAME_WIDTH; j++) { buffer.append (BLANK); } } return buffer.toString(); } /** * * @param position * @return string */ private String adjustPosition(String position) { StringBuffer buffer1 = new StringBuffer( ); StringBuffer buffer2 = new StringBuffer( ); if (position.length() > POSITION_WIDTH) { buffer1.append(position.substring(position.length() - POSITION_WIDTH, position.length())); } else { buffer1.append(position); } for (int j = 0, n = POSITION_WIDTH - buffer1.length(); j < n; j++) { buffer2.append(BLANK); } buffer2.append(buffer1.toString()); return buffer2.toString(); } }JAligner-1.0/src/jaligner/formats/package.html000066400000000000000000000002621216526722600213740ustar00rootroot00000000000000 Group of formats for output alignments. @author Ahmed Moustafa JAligner-1.0/src/jaligner/matrix/000077500000000000000000000000001216526722600167445ustar00rootroot00000000000000JAligner-1.0/src/jaligner/matrix/MatricesCompartor.java000066400000000000000000000035111216526722600232450ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.matrix; import java.util.Comparator; /** * Comparator to sort the scoring matrices by their names. * * @author Ahmed Moustafa */ public class MatricesCompartor implements Comparator { /* (non-Javadoc) * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object) */ public int compare(String s1, String s2) { int index1 = firstDigitIndex(s1); int index2 = firstDigitIndex(s2); if (index1 == -1 || index2 == -1) { return s1.compareToIgnoreCase(s2); } else { String s3 = s1.substring(0, index1); String s4 = s2.substring(0, index2); if (s3.equalsIgnoreCase(s4)) { return new Integer(s1.substring(index1)).compareTo(new Integer(s2.substring(index2))); } else { return s1.compareToIgnoreCase(s2); } } } /** * Returns the index of the first digit in a String. * If there are no digits, returns -1. * @param s String to be searched for the digits in * @return int */ private int firstDigitIndex (String s) { for (int i = 0; i < s.length(); i++) { if (s.charAt(i) >= '0' && s.charAt(i) <= '9') { return i; } } return -1; } }JAligner-1.0/src/jaligner/matrix/Matrix.java000066400000000000000000000032721216526722600210570ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.matrix; import java.io.Serializable; /** * Scoring matrix. * * @author Ahmed Moustafa */ public class Matrix implements Serializable { /** * */ private static final long serialVersionUID = 3833742170619524400L; /** * The size of the scoring matrix. It is the number of the characters in the * ASCII table. It is more than the 20 amino acids just to save the * processing time of the mapping. */ public static final int SIZE = 127; /** * Matrix id (or name) */ private final String id; /** * Scores */ private final float[][] scores; public Matrix(String id, float[][] scores) { this.id = id; this.scores = scores; } /** * @return Returns the id. */ public String getId() { return this.id; } /** * @return Returns the scores. */ public float[][] getScores() { return this.scores; } /** * * @param a * @param b * @return score */ public float getScore(char a, char b) { return this.scores[a][b]; } }JAligner-1.0/src/jaligner/matrix/MatrixGenerator.java000066400000000000000000000035241216526722600227260ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.matrix; /** * A utility class to generate a scoring matrix from a fixed match and mismatch * scoring scheme. * * @author Ahmed Moustafa */ public final class MatrixGenerator { /** * Returns scoring matrix from a fixed match/mismatch scoring scheme. * * @param match * match score * @param mismatch * mistmatch score * * @return scoring matrix */ public static Matrix generate(float match, float mismatch) { float[][] scores = new float[Matrix.SIZE][Matrix.SIZE]; // Fill the matrix with the scores for (int i = 0; i < Matrix.SIZE; i++) { for (int j = 0; j < Matrix.SIZE; j++) { if (i == j || i == 'N' || j == 'N') { scores[i][j] = match; } else { scores[i][j] = mismatch; } } } // Generate some id for the matrix (hopefully to be somehow unique) String id = new Long(System.currentTimeMillis()).toString(); Matrix matrix = new Matrix(id, scores); return matrix; } } JAligner-1.0/src/jaligner/matrix/MatrixLoader.java000066400000000000000000000155341216526722600222120ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.matrix; import jaligner.ui.filechooser.NamedInputStream; import jaligner.util.Commons; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; import java.io.InputStream; import java.io.InputStreamReader; import java.net.JarURLConnection; import java.net.URL; import java.net.URLDecoder; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; import java.util.Enumeration; import java.util.List; import java.util.StringTokenizer; import java.util.jar.JarEntry; import java.util.jar.JarFile; import java.util.logging.Level; import java.util.logging.Logger; /** * Scoring matrices loader from a jar file or a file system. * * @author Ahmed Moustafa */ public class MatrixLoader { /** * The starter character of a comment line. */ private static final char COMMENT_STARTER = '#'; /** * The path to the matrices within the package. */ private static final String MATRICES_HOME = "jaligner/matrix/matrices/"; /** * Logger */ private static final Logger logger = Logger.getLogger(MatrixLoader.class .getName()); /** * Loads scoring matrix from Jar file or file system. * * @param matrix * to load * @return loaded matrix * @throws MatrixLoaderException * @see Matrix */ public static Matrix load(String matrix) throws MatrixLoaderException { InputStream is = null; if (new StringTokenizer(matrix, Commons.getFileSeparator()) .countTokens() == 1) { // Matrix does not include the path // Load the matrix from matrices.jar is = MatrixLoader.class.getClassLoader().getResourceAsStream( MATRICES_HOME + matrix); } else { // Matrix includes the path information // Load the matrix from the file system try { is = new FileInputStream(matrix); } catch (Exception e) { String message = "Failed opening input stream: " + e.getMessage(); logger.log(Level.SEVERE, message, e); throw new MatrixLoaderException(message); } } return load(new NamedInputStream(matrix, is)); } /** * Loads scoring matrix from {@link InputStream} * * @param nis * named input stream * @return loaded matrix * @throws MatrixLoaderException * @see Matrix * @see NamedInputStream */ public static Matrix load(NamedInputStream nis) throws MatrixLoaderException { logger.info("Loading scoring matrix..."); char[] acids = new char[Matrix.SIZE]; // Initialize the acids array to null values (ascii = 0) for (int i = 0; i < Matrix.SIZE; i++) { acids[i] = 0; } float[][] scores = new float[Matrix.SIZE][Matrix.SIZE]; BufferedReader reader = new BufferedReader(new InputStreamReader(nis .getInputStream())); String line; try { // Skip the comment lines while ((line = reader.readLine()) != null && line.trim().charAt(0) == COMMENT_STARTER) ; } catch (Exception e) { String message = "Failed reading from input stream: " + e.getMessage(); logger.log(Level.SEVERE, message, e); throw new MatrixLoaderException(message); } // Read the headers line (the letters of the acids) StringTokenizer tokenizer; tokenizer = new StringTokenizer(line.trim()); for (int j = 0; tokenizer.hasMoreTokens(); j++) { acids[j] = tokenizer.nextToken().charAt(0); } try { // Read the scores while ((line = reader.readLine()) != null) { tokenizer = new StringTokenizer(line.trim()); char acid = tokenizer.nextToken().charAt(0); for (int i = 0; i < Matrix.SIZE; i++) { if (acids[i] != 0) { scores[acid][acids[i]] = Float.parseFloat(tokenizer .nextToken()); } } } } catch (Exception e) { String message = "Failed reading from input stream: " + e.getMessage(); logger.log(Level.SEVERE, message, e); throw new MatrixLoaderException(message); } logger.info("Finished loading scoring matrix"); return new Matrix(nis.getName(), scores); } /** * Returns a list of the scoring matrices in the matrices home directory * * @param sort * flag to sort the list or not * @return sorted array of scoring matrices * @throws MatrixLoaderException */ public static Collection list(boolean sort) throws MatrixLoaderException { logger.info("Loading list of scoring matrices..."); List matrices = new ArrayList(); URL url = MatrixLoader.class.getClassLoader() .getResource(MATRICES_HOME); if (url.getFile().toString().indexOf("!") != -1) { // Load from Jar JarURLConnection connection = null; JarFile jar = null; try { connection = (JarURLConnection) url.openConnection(); jar = connection.getJarFile(); } catch (Exception e) { String message = "Failed opening a connection to jar: " + e.getMessage(); logger.log(Level.SEVERE, message, e); throw new MatrixLoaderException(message); } Enumeration entries = jar.entries(); JarEntry entry; String entryName; int length = MATRICES_HOME.length(); while (entries.hasMoreElements()) { entry = entries.nextElement(); if (!entry.isDirectory()) { entryName = entry.getName(); if (entryName.startsWith(MATRICES_HOME)) { matrices.add(entryName.substring(length)); } } } } else { // Load from file system String home = null; try { home = URLDecoder.decode(url.getFile(), "UTF-8"); } catch (Exception e) { String message = "Failed decoding matrices url: " + e.getMessage(); logger.log(Level.SEVERE, message, e); throw new MatrixLoaderException(message); } File dir = new File(home); String files[] = dir.list(); File file; for (int i = 0, n = files.length; i < n; i++) { file = new File(home + files[i]); if (file.isFile() && file.canRead()) { matrices.add(file.getName()); } } } if (sort) { Collections.sort(matrices, new MatricesCompartor()); } logger.info("Finished loading list of scoring matrices"); return matrices; } /** * Returns a list of the scoring matrices in the matrices home directory * * @return sorted array of scoring matrices * @throws MatrixLoaderException */ public static Collection list() throws MatrixLoaderException { return list(false); } }JAligner-1.0/src/jaligner/matrix/MatrixLoaderException.java000066400000000000000000000020201216526722600240530ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.matrix; /** * * @author Ahmed Moustafa */ public class MatrixLoaderException extends Exception { /** * */ private static final long serialVersionUID = 3906364935142586680L; /** * @param message */ public MatrixLoaderException(String message) { super(message); } } JAligner-1.0/src/jaligner/matrix/matrices/000077500000000000000000000000001216526722600205535ustar00rootroot00000000000000JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM100000066400000000000000000000041761216526722600217300ustar00rootroot00000000000000# Matrix made by matblas from blosum100_3.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 100 # Entropy = 1.4516, Expected = -1.0948 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10 R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10 N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10 D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10 C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10 Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10 E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10 G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10 H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10 I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10 L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10 K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10 M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10 F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10 P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10 S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10 T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10 W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10 Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10 V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10 B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10 Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10 X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM30000066400000000000000000000041121216526722600216400ustar00rootroot00000000000000# Matrix made by matblas from blosum30.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/5 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 30 # Entropy = 0.1424, Expected = -0.1074 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -1 0 0 -3 1 0 0 -2 0 -1 0 1 -2 -1 1 1 -5 -4 1 0 0 0 -7 R -1 8 -2 -1 -2 3 -1 -2 -1 -3 -2 1 0 -1 -1 -1 -3 0 0 -1 -2 0 -1 -7 N 0 -2 8 1 -1 -1 -1 0 -1 0 -2 0 0 -1 -3 0 1 -7 -4 -2 4 -1 0 -7 D 0 -1 1 9 -3 -1 1 -1 -2 -4 -1 0 -3 -5 -1 0 -1 -4 -1 -2 5 0 -1 -7 C -3 -2 -1 -3 17 -2 1 -4 -5 -2 0 -3 -2 -3 -3 -2 -2 -2 -6 -2 -2 0 -2 -7 Q 1 3 -1 -1 -2 8 2 -2 0 -2 -2 0 -1 -3 0 -1 0 -1 -1 -3 -1 4 0 -7 E 0 -1 -1 1 1 2 6 -2 0 -3 -1 2 -1 -4 1 0 -2 -1 -2 -3 0 5 -1 -7 G 0 -2 0 -1 -4 -2 -2 8 -3 -1 -2 -1 -2 -3 -1 0 -2 1 -3 -3 0 -2 -1 -7 H -2 -1 -1 -2 -5 0 0 -3 14 -2 -1 -2 2 -3 1 -1 -2 -5 0 -3 -2 0 -1 -7 I 0 -3 0 -4 -2 -2 -3 -1 -2 6 2 -2 1 0 -3 -1 0 -3 -1 4 -2 -3 0 -7 L -1 -2 -2 -1 0 -2 -1 -2 -1 2 4 -2 2 2 -3 -2 0 -2 3 1 -1 -1 0 -7 K 0 1 0 0 -3 0 2 -1 -2 -2 -2 4 2 -1 1 0 -1 -2 -1 -2 0 1 0 -7 M 1 0 0 -3 -2 -1 -1 -2 2 1 2 2 6 -2 -4 -2 0 -3 -1 0 -2 -1 0 -7 F -2 -1 -1 -5 -3 -3 -4 -3 -3 0 2 -1 -2 10 -4 -1 -2 1 3 1 -3 -4 -1 -7 P -1 -1 -3 -1 -3 0 1 -1 1 -3 -3 1 -4 -4 11 -1 0 -3 -2 -4 -2 0 -1 -7 S 1 -1 0 0 -2 -1 0 0 -1 -1 -2 0 -2 -1 -1 4 2 -3 -2 -1 0 -1 0 -7 T 1 -3 1 -1 -2 0 -2 -2 -2 0 0 -1 0 -2 0 2 5 -5 -1 1 0 -1 0 -7 W -5 0 -7 -4 -2 -1 -1 1 -5 -3 -2 -2 -3 1 -3 -3 -5 20 5 -3 -5 -1 -2 -7 Y -4 0 -4 -1 -6 -1 -2 -3 0 -1 3 -1 -1 3 -2 -2 -1 5 9 1 -3 -2 -1 -7 V 1 -1 -2 -2 -2 -3 -3 -3 -3 4 1 -2 0 1 -4 -1 1 -3 1 5 -2 -3 0 -7 B 0 -2 4 5 -2 -1 0 0 -2 -2 -1 0 -2 -3 -2 0 0 -5 -3 -2 5 0 -1 -7 Z 0 0 -1 0 0 4 5 -2 0 -3 -1 1 -1 -4 0 -1 -1 -1 -2 -3 0 4 0 -7 X 0 -1 0 -1 -2 0 -1 -1 -1 0 0 0 0 -1 -1 0 0 -2 -1 0 -1 0 -1 -7 * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM35000066400000000000000000000041121216526722600216450ustar00rootroot00000000000000# Matrix made by matblas from blosum35.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/4 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 35 # Entropy = 0.2111, Expected = -0.1550 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5 R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5 N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5 D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5 C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5 Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5 E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5 G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5 H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5 I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5 L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5 K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5 M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5 F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5 P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5 S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5 T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5 W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5 Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5 V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5 B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5 Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5 X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM40000066400000000000000000000041121216526722600216410ustar00rootroot00000000000000# Matrix made by matblas from blosum40.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/4 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 40 # Entropy = 0.2851, Expected = -0.2090 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6 R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6 N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6 D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6 C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6 Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6 E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6 G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6 H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6 I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6 L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6 K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6 M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6 F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6 P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6 S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6 T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6 W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6 Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6 V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6 B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6 Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6 * -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM45000066400000000000000000000041121216526722600216460ustar00rootroot00000000000000# Matrix made by matblas from blosum45.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 45 # Entropy = 0.3795, Expected = -0.2789 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5 R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5 N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5 D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5 C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5 Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5 E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5 G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5 H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5 I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5 L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5 K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5 M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5 F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5 P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5 S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5 W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5 Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5 V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5 B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5 Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM50000066400000000000000000000041121216526722600216420ustar00rootroot00000000000000# Matrix made by matblas from blosum50.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 50 # Entropy = 0.4808, Expected = -0.3573 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5 R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1 -5 N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1 -5 D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1 -5 C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5 Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1 -5 E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1 -5 G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2 -5 H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1 -5 I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1 -5 L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1 -5 K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1 -5 M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1 -5 F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2 -5 P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5 S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0 -5 W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5 Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5 V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5 B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1 -5 Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1 -5 X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM55000066400000000000000000000041121216526722600216470ustar00rootroot00000000000000# Matrix made by matblas from blosum55.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 55 # Entropy = 0.5637, Expected = -0.4179 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -2 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -2 0 -2 -1 -1 -5 R -2 8 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -2 -3 -1 0 -1 -5 N -2 -1 8 2 -3 0 0 0 1 -4 -4 0 -3 -4 -2 1 0 -5 -2 -4 4 0 -1 -5 D -2 -2 2 8 -4 0 2 -2 -1 -4 -5 -1 -4 -5 -2 0 -1 -5 -3 -4 5 1 -2 -5 C 0 -4 -3 -4 13 -4 -4 -3 -4 -2 -2 -4 -2 -3 -3 -1 -1 -4 -3 -1 -4 -4 -2 -5 Q -1 1 0 0 -4 7 2 -2 1 -4 -3 2 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5 E -1 0 0 2 -4 2 7 -3 -1 -4 -4 1 -3 -4 -1 0 -1 -3 -2 -3 1 5 -1 -5 G 0 -3 0 -2 -3 -2 -3 8 -2 -5 -5 -2 -3 -4 -3 0 -2 -3 -4 -4 -1 -3 -2 -5 H -2 0 1 -1 -4 1 -1 -2 11 -4 -3 0 -2 -1 -3 -1 -2 -3 2 -4 0 0 -1 -5 I -2 -4 -4 -4 -2 -4 -4 -5 -4 6 2 -4 2 0 -3 -3 -1 -3 -1 4 -4 -4 -1 -5 L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 6 -3 3 1 -4 -3 -2 -3 -1 1 -4 -3 -1 -5 K -1 3 0 -1 -4 2 1 -2 0 -4 -3 6 -2 -4 -1 0 -1 -4 -2 -3 0 1 -1 -5 M -1 -2 -3 -4 -2 0 -3 -3 -2 2 3 -2 8 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 F -3 -3 -4 -5 -3 -4 -4 -4 -1 0 1 -4 0 9 -5 -3 -3 2 4 -1 -5 -4 -2 -5 P -1 -3 -2 -2 -3 -1 -1 -3 -3 -3 -4 -1 -3 -5 10 -1 -1 -5 -4 -3 -2 -1 -2 -5 S 2 -1 1 0 -1 0 0 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -3 -1 2 6 -3 -2 0 -1 -1 -1 -5 W -4 -3 -5 -5 -4 -2 -3 -3 -3 -3 -3 -4 -2 2 -5 -4 -3 15 3 -4 -5 -3 -3 -5 Y -2 -2 -2 -3 -3 -1 -2 -4 2 -1 -1 -2 -1 4 -4 -2 -2 3 9 -2 -3 -2 -1 -5 V 0 -3 -4 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -4 -2 5 -4 -3 -1 -5 B -2 -1 4 5 -4 0 1 -1 0 -4 -4 0 -3 -5 -2 0 -1 -5 -3 -4 5 2 -1 -5 Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -2 -4 -1 0 -1 -3 -2 -3 2 5 -1 -5 X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -1 -1 -1 -1 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM60000066400000000000000000000041121216526722600216430ustar00rootroot00000000000000# Matrix made by matblas from blosum60.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 60 # Entropy = 0.6603, Expected = -0.4917 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -1 -1 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 R -1 5 0 -1 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -2 -1 0 -1 -4 N -1 0 6 1 -2 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 D -2 -1 1 6 -3 0 2 -1 -1 -3 -3 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 C 0 -3 -2 -3 9 -3 -3 -2 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 Q -1 1 0 0 -3 5 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 E -1 0 0 2 -3 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 G 0 -2 0 -1 -2 -2 -2 6 -2 -3 -4 -1 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 H -2 0 1 -1 -3 1 0 -2 7 -3 -3 -1 -1 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 I -1 -3 -3 -3 -1 -3 -3 -3 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -4 L -1 -2 -3 -3 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -4 K -1 2 0 -1 -3 1 1 -1 -1 -3 -2 4 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 M -1 -1 -2 -3 -1 0 -2 -2 -1 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 4 -2 -2 0 0 -1 0 -4 W -3 -3 -4 -4 -2 -2 -3 -2 -2 -2 -2 -3 -1 1 -4 -3 -2 10 2 -3 -4 -2 -2 -4 Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 -2 -2 -1 -4 V 0 -2 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 B -2 -1 3 4 -3 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -2 -3 4 1 -1 -4 Z -1 0 0 1 -3 3 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -2 1 3 -1 -4 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM62000066400000000000000000000041121216526722600216450ustar00rootroot00000000000000# Matrix made by matblas from blosum62.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 62 # Entropy = 0.6979, Expected = -0.5209 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM65000066400000000000000000000041121216526722600216500ustar00rootroot00000000000000# Matrix made by matblas from blosum65.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 65 # Entropy = 0.7576, Expected = -0.5675 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5 R -1 6 0 -2 -4 1 0 -2 0 -3 -2 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 N -2 0 6 1 -3 0 0 -1 1 -3 -4 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -5 D -2 -2 1 6 -4 0 2 -1 -1 -3 -4 -1 -3 -4 -2 0 -1 -5 -3 -3 4 1 -1 -5 C 0 -4 -3 -4 9 -3 -4 -3 -3 -1 -1 -3 -2 -2 -3 -1 -1 -2 -2 -1 -3 -4 -2 -5 Q -1 1 0 0 -3 6 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -2 -2 0 3 -1 -5 E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -3 1 4 -1 -5 G 0 -2 -1 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -3 -3 -3 -1 -2 -2 -5 H -2 0 1 -1 -3 1 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -5 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -5 L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 -4 -3 -1 -5 K -1 2 0 -1 -3 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -2 0 1 -1 -5 M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 F -2 -3 -3 -4 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -2 -5 P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -2 -2 -1 -2 -5 S 1 -1 1 0 -1 0 0 0 -1 -2 -3 0 -2 -2 -1 4 1 -3 -2 -2 0 0 -1 -5 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 W -3 -3 -4 -5 -2 -2 -3 -3 -2 -2 -2 -3 -2 1 -4 -3 -3 10 2 -3 -4 -3 -2 -5 Y -2 -2 -2 -3 -2 -2 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -5 V 0 -3 -3 -3 -1 -2 -3 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -5 B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -5 Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -5 X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM70000066400000000000000000000041121216526722600216440ustar00rootroot00000000000000# Matrix made by matblas from blosum70.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 70 # Entropy = 0.8391, Expected = -0.6313 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5 R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 N -2 -1 6 1 -3 0 0 -1 0 -4 -4 0 -2 -3 -2 0 0 -4 -2 -3 3 0 -1 -5 D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -4 -4 4 1 -2 -5 C -1 -4 -3 -4 9 -3 -4 -3 -4 -1 -2 -4 -2 -2 -3 -1 -1 -3 -3 -1 -4 -4 -2 -5 Q -1 1 0 -1 -3 6 2 -2 1 -3 -2 1 0 -3 -2 0 -1 -2 -2 -2 0 3 -1 -5 E -1 0 0 1 -4 2 5 -2 0 -4 -3 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5 G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5 H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 -1 0 -1 -5 I -2 -3 -4 -4 -1 -3 -4 -4 -4 4 2 -3 1 0 -3 -3 -1 -3 -1 3 -4 -3 -1 -5 L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5 K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -3 -1 1 -1 -5 M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5 F -2 -3 -3 -4 -2 -3 -4 -4 -1 0 0 -3 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5 P -1 -2 -2 -2 -3 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -3 -2 -1 -2 -5 S 1 -1 0 0 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 4 1 -3 -2 -2 0 0 -1 -5 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -3 -2 1 -4 -3 -3 11 2 -3 -4 -3 -3 -5 Y -2 -2 -2 -4 -3 -2 -3 -4 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -2 -3 -2 -2 -5 V 0 -3 -3 -4 -1 -2 -3 -4 -3 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -3 -3 -1 -5 B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -4 -3 -3 4 0 -1 -5 Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -4 -1 0 -1 -3 -2 -3 0 4 -1 -5 X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -1 -1 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM75000066400000000000000000000041121216526722600216510ustar00rootroot00000000000000# Matrix made by matblas from blosum75.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 75 # Entropy = 0.9077, Expected = -0.6845 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5 R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5 N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -3 3 0 -1 -5 D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -4 -4 -2 -1 -1 -5 -4 -4 4 1 -2 -5 C -1 -4 -3 -4 9 -3 -5 -3 -4 -1 -2 -4 -2 -2 -4 -1 -1 -3 -3 -1 -4 -4 -2 -5 Q -1 1 0 -1 -3 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -2 -2 -2 0 3 -1 -5 E -1 0 -1 1 -5 2 5 -3 0 -4 -4 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5 G 0 -3 -1 -2 -3 -2 -3 6 -2 -5 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5 H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -2 -2 -1 -2 -2 2 -4 -1 0 -1 -5 I -2 -3 -4 -4 -1 -3 -4 -5 -4 4 1 -3 1 0 -3 -3 -1 -3 -2 3 -4 -4 -2 -5 L -2 -3 -4 -4 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5 K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 0 -1 -4 -2 -3 -1 1 -1 -5 M -1 -2 -3 -4 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -5 F -3 -3 -4 -4 -2 -4 -4 -4 -2 0 0 -4 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5 P -1 -2 -3 -2 -4 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -5 -4 -3 -2 -2 -2 -5 S 1 -1 0 -1 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 5 1 -3 -2 -2 0 0 -1 -5 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5 W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -4 -2 1 -5 -3 -3 11 2 -3 -5 -3 -3 -5 Y -2 -2 -3 -4 -3 -2 -3 -4 2 -2 -1 -2 -2 3 -4 -2 -2 2 7 -2 -3 -3 -2 -5 V 0 -3 -3 -4 -1 -2 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -5 B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -2 -5 Z -1 0 0 1 -4 3 4 -2 0 -4 -3 1 -2 -4 -2 0 -1 -3 -3 -3 0 4 -1 -5 X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM80000066400000000000000000000041141216526722600216470ustar00rootroot00000000000000# Matrix made by matblas from blosum80_3.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 80 # Entropy = 0.9868, Expected = -0.7442 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8 R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8 N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8 D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8 C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8 Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8 E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8 G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8 H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8 I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8 L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8 K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8 M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8 F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8 P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8 S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8 T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8 W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8 Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8 V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8 B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8 Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8 X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM85000066400000000000000000000041121216526722600216520ustar00rootroot00000000000000# Matrix made by matblas from blosum85.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 85 # Entropy = 1.0805, Expected = -0.8153 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -3 -3 -1 -2 -1 -1 -6 R -2 6 -1 -2 -4 1 -1 -3 0 -4 -3 2 -2 -4 -2 -1 -2 -4 -3 -3 -2 0 -2 -6 N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6 D -2 -2 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -4 -2 -1 -2 -6 -4 -4 4 1 -2 -6 C -1 -4 -4 -5 9 -4 -5 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -3 -1 -4 -5 -3 -6 Q -1 1 0 -1 -4 6 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -2 -3 -1 4 -1 -6 E -1 -1 -1 1 -5 2 6 -3 -1 -4 -4 0 -3 -4 -2 -1 -1 -4 -4 -3 0 4 -1 -6 G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -5 -4 -1 -3 -2 -6 H -2 0 0 -2 -5 1 -1 -3 8 -4 -3 -1 -3 -2 -3 -1 -2 -3 2 -4 -1 0 -2 -6 I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -5 -4 -2 -6 L -2 -3 -4 -5 -2 -3 -4 -5 -3 1 4 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6 K -1 2 0 -1 -4 1 0 -2 -1 -3 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6 M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6 F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -1 -4 -4 -2 -6 P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -1 -2 -5 -4 -3 -3 -2 -2 -6 S 1 -1 0 -1 -2 -1 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -1 -1 -6 T 0 -2 0 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -3 -2 1 5 -4 -2 0 -1 -1 -1 -6 W -3 -4 -5 -6 -4 -3 -4 -4 -3 -3 -3 -5 -2 0 -5 -4 -4 11 2 -3 -5 -4 -3 -6 Y -3 -3 -3 -4 -3 -2 -4 -5 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -4 -3 -2 -6 V -1 -3 -4 -4 -1 -3 -3 -4 -4 3 0 -3 0 -1 -3 -2 0 -3 -2 5 -4 -3 -1 -6 B -2 -2 4 4 -4 -1 0 -1 -1 -5 -5 -1 -4 -4 -3 0 -1 -5 -4 -4 4 0 -2 -6 Z -1 0 -1 1 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6 X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -6 * -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUM90000066400000000000000000000041121216526722600216460ustar00rootroot00000000000000# Matrix made by matblas from blosum90.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 90 # Entropy = 1.1806, Expected = -0.8887 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -1 -1 -6 R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 0 -2 -6 N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6 D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 4 0 -2 -6 C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -5 -3 -6 Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 4 -1 -6 E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 0 4 -2 -6 G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -3 -2 -6 H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 0 -2 -6 I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 -4 -2 -6 L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6 K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6 M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6 F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 -4 -2 -6 P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -2 -2 -6 S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -1 -1 -6 T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -1 -1 -6 W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -4 -3 -6 Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -3 -2 -6 V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 -3 -2 -6 B -2 -2 4 4 -4 -1 0 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 4 0 -2 -6 Z -1 0 -1 0 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6 X -1 -2 -2 -2 -3 -1 -2 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -6 * -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 JAligner-1.0/src/jaligner/matrix/matrices/BLOSUMN000066400000000000000000000041111216526722600216120ustar00rootroot00000000000000# Matrix made by matblas from blosumn.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/2 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= -2 # Entropy = 1.5172, Expected = -1.1484 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 6 -2 -2 -3 -2 -1 -2 -1 -3 -3 -3 -2 -2 -4 -1 1 -1 -4 -4 -1 -3 -2 -1 -7 R -2 7 -1 -3 -6 0 -2 -4 -1 -5 -4 2 -3 -4 -3 -2 -2 -5 -4 -4 -2 -1 -2 -7 N -2 -1 7 1 -4 -1 -1 -2 0 -5 -5 -1 -4 -5 -4 0 -1 -6 -4 -4 4 -1 -2 -7 D -3 -3 1 7 -6 -2 1 -3 -2 -6 -6 -2 -5 -5 -3 -2 -2 -7 -5 -5 4 0 -3 -7 C -2 -6 -4 -6 9 -5 -7 -5 -6 -2 -3 -5 -3 -3 -5 -2 -2 -5 -4 -2 -5 -6 -4 -7 Q -1 0 -1 -2 -5 7 1 -4 0 -4 -3 1 -1 -4 -2 -1 -2 -4 -3 -4 -1 4 -2 -7 E -2 -2 -1 1 -7 1 6 -4 -1 -5 -5 0 -4 -5 -3 -1 -2 -5 -4 -4 0 5 -2 -7 G -1 -4 -2 -3 -5 -4 -4 6 -4 -6 -6 -3 -5 -5 -4 -1 -3 -5 -6 -5 -2 -4 -3 -7 H -3 -1 0 -2 -6 0 -1 -4 9 -5 -4 -2 -3 -3 -4 -2 -3 -4 1 -5 -1 -1 -3 -7 I -3 -5 -5 -6 -2 -4 -5 -6 -5 6 1 -4 1 -1 -5 -4 -2 -4 -3 2 -5 -5 -2 -7 L -3 -4 -5 -6 -3 -3 -5 -6 -4 1 5 -4 2 0 -5 -4 -3 -4 -3 0 -5 -4 -2 -7 K -2 2 -1 -2 -5 1 0 -3 -2 -4 -4 6 -2 -4 -2 -1 -2 -6 -4 -4 -1 0 -2 -7 M -2 -3 -4 -5 -3 -1 -4 -5 -3 1 2 -2 8 -1 -4 -3 -2 -2 -3 0 -5 -3 -2 -7 F -4 -4 -5 -5 -3 -4 -5 -5 -3 -1 0 -4 -1 7 -5 -4 -3 0 3 -2 -5 -5 -3 -7 P -1 -3 -4 -3 -5 -2 -3 -4 -4 -5 -5 -2 -4 -5 8 -2 -3 -5 -5 -4 -4 -3 -3 -7 S 1 -2 0 -2 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 6 1 -4 -3 -3 -1 -1 -1 -7 T -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -3 -2 -2 -3 -3 1 6 -5 -3 -1 -2 -2 -1 -7 W -4 -5 -6 -7 -5 -4 -5 -5 -4 -4 -4 -6 -2 0 -5 -4 -5 11 1 -3 -6 -4 -4 -7 Y -4 -4 -4 -5 -4 -3 -4 -6 1 -3 -3 -4 -3 3 -5 -3 -3 1 8 -3 -4 -4 -3 -7 V -1 -4 -4 -5 -2 -4 -4 -5 -5 2 0 -4 0 -2 -4 -3 -1 -3 -3 5 -5 -4 -2 -7 B -3 -2 4 4 -5 -1 0 -2 -1 -5 -5 -1 -5 -5 -4 -1 -2 -6 -4 -5 4 1 -2 -7 Z -2 -1 -1 0 -6 4 5 -4 -1 -5 -4 0 -3 -5 -3 -1 -2 -4 -4 -4 1 4 -2 -7 X -1 -2 -2 -3 -4 -2 -2 -3 -3 -2 -2 -2 -2 -3 -3 -1 -1 -4 -3 -2 -2 -2 -2 -7 * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1 JAligner-1.0/src/jaligner/matrix/matrices/DAYHOFF000066400000000000000000000040411216526722600215550ustar00rootroot00000000000000#Date: Wed, 18 Sep 91 17:36:51 EDT #From: altschul@ray.nlm.nih.gov (Stephen Altschul) #To: gish@ray.nlm.nih.gov #Subject: Vanilla-flavored PAM-250 # # substitution scores for B, Z, X, and * were obtained with "pam" version 1.0.5 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -3 0 0 0 0 -8 R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8 D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8 C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8 Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8 E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8 G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8 H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8 I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8 K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8 M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8 F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8 P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8 S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8 W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8 Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8 B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8 Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/EDNAFULL000066400000000000000000000024221216526722600216700ustar00rootroot00000000000000# # This matrix was created by Todd Lowe 12/10/92 # # Uses ambiguous nucleotide codes, probabilities rounded to # nearest integer # # Lowest score = -4, Highest score = 5 # A T G C S W R Y K M B V H D N U A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2 -4 T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5 G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2 -4 C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2 -4 S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 -4 W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1 1 R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 -4 Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1 1 K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1 1 M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 -4 B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 -1 V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 -4 H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 -1 D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 -1 N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 U -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5 JAligner-1.0/src/jaligner/matrix/matrices/GONNET000066400000000000000000000032171216526722600214730ustar00rootroot00000000000000# PAM 250 matrix recommended by Gonnet, Cohen & Benner # Science June 5, 1992. # Values rounded to nearest integer C S T P A G N D E Q H R K M I L V F Y W X * C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8 S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8 T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8 P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8 A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8 G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8 N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8 D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8 E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8 Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8 H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8 R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8 K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8 M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8 I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8 L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8 V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8 F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8 Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8 W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8 X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/IDENTITY000066400000000000000000000077311216526722600217370ustar00rootroot00000000000000 A R N B D C Q Z E G H I L K M F P S T W Y V X * A 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 R -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 N -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 B -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 D -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 C -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 Q -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 Z -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 E -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 G -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 H -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 I -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 L -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 K -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 M -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 F -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 P -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 S -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 T -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 W -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 Y -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 V -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 X -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0 -10000 * -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0 JAligner-1.0/src/jaligner/matrix/matrices/MATCH000066400000000000000000000034721216526722600213400ustar00rootroot00000000000000 A R N B D C Q Z E G H I L K M F P S T W Y V X * A 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 R -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 N -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 B -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 D -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 C -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 Q -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 Z -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 E -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 G -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 I -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 L -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 F -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 * -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 JAligner-1.0/src/jaligner/matrix/matrices/PAM10000066400000000000000000000051521216526722600212570ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 10 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -8.27, Entropy = 3.43 bits # # Lowest score = -23, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 7 -10 -7 -6 -10 -7 -5 -4 -11 -8 -9 -10 -8 -12 -4 -3 -3 -20 -11 -5 -6 -6 -6 -23 R -10 9 -9 -17 -11 -4 -15 -13 -4 -8 -12 -2 -7 -12 -7 -6 -10 -5 -14 -11 -11 -7 -9 -23 N -7 -9 9 -1 -17 -7 -5 -6 -2 -8 -10 -4 -15 -12 -9 -2 -5 -11 -7 -12 7 -6 -6 -23 D -6 -17 -1 8 -21 -6 0 -6 -7 -11 -19 -8 -17 -21 -12 -7 -8 -21 -17 -11 7 -1 -9 -23 C -10 -11 -17 -21 10 -20 -20 -13 -10 -9 -21 -20 -20 -19 -11 -6 -11 -22 -7 -9 -18 -20 -13 -23 Q -7 -4 -7 -6 -20 9 -1 -10 -2 -11 -8 -6 -7 -19 -6 -8 -9 -19 -18 -10 -6 7 -8 -23 E -5 -15 -5 0 -20 -1 8 -7 -9 -8 -13 -7 -10 -20 -9 -7 -9 -23 -11 -10 -1 7 -8 -23 G -4 -13 -6 -6 -13 -10 -7 7 -13 -17 -14 -10 -12 -12 -10 -4 -10 -21 -20 -9 -6 -8 -8 -23 H -11 -4 -2 -7 -10 -2 -9 -13 10 -13 -9 -10 -17 -9 -7 -9 -11 -10 -6 -9 -4 -4 -8 -23 I -8 -8 -8 -11 -9 -11 -8 -17 -13 9 -4 -9 -3 -5 -12 -10 -5 -20 -9 -1 -9 -9 -8 -23 L -9 -12 -10 -19 -21 -8 -13 -14 -9 -4 7 -11 -2 -5 -10 -12 -10 -9 -10 -5 -12 -10 -9 -23 K -10 -2 -4 -8 -20 -6 -7 -10 -10 -9 -11 7 -4 -20 -10 -7 -6 -18 -12 -13 -5 -6 -8 -23 M -8 -7 -15 -17 -20 -7 -10 -12 -17 -3 -2 -4 12 -7 -11 -8 -7 -19 -17 -4 -16 -8 -9 -23 F -12 -12 -12 -21 -19 -19 -20 -12 -9 -5 -5 -20 -7 9 -13 -9 -12 -7 -1 -12 -14 -20 -12 -23 P -4 -7 -9 -12 -11 -6 -9 -10 -7 -12 -10 -10 -11 -13 8 -4 -7 -20 -20 -9 -10 -7 -8 -23 S -3 -6 -2 -7 -6 -8 -7 -4 -9 -10 -12 -7 -8 -9 -4 7 -2 -8 -10 -10 -4 -8 -6 -23 T -3 -10 -5 -8 -11 -9 -9 -10 -11 -5 -10 -6 -7 -12 -7 -2 8 -19 -9 -6 -6 -9 -7 -23 W -20 -5 -11 -21 -22 -19 -23 -21 -10 -20 -9 -18 -19 -7 -20 -8 -19 13 -8 -22 -13 -21 -16 -23 Y -11 -14 -7 -17 -7 -18 -11 -20 -6 -9 -10 -12 -17 -1 -20 -10 -9 -8 10 -10 -9 -13 -11 -23 V -5 -11 -12 -11 -9 -10 -10 -9 -9 -1 -5 -13 -4 -12 -9 -10 -6 -22 -10 8 -11 -10 -8 -23 B -6 -11 7 7 -18 -6 -1 -6 -4 -9 -12 -5 -16 -14 -10 -4 -6 -13 -9 -11 7 -3 -8 -23 Z -6 -7 -6 -1 -20 7 7 -8 -4 -9 -10 -6 -8 -20 -7 -8 -9 -21 -13 -10 -3 7 -8 -23 X -6 -9 -6 -9 -13 -8 -8 -8 -8 -8 -9 -8 -9 -12 -8 -6 -7 -16 -11 -8 -8 -8 -8 -23 * -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM100000066400000000000000000000040221216526722600213320ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 100 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.99, Entropy = 1.18 bits # # Lowest score = -9, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -3 -1 -1 -3 -2 0 1 -3 -2 -3 -3 -2 -5 1 1 1 -7 -4 0 -1 -1 -1 -9 R -3 7 -2 -4 -5 1 -3 -5 1 -3 -5 2 -1 -6 -1 -1 -3 1 -6 -4 -3 -1 -2 -9 N -1 -2 5 3 -5 -1 1 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -3 4 0 -1 -9 D -1 -4 3 5 -7 0 4 -1 -1 -4 -6 -1 -5 -8 -3 -1 -2 -9 -6 -4 4 3 -2 -9 C -3 -5 -5 -7 9 -8 -8 -5 -4 -3 -8 -8 -7 -7 -4 -1 -4 -9 -1 -3 -6 -8 -5 -9 Q -2 1 -1 0 -8 6 2 -3 3 -4 -2 0 -2 -7 -1 -2 -2 -7 -6 -3 0 5 -2 -9 E 0 -3 1 4 -8 2 5 -1 -1 -3 -5 -1 -4 -8 -2 -1 -2 -9 -5 -3 3 4 -2 -9 G 1 -5 -1 -1 -5 -3 -1 5 -4 -5 -6 -3 -4 -6 -2 0 -2 -9 -7 -3 -1 -2 -2 -9 H -3 1 2 -1 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9 I -2 -3 -3 -4 -3 -4 -3 -5 -4 6 1 -3 1 0 -4 -3 0 -7 -3 3 -3 -3 -2 -9 L -3 -5 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 0 -5 -4 -3 -9 K -3 2 1 -1 -8 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -6 -6 -4 0 -1 -2 -9 M -2 -1 -4 -5 -7 -2 -4 -4 -4 1 3 0 9 -1 -4 -3 -1 -6 -5 1 -4 -2 -2 -9 F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -7 -1 8 -6 -4 -5 -1 4 -3 -6 -7 -4 -9 P 1 -1 -2 -3 -4 -1 -2 -2 -1 -4 -4 -3 -4 -6 7 0 -1 -7 -7 -3 -3 -1 -2 -9 S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -3 -4 0 4 2 -3 -4 -2 0 -2 -1 -9 T 1 -3 0 -2 -4 -2 -2 -2 -3 0 -3 -1 -1 -5 -1 2 5 -7 -4 0 -1 -2 -1 -9 W -7 1 -5 -9 -9 -7 -9 -9 -4 -7 -3 -6 -6 -1 -7 -3 -7 12 -2 -9 -6 -8 -6 -9 Y -4 -6 -2 -6 -1 -6 -5 -7 -1 -3 -3 -6 -5 4 -7 -4 -4 -2 9 -4 -4 -6 -4 -9 V 0 -4 -3 -4 -3 -3 -3 -3 -3 3 0 -4 1 -3 -3 -2 0 -9 -4 5 -4 -3 -2 -9 B -1 -3 4 4 -6 0 3 -1 1 -3 -5 0 -4 -6 -3 0 -1 -6 -4 -4 4 2 -2 -9 Z -1 -1 0 3 -8 5 4 -2 1 -3 -4 -1 -2 -7 -1 -2 -2 -8 -6 -3 2 5 -2 -9 X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM110000066400000000000000000000040221216526722600213330ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 110 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.81, Entropy = 1.07 bits # # Lowest score = -9, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -3 -1 -1 -3 -1 0 1 -3 -1 -3 -3 -2 -4 1 1 1 -7 -4 0 -1 -1 -1 -9 R -3 7 -1 -4 -4 1 -3 -4 1 -3 -4 2 -1 -5 -1 -1 -2 1 -5 -4 -2 -1 -2 -9 N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -5 -2 -3 3 0 -1 -9 D -1 -4 2 5 -7 1 4 0 0 -3 -6 -1 -5 -7 -3 -1 -1 -8 -5 -4 4 3 -2 -9 C -3 -4 -5 -7 9 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 -1 -3 -9 -1 -3 -6 -7 -4 -9 Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -6 -3 0 4 -1 -9 E 0 -3 1 4 -7 2 5 -1 -1 -3 -5 -1 -3 -7 -2 -1 -2 -9 -5 -3 3 4 -2 -9 G 1 -4 0 0 -5 -3 -1 5 -4 -4 -6 -3 -4 -5 -2 0 -2 -8 -7 -2 0 -2 -2 -9 H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9 I -1 -3 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -4 -3 0 -7 -2 3 -3 -3 -2 -9 L -3 -4 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 1 -5 -3 -2 -9 K -3 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -5 -5 -4 0 -1 -2 -9 M -2 -1 -3 -5 -7 -1 -3 -4 -4 1 3 0 8 -1 -4 -2 -1 -6 -5 1 -4 -2 -2 -9 F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -6 -4 -4 -1 4 -3 -6 -7 -4 -9 P 1 -1 -2 -3 -4 0 -2 -2 -1 -4 -4 -3 -4 -6 6 0 -1 -7 -7 -2 -2 -1 -2 -9 S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -2 -4 0 3 2 -3 -3 -2 0 -1 -1 -9 T 1 -2 0 -1 -3 -2 -2 -2 -3 0 -3 -1 -1 -4 -1 2 5 -6 -3 0 -1 -2 -1 -9 W -7 1 -5 -8 -9 -6 -9 -8 -4 -7 -3 -5 -6 -1 -7 -3 -6 12 -2 -8 -6 -7 -5 -9 Y -4 -5 -2 -5 -1 -6 -5 -7 -1 -2 -3 -5 -5 4 -7 -3 -3 -2 8 -4 -3 -5 -3 -9 V 0 -4 -3 -4 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -4 5 -3 -3 -2 -9 B -1 -2 3 4 -6 0 3 0 1 -3 -5 0 -4 -6 -2 0 -1 -6 -3 -3 4 2 -1 -9 Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -7 -1 -1 -2 -7 -5 -3 2 4 -2 -9 X -1 -2 -1 -2 -4 -1 -2 -2 -2 -2 -2 -2 -2 -4 -2 -1 -1 -5 -3 -2 -1 -2 -2 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM120000066400000000000000000000040231216526722600213350ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.64, Entropy = 0.979 bits # # Lowest score = -8, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -3 -1 0 -3 -1 0 1 -3 -1 -3 -2 -2 -4 1 1 1 -7 -4 0 0 -1 -1 -8 R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8 N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -4 -2 -3 3 0 -1 -8 D 0 -3 2 5 -7 1 3 0 0 -3 -5 -1 -4 -7 -3 0 -1 -8 -5 -3 4 3 -2 -8 C -3 -4 -5 -7 9 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -8 -1 -3 -6 -7 -4 -8 Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -5 -3 0 4 -1 -8 E 0 -3 1 3 -7 2 5 -1 -1 -3 -4 -1 -3 -7 -2 -1 -2 -8 -5 -3 3 4 -1 -8 G 1 -4 0 0 -4 -3 -1 5 -4 -4 -5 -3 -4 -5 -2 1 -1 -8 -6 -2 0 -2 -2 -8 H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -3 -1 -3 1 1 -2 -8 I -1 -2 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8 L -3 -4 -4 -5 -7 -2 -4 -5 -3 1 5 -4 3 0 -3 -4 -3 -3 -2 1 -4 -3 -2 -8 K -2 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -2 -1 -1 -5 -5 -4 0 -1 -2 -8 M -2 -1 -3 -4 -6 -1 -3 -4 -4 1 3 0 8 -1 -3 -2 -1 -6 -4 1 -4 -2 -2 -8 F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -5 -3 -4 -1 4 -3 -5 -6 -3 -8 P 1 -1 -2 -3 -4 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -7 -6 -2 -2 -1 -2 -8 S 1 -1 1 0 0 -2 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8 T 1 -2 0 -1 -3 -2 -2 -1 -3 0 -3 -1 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8 W -7 1 -4 -8 -8 -6 -8 -8 -3 -6 -3 -5 -6 -1 -7 -2 -6 12 -2 -8 -6 -7 -5 -8 Y -4 -5 -2 -5 -1 -5 -5 -6 -1 -2 -2 -5 -4 4 -6 -3 -3 -2 8 -3 -3 -5 -3 -8 V 0 -3 -3 -3 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -3 5 -3 -3 -1 -8 B 0 -2 3 4 -6 0 3 0 1 -3 -4 0 -4 -5 -2 0 0 -6 -3 -3 4 2 -1 -8 Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8 X -1 -2 -1 -2 -4 -1 -1 -2 -2 -1 -2 -2 -2 -3 -2 -1 -1 -5 -3 -1 -1 -1 -2 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM130000066400000000000000000000040231216526722600213360ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 130 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.48, Entropy = 0.895 bits # # Lowest score = -8, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8 R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8 N 0 -1 4 2 -4 0 1 0 2 -2 -3 1 -3 -4 -1 1 0 -4 -2 -3 3 0 -1 -8 D 0 -3 2 5 -6 1 3 0 0 -3 -5 -1 -4 -7 -2 0 -1 -7 -5 -3 4 3 -1 -8 C -3 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8 Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -6 0 -1 -2 -6 -5 -3 0 4 -1 -8 E 0 -3 1 3 -6 2 5 -1 0 -2 -4 -1 -3 -6 -2 -1 -1 -8 -5 -3 2 4 -1 -8 G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -4 -5 -2 1 -1 -7 -6 -2 0 -1 -2 -8 H -2 1 2 0 -4 3 0 -3 7 -3 -3 -1 -3 -2 -1 -2 -2 -3 0 -3 1 1 -1 -8 I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8 L -3 -4 -3 -5 -7 -2 -4 -5 -3 1 5 -4 3 1 -3 -4 -2 -2 -2 1 -4 -3 -2 -8 K -2 2 1 -1 -6 0 -1 -3 -1 -2 -4 5 0 -6 -2 -1 0 -5 -5 -4 0 0 -1 -8 M -2 -1 -3 -4 -6 -1 -3 -4 -3 2 3 0 8 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8 F -4 -5 -4 -7 -5 -6 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8 P 1 -1 -1 -2 -3 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -6 -6 -2 -2 -1 -1 -8 S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8 T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8 W -6 1 -4 -7 -8 -6 -8 -7 -3 -6 -2 -5 -5 -1 -6 -2 -6 12 -1 -7 -5 -7 -5 -8 Y -4 -5 -2 -5 -1 -5 -5 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -5 -3 -8 V 0 -3 -3 -3 -2 -3 -3 -2 -3 3 1 -4 1 -2 -2 -2 0 -7 -3 5 -3 -3 -1 -8 B 0 -2 3 4 -5 0 2 0 1 -3 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8 Z 0 -1 0 3 -6 4 4 -1 1 -3 -3 0 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8 X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 -1 -1 -5 -3 -1 -1 -1 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM140000066400000000000000000000040231216526722600213370ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 140 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.35, Entropy = 0.820 bits # # Lowest score = -8, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8 R -2 6 -1 -3 -4 1 -2 -4 1 -2 -4 3 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -1 -8 N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -8 D 0 -3 2 4 -6 1 3 0 0 -3 -5 -1 -4 -6 -2 0 -1 -7 -5 -3 4 3 -1 -8 C -2 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8 Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -2 -5 -5 -2 1 4 -1 -8 E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -3 -6 -1 -1 -1 -8 -4 -2 2 4 -1 -8 G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -3 -5 -1 1 -1 -7 -6 -2 0 -1 -1 -8 H -2 1 2 0 -4 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -8 I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -2 -2 -1 -8 L -2 -4 -3 -5 -7 -2 -4 -5 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -8 K -2 3 1 -1 -6 0 -1 -3 -1 -2 -3 5 0 -6 -2 -1 0 -4 -5 -3 0 0 -1 -8 M -2 -1 -2 -4 -6 -1 -3 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8 F -4 -5 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8 P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -6 -2 -2 -1 -1 -8 S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 0 -8 T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -5 -3 0 0 -1 -1 -8 W -6 1 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 -1 -6 -2 -5 12 -1 -7 -5 -6 -5 -8 Y -4 -5 -2 -5 -1 -5 -4 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -4 -3 -8 V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -2 0 -7 -3 5 -3 -2 -1 -8 B 0 -2 3 4 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8 Z 0 -1 1 3 -6 4 4 -1 1 -2 -3 0 -2 -6 -1 -1 -1 -6 -4 -2 2 4 -1 -8 X -1 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -5 -3 -1 -1 -1 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM150000066400000000000000000000040231216526722600213400ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 150 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.25, Entropy = 0.754 bits # # Lowest score = -7, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -6 -3 0 0 0 -1 -7 R -2 6 -1 -2 -4 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -2 1 -4 -3 -2 0 -1 -7 N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -7 D 0 -2 2 4 -6 1 3 0 0 -3 -5 -1 -3 -6 -2 0 -1 -7 -4 -3 3 2 -1 -7 C -2 -4 -4 -6 9 -6 -6 -4 -3 -2 -6 -6 -5 -5 -3 0 -3 -7 0 -2 -5 -6 -3 -7 Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -7 E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -2 -6 -1 -1 -1 -7 -4 -2 2 4 -1 -7 G 1 -3 0 0 -4 -2 -1 4 -3 -3 -4 -2 -3 -5 -1 1 -1 -7 -5 -2 0 -1 -1 -7 H -2 1 2 0 -3 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -7 I -1 -2 -2 -3 -2 -3 -2 -3 -3 5 1 -2 2 0 -3 -2 0 -5 -2 3 -2 -2 -1 -7 L -2 -3 -3 -5 -6 -2 -4 -4 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7 K -2 3 1 -1 -6 0 -1 -2 -1 -2 -3 4 0 -6 -2 -1 0 -4 -4 -3 0 0 -1 -7 M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -3 1 -3 -2 -1 -7 F -4 -4 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -3 -1 5 -2 -5 -5 -3 -7 P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -5 -2 -2 -1 -1 -7 S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7 T 1 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 4 -5 -3 0 0 -1 -1 -7 W -6 1 -4 -7 -7 -5 -7 -7 -3 -5 -2 -4 -5 -1 -6 -2 -5 12 -1 -6 -5 -6 -4 -7 Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7 V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7 B 0 -2 3 3 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -2 3 2 -1 -7 Z 0 0 1 2 -6 4 4 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 4 -1 -7 X -1 -1 -1 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -4 -3 -1 -1 -1 -1 -7 * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM160000066400000000000000000000040231216526722600213410ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 160 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.14, Entropy = 0.694 bits # # Lowest score = -7, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -3 1 1 1 -5 -3 0 0 0 0 -7 R -2 6 -1 -2 -3 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -1 1 -4 -3 -1 0 -1 -7 N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -3 -1 1 0 -4 -2 -2 2 1 0 -7 D 0 -2 2 4 -5 1 3 0 0 -3 -4 0 -3 -6 -2 0 -1 -6 -4 -3 3 2 -1 -7 C -2 -3 -4 -5 9 -5 -5 -3 -3 -2 -6 -5 -5 -5 -3 0 -2 -7 0 -2 -4 -5 -3 -7 Q -1 1 0 1 -5 5 2 -2 2 -2 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -7 E 0 -2 1 3 -5 2 4 0 0 -2 -3 -1 -2 -5 -1 0 -1 -7 -4 -2 2 3 -1 -7 G 1 -3 0 0 -3 -2 0 4 -3 -3 -4 -2 -3 -4 -1 1 -1 -7 -5 -2 0 -1 -1 -7 H -2 1 2 0 -3 2 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -2 1 1 -1 -7 I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 0 -2 -2 0 -5 -2 3 -2 -2 -1 -7 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7 K -2 3 1 0 -5 0 -1 -2 -1 -2 -3 4 0 -5 -2 -1 0 -4 -4 -3 0 0 -1 -7 M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 0 -2 -2 -1 -4 -3 1 -3 -2 -1 -7 F -3 -4 -3 -6 -5 -5 -5 -4 -2 0 1 -5 0 7 -4 -3 -3 -1 5 -2 -4 -5 -3 -7 P 1 -1 -1 -2 -3 0 -1 -1 -1 -2 -3 -2 -2 -4 5 1 0 -5 -5 -2 -1 -1 -1 -7 S 1 -1 1 0 0 -1 0 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7 T 1 -1 0 -1 -2 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -7 W -5 1 -4 -6 -7 -5 -7 -7 -3 -5 -2 -4 -4 -1 -5 -2 -5 12 -1 -6 -5 -6 -4 -7 Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7 V 0 -3 -2 -3 -2 -2 -2 -2 -2 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7 B 0 -1 2 3 -4 1 2 0 1 -2 -4 0 -3 -4 -1 0 0 -5 -3 -2 3 2 -1 -7 Z 0 0 1 2 -5 3 3 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 3 -1 -7 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -7 * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM170000066400000000000000000000051541216526722600213500ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 170 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -1.57, Entropy = 0.640 bits # # Lowest score = -10, Highest score = 18 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -3 0 0 -3 -1 0 1 -3 -1 -3 -2 -2 -5 1 2 2 -8 -5 0 0 0 -1 -10 R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10 N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -3 -3 3 1 -1 -10 D 0 -3 3 6 -7 2 5 0 0 -4 -6 -1 -4 -8 -2 0 -1 -9 -6 -4 5 4 -1 -10 C -3 -5 -5 -7 13 -8 -8 -5 -5 -3 -9 -8 -7 -6 -4 0 -3 -10 0 -3 -6 -8 -4 -10 Q -1 1 0 2 -8 6 3 -2 4 -3 -2 0 -1 -7 0 -1 -2 -7 -6 -3 1 5 -1 -10 E 0 -2 2 5 -8 3 6 0 0 -3 -5 -1 -3 -8 -1 -1 -1 -10 -6 -3 3 5 -1 -10 G 1 -4 0 0 -5 -2 0 6 -4 -4 -6 -3 -4 -6 -2 1 -1 -9 -7 -2 0 -1 -2 -10 H -3 2 2 0 -5 4 0 -4 9 -4 -3 -1 -4 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10 I -1 -3 -3 -4 -3 -3 -3 -4 -4 7 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10 L -3 -4 -4 -6 -9 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -4 -2 -10 K -2 4 1 -1 -8 0 -1 -3 -1 -3 -4 6 1 -8 -2 -1 0 -5 -6 -4 0 0 -2 -10 M -2 -1 -3 -4 -7 -1 -3 -4 -4 2 4 1 10 0 -3 -2 -1 -6 -4 2 -4 -2 -1 -10 F -5 -6 -5 -8 -6 -7 -8 -6 -3 1 1 -8 0 10 -6 -4 -5 -1 7 -2 -6 -7 -4 -10 P 1 -1 -1 -2 -4 0 -1 -2 -1 -3 -4 -2 -3 -6 8 1 0 -8 -7 -2 -2 -1 -1 -10 S 2 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10 T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -5 0 2 5 -7 -4 0 0 -1 -1 -10 W -8 2 -5 -9 -10 -7 -10 -9 -4 -7 -3 -5 -6 -1 -8 -3 -7 18 -1 -9 -7 -8 -6 -10 Y -5 -6 -3 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 12 -4 -4 -6 -4 -10 V 0 -4 -3 -4 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -9 -4 6 -3 -3 -1 -10 B 0 -2 3 5 -6 1 3 0 1 -3 -5 0 -4 -6 -2 1 0 -7 -4 -3 4 3 -1 -10 Z 0 0 1 4 -8 5 5 -1 2 -3 -4 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10 X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -2 -1 -4 -1 0 -1 -6 -4 -1 -1 -1 -2 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM180000066400000000000000000000051541216526722600213510ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 180 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -1.51, Entropy = 0.591 bits # # Lowest score = -10, Highest score = 18 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -8 -5 0 0 0 -1 -10 R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10 N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -2 -3 3 1 -1 -10 D 0 -3 3 5 -7 2 4 0 0 -3 -6 0 -4 -8 -2 0 -1 -9 -6 -3 4 3 -1 -10 C -3 -5 -5 -7 13 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 0 -3 -10 0 -3 -6 -7 -4 -10 Q -1 1 0 2 -7 6 3 -2 4 -3 -2 0 -1 -6 0 -1 -2 -6 -6 -3 1 5 -1 -10 E 0 -2 2 4 -7 3 5 0 0 -3 -5 -1 -3 -7 -1 -1 -1 -9 -6 -3 3 5 -1 -10 G 1 -4 0 0 -5 -2 0 6 -3 -4 -6 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -2 -10 H -2 2 2 0 -4 4 0 -3 8 -4 -3 -1 -3 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10 I -1 -3 -3 -3 -3 -3 -3 -4 -4 6 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10 L -3 -4 -4 -6 -8 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -3 -2 -10 K -2 4 1 0 -7 0 -1 -3 -1 -3 -4 6 1 -7 -2 -1 0 -5 -6 -4 0 0 -1 -10 M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -10 F -5 -6 -5 -8 -6 -6 -7 -6 -3 1 1 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -10 P 1 -1 -1 -2 -4 0 -1 -1 -1 -3 -4 -2 -3 -6 8 1 0 -7 -7 -2 -2 -1 -1 -10 S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10 T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -4 0 2 4 -7 -4 0 0 -1 -1 -10 W -8 2 -5 -9 -10 -6 -9 -9 -4 -7 -3 -5 -6 0 -7 -3 -7 18 -1 -8 -7 -8 -6 -10 Y -5 -6 -2 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 11 -4 -4 -6 -3 -10 V 0 -4 -3 -3 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -8 -4 6 -3 -3 -1 -10 B 0 -2 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -2 1 0 -7 -4 -3 4 3 -1 -10 Z 0 0 1 3 -7 5 5 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10 X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 0 -1 -6 -3 -1 -1 -1 -1 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM190000066400000000000000000000040231216526722600213440ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 190 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -1.35, Entropy = 0.547 bits # # Lowest score = -9, Highest score = 18 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -2 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -7 -4 0 0 0 0 -9 R -2 8 -1 -2 -5 1 -2 -4 2 -3 -4 4 -1 -6 0 -1 -2 2 -5 -3 -1 0 -1 -9 N 0 -1 3 3 -5 1 2 0 2 -2 -4 1 -3 -4 -1 1 0 -5 -2 -3 3 1 -1 -9 D 0 -2 3 5 -7 2 4 0 0 -3 -5 0 -4 -7 -2 0 -1 -8 -5 -3 4 3 -1 -9 C -3 -5 -5 -7 13 -7 -7 -4 -4 -3 -8 -7 -7 -6 -4 0 -3 -9 0 -3 -6 -7 -4 -9 Q -1 1 1 2 -7 6 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9 E 0 -2 2 4 -7 3 5 0 0 -3 -4 -1 -3 -7 -1 0 -1 -9 -5 -3 3 4 -1 -9 G 1 -4 0 0 -4 -2 0 6 -3 -4 -5 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -1 -9 H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9 I -1 -3 -2 -3 -3 -3 -3 -4 -3 6 2 -3 2 1 -3 -2 0 -7 -2 4 -3 -3 -1 -9 L -3 -4 -4 -5 -8 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -3 -2 2 -5 -3 -2 -9 K -2 4 1 0 -7 1 -1 -3 -1 -3 -4 6 1 -7 -2 0 0 -5 -6 -3 0 0 -1 -9 M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -9 F -5 -6 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -9 P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9 S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -9 T 2 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9 W -7 2 -5 -8 -9 -6 -9 -9 -3 -7 -3 -5 -6 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9 Y -4 -5 -2 -5 0 -5 -5 -7 0 -2 -2 -6 -4 7 -6 -4 -3 -1 11 -3 -4 -5 -3 -9 V 0 -3 -3 -3 -3 -3 -3 -2 -3 4 2 -3 2 -2 -2 -2 0 -8 -3 6 -3 -3 -1 -9 B 0 -1 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -1 1 0 -6 -4 -3 4 2 -1 -9 Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -7 -5 -3 2 4 -1 -9 X 0 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM20000066400000000000000000000051521216526722600212600ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 20 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -6.18, Entropy = 2.95 bits # # Lowest score = -19, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 6 -8 -5 -4 -8 -5 -3 -3 -8 -6 -7 -8 -6 -9 -2 -1 -1 -16 -9 -3 -5 -4 -4 -19 R -8 9 -7 -12 -9 -2 -11 -11 -3 -6 -10 -1 -5 -10 -5 -4 -8 -3 -11 -9 -9 -5 -7 -19 N -5 -7 8 1 -13 -5 -3 -4 -1 -6 -8 -2 -11 -10 -7 -1 -3 -9 -5 -9 6 -4 -4 -19 D -4 -12 1 8 -16 -4 2 -4 -5 -9 -15 -6 -13 -17 -9 -5 -6 -17 -13 -9 6 0 -7 -19 C -8 -9 -13 -16 10 -16 -16 -11 -8 -7 -17 -16 -16 -15 -9 -4 -9 -18 -5 -7 -14 -16 -11 -19 Q -5 -2 -5 -4 -16 9 0 -8 0 -9 -6 -4 -5 -15 -4 -6 -7 -15 -14 -8 -4 7 -6 -19 E -3 -11 -3 2 -16 0 8 -5 -6 -6 -10 -5 -8 -16 -7 -5 -7 -19 -9 -8 0 6 -6 -19 G -3 -11 -4 -4 -11 -8 -5 7 -10 -13 -12 -8 -10 -10 -7 -3 -7 -17 -16 -7 -4 -6 -6 -19 H -8 -3 -1 -5 -8 0 -6 -10 9 -11 -7 -8 -13 -7 -5 -7 -8 -8 -4 -7 -2 -2 -6 -19 I -6 -6 -6 -9 -7 -9 -6 -13 -11 9 -2 -7 -2 -3 -10 -8 -3 -16 -7 1 -7 -7 -6 -19 L -7 -10 -8 -15 -17 -6 -10 -12 -7 -2 7 -9 0 -4 -8 -9 -8 -7 -8 -3 -10 -8 -7 -19 K -8 -1 -2 -6 -16 -4 -5 -8 -8 -7 -9 7 -3 -16 -8 -5 -4 -14 -10 -10 -3 -5 -6 -19 M -6 -5 -11 -13 -16 -5 -8 -10 -13 -2 0 -3 11 -5 -9 -6 -5 -15 -13 -2 -12 -6 -6 -19 F -9 -10 -10 -17 -15 -15 -16 -10 -7 -3 -4 -16 -5 9 -11 -7 -10 -6 1 -9 -12 -16 -9 -19 P -2 -5 -7 -9 -9 -4 -7 -7 -5 -10 -8 -8 -9 -11 8 -3 -5 -16 -16 -7 -8 -5 -6 -19 S -1 -4 -1 -5 -4 -6 -5 -3 -7 -8 -9 -5 -6 -7 -3 7 0 -6 -8 -8 -2 -6 -4 -19 T -1 -8 -3 -6 -9 -7 -7 -7 -8 -3 -8 -4 -5 -10 -5 0 7 -15 -7 -4 -4 -7 -5 -19 W -16 -3 -9 -17 -18 -15 -19 -17 -8 -16 -7 -14 -15 -6 -16 -6 -15 13 -6 -18 -11 -17 -13 -19 Y -9 -11 -5 -13 -5 -14 -9 -16 -4 -7 -8 -10 -13 1 -16 -8 -7 -6 10 -8 -7 -11 -9 -19 V -3 -9 -9 -9 -7 -8 -8 -7 -7 1 -3 -10 -2 -9 -7 -8 -4 -18 -8 7 -9 -8 -6 -19 B -5 -9 6 6 -14 -4 0 -4 -2 -7 -10 -3 -12 -12 -8 -2 -4 -11 -7 -9 6 -1 -6 -19 Z -4 -5 -4 0 -16 7 6 -6 -2 -7 -8 -5 -6 -16 -5 -6 -7 -17 -11 -8 -1 6 -6 -19 X -4 -7 -4 -7 -11 -6 -6 -6 -6 -6 -7 -6 -6 -9 -6 -4 -5 -13 -9 -6 -6 -6 -6 -19 * -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM200000066400000000000000000000040231216526722600213340ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 200 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -1.23, Entropy = 0.507 bits # # Lowest score = -9, Highest score = 18 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 3 -2 0 0 -3 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -7 -4 0 0 0 0 -9 R -2 7 0 -2 -4 1 -2 -4 2 -2 -4 4 -1 -5 0 -1 -1 2 -5 -3 -1 0 -1 -9 N 0 0 3 3 -5 1 2 0 2 -2 -4 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9 D 0 -2 3 5 -6 2 4 0 0 -3 -5 0 -4 -7 -2 0 0 -8 -5 -3 4 3 -1 -9 C -3 -4 -5 -6 12 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -9 0 -2 -5 -7 -4 -9 Q -1 1 1 2 -7 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9 E 0 -2 2 4 -7 3 5 0 0 -3 -4 0 -3 -7 -1 0 -1 -9 -5 -2 3 4 -1 -9 G 1 -4 0 0 -4 -2 0 6 -3 -3 -5 -2 -4 -6 -1 1 0 -8 -6 -2 0 -1 -1 -9 H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9 I -1 -2 -2 -3 -3 -3 -3 -3 -3 6 2 -2 2 1 -3 -2 0 -6 -2 4 -3 -3 -1 -9 L -2 -4 -4 -5 -7 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -2 -2 2 -4 -3 -2 -9 K -2 4 1 0 -7 1 0 -2 -1 -2 -4 6 1 -7 -2 0 0 -4 -5 -3 0 0 -1 -9 M -2 -1 -2 -4 -6 -1 -3 -4 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9 F -4 -5 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -6 -3 -9 P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9 S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 2 2 -3 -3 -1 1 -1 0 -9 T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9 W -7 2 -5 -8 -9 -6 -9 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9 Y -4 -5 -2 -5 0 -5 -5 -6 0 -2 -2 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9 V 0 -3 -2 -3 -2 -3 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -8 -3 5 -3 -2 -1 -9 B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -6 -1 1 0 -6 -4 -3 3 2 -1 -9 Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -6 -1 -1 -1 -7 -5 -2 2 4 -1 -9 X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM210000066400000000000000000000040231216526722600213350ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 210 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -1.12, Entropy = 0.470 bits # # Lowest score = -9, Highest score = 18 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -7 -4 0 0 0 0 -9 R -2 7 0 -2 -4 1 -2 -3 2 -2 -4 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -9 N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9 D 0 -2 2 5 -6 2 4 0 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -9 C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 0 -2 -5 -6 -4 -9 Q -1 1 1 2 -6 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -2 1 4 -1 -9 E 0 -2 2 4 -6 3 5 0 0 -2 -4 0 -3 -6 -1 0 -1 -8 -5 -2 3 4 -1 -9 G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -9 H -2 2 2 1 -4 3 0 -3 8 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -9 I -1 -2 -2 -3 -3 -3 -2 -3 -3 5 2 -2 2 1 -3 -2 0 -6 -1 4 -3 -3 -1 -9 L -2 -4 -3 -5 -7 -2 -4 -5 -2 2 7 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -9 K -2 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -2 0 0 -4 -5 -3 0 0 -1 -9 M -1 -1 -2 -3 -6 -1 -3 -3 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9 F -4 -5 -4 -7 -5 -6 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -9 P 1 0 -1 -1 -3 0 -1 -1 0 -3 -3 -2 -3 -5 7 1 0 -7 -6 -2 -1 0 -1 -9 S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 1 0 0 -9 T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -9 W -7 2 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -7 -6 -7 -5 -9 Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9 V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -7 -3 5 -2 -2 -1 -9 B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -5 -1 1 0 -6 -4 -2 3 2 -1 -9 Z 0 0 1 3 -6 4 4 -1 2 -3 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -9 X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM220000066400000000000000000000040231216526722600213360ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 220 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -1.06, Entropy = 0.437 bits # # Lowest score = -8, Highest score = 17 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8 R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8 N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8 D 0 -2 2 4 -6 2 4 0 1 -3 -5 0 -3 -6 -1 0 0 -8 -5 -3 4 3 -1 -8 C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 0 -2 -5 -6 -3 -8 Q -1 1 1 2 -6 5 3 -2 3 -2 -2 1 -1 -5 0 -1 -1 -5 -5 -2 1 4 -1 -8 E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8 G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -8 H -2 2 2 1 -4 3 1 -3 7 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -8 I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8 L -2 -3 -3 -5 -7 -2 -4 -5 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8 K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -1 0 0 -4 -5 -3 0 0 -1 -8 M -1 -1 -2 -3 -6 -1 -2 -3 -3 2 4 1 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -8 F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -8 P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 7 1 0 -6 -6 -1 -1 0 -1 -8 S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 0 0 0 -8 T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -8 W -6 2 -4 -8 -8 -5 -8 -8 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -7 -5 -8 Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 0 11 -3 -3 -5 -3 -8 V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -1 -1 0 -7 -3 5 -2 -2 -1 -8 B 0 -1 2 4 -5 1 3 0 1 -2 -4 0 -3 -5 -1 0 0 -6 -3 -2 3 2 -1 -8 Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -8 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM230000066400000000000000000000040241216526722600213400ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 230 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -0.991, Entropy = 0.407 bits # # Lowest score = -8, Highest score = 17 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8 R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8 D 0 -2 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -8 C -2 -4 -4 -6 12 -6 -6 -4 -4 -2 -7 -6 -6 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8 Q -1 1 1 2 -6 5 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -8 E 0 -1 1 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8 G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -6 -2 0 -1 -1 -8 H -2 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -2 -3 0 -2 1 2 -1 -8 I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8 L -2 -3 -3 -4 -7 -2 -4 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8 K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -8 M -1 -1 -2 -3 -6 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -8 F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 9 -5 -3 -3 0 7 -1 -5 -6 -3 -8 P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8 S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -3 1 2 2 -3 -3 -1 0 0 0 -8 T 1 -1 0 0 -2 -1 -1 0 -2 0 -2 0 -1 -3 0 2 3 -6 -3 0 0 -1 0 -8 W -6 2 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -6 -4 -8 Y -4 -5 -2 -5 0 -4 -5 -6 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -5 -3 -8 V 0 -3 -2 -2 -2 -2 -2 -2 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -8 B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -6 -3 -2 3 2 -1 -8 Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -6 -5 -2 2 4 -1 -8 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM240000066400000000000000000000040241216526722600213410ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 240 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -0.923, Entropy = 0.379 bits # # Lowest score = -8, Highest score = 17 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8 R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -5 0 0 -1 2 -4 -3 -1 0 -1 -8 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8 D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8 C -2 -4 -4 -5 12 -6 -6 -4 -4 -2 -6 -6 -5 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8 Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8 E 0 -1 1 4 -6 3 4 0 1 -2 -3 0 -2 -6 -1 0 0 -7 -4 -2 3 3 -1 -8 G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8 H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8 I -1 -2 -2 -2 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -8 K -1 3 1 0 -6 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -4 -5 -3 1 0 -1 -8 M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -4 -3 2 -2 -2 -1 -8 F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -5 -5 -2 -8 P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8 S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -3 -3 -1 0 0 0 -8 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8 W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -4 -4 0 -6 -3 -5 17 0 -6 -5 -6 -4 -8 Y -4 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -4 -2 -8 V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -6 -3 4 -2 -2 -1 -8 B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -5 -3 -2 3 2 -1 -8 Z 0 0 1 3 -6 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM250000066400000000000000000000040241216526722600213420ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -0.844, Entropy = 0.354 bits # # Lowest score = -8, Highest score = 17 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8 R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8 D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8 C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8 Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8 E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8 G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 -8 H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8 I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8 K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8 M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8 F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8 P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8 S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8 W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8 Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8 B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8 Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM260000066400000000000000000000040241216526722600213430ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 260 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -0.794, Entropy = 0.330 bits # # Lowest score = -7, Highest score = 17 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -7 R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -7 N 0 0 2 2 -3 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -7 D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -5 -1 0 0 -6 -4 -2 3 3 -1 -7 C -2 -4 -3 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -7 0 -2 -4 -5 -3 -7 Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -4 0 0 -1 -5 -4 -2 1 3 0 -7 E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 3 3 -1 -7 G 1 -2 0 1 -3 -1 0 5 -2 -2 -4 -2 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -7 H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -7 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -7 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -2 -3 -2 -2 -1 2 -3 -2 -1 -7 K -1 3 1 0 -5 1 0 -2 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -7 M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -1 -1 -4 -2 2 -2 -2 -1 -7 F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 2 -5 0 9 -4 -3 -3 0 7 -1 -4 -5 -2 -7 P 1 0 0 -1 -3 0 0 0 0 -2 -2 -1 -2 -4 6 1 0 -5 -5 -1 -1 0 -1 -7 S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -2 -3 -1 0 0 0 -7 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 2 -5 -3 0 0 0 0 -7 W -6 2 -4 -6 -7 -5 -7 -7 -3 -5 -2 -3 -4 0 -5 -2 -5 17 0 -6 -5 -6 -4 -7 Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -7 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -7 B 0 -1 2 3 -4 1 3 1 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 0 -7 Z 0 0 1 3 -5 3 3 0 2 -2 -2 0 -2 -5 0 0 0 -6 -4 -2 2 3 -1 -7 X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 0 -1 -1 -7 * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM270000066400000000000000000000051551216526722600213520ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 270 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.969, Entropy = 0.309 bits # # Lowest score = -10, Highest score = 23 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 0 0 2 -2 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -10 R -2 8 0 -1 -5 2 -1 -3 2 -2 -4 4 -1 -5 0 0 -1 3 -5 -3 -1 0 -1 -10 N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10 D 0 -1 2 5 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -10 C -2 -5 -4 -6 16 -7 -6 -4 -4 -3 -7 -7 -6 -5 -3 0 -3 -10 1 -2 -5 -7 -4 -10 Q 0 2 1 2 -7 5 3 -1 4 -2 -2 1 -1 -6 0 -1 -1 -6 -5 -2 2 4 -1 -10 E 0 -1 2 4 -6 3 5 0 1 -2 -4 0 -3 -7 -1 0 0 -9 -5 -2 3 4 -1 -10 G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -9 -6 -2 1 0 -1 -10 H -2 2 2 1 -4 4 1 -2 8 -3 -3 0 -3 -2 0 -1 -1 -3 0 -3 1 2 -1 -10 I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 5 -3 -2 -1 -10 L -2 -4 -3 -5 -7 -2 -4 -5 -3 3 8 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -10 K -1 4 1 0 -7 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -10 M -1 -1 -2 -3 -6 -1 -3 -3 -3 3 5 0 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -10 F -4 -5 -4 -7 -5 -6 -7 -6 -2 1 2 -6 0 12 -6 -4 -4 1 9 -1 -6 -6 -3 -10 P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -6 7 1 0 -7 -6 -1 -1 0 -1 -10 S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -4 -1 1 0 0 -10 T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -10 W -7 3 -5 -8 -10 -6 -9 -9 -3 -6 -2 -4 -5 1 -7 -3 -6 23 0 -8 -7 -7 -5 -10 Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -4 -3 0 13 -3 -4 -5 -3 -10 V 0 -3 -2 -3 -2 -2 -2 -2 -3 5 2 -3 2 -1 -1 -1 0 -8 -3 5 -2 -2 -1 -10 B 0 -1 2 4 -5 2 3 1 1 -3 -4 1 -3 -6 -1 1 0 -7 -4 -2 3 3 -1 -10 Z 0 0 2 3 -7 4 4 0 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 3 4 -1 -10 X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM280000066400000000000000000000040241216526722600213450ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 280 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.916, Entropy = 0.289 bits # # Lowest score = -9, Highest score = 22 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9 R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 -1 0 -1 -9 N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9 D 0 -1 2 4 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -2 4 3 -1 -9 C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 1 -2 -5 -6 -3 -9 Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -6 -5 -2 2 4 -1 -9 E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9 G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9 H -1 2 2 1 -4 3 1 -2 8 -3 -2 0 -2 -2 0 -1 -1 -3 0 -3 1 2 -1 -9 I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 4 -2 -2 -1 -9 L -2 -3 -3 -5 -7 -2 -4 -5 -2 3 7 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -9 K -1 4 1 0 -6 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9 M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -9 F -4 -5 -4 -7 -5 -5 -6 -6 -2 1 2 -6 0 11 -5 -4 -4 1 9 -1 -5 -6 -3 -9 P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -7 -6 -1 -1 0 -1 -9 S 1 0 1 0 0 0 0 1 -1 -2 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9 T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 1 1 3 -6 -3 0 0 0 0 -9 W -7 3 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 22 0 -7 -6 -7 -5 -9 Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -3 -3 0 13 -3 -4 -5 -3 -9 V 0 -3 -2 -2 -2 -2 -2 -1 -3 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9 B 0 -1 2 4 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 -1 -9 Z 0 0 1 3 -6 4 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM290000066400000000000000000000040241216526722600213460ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 290 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.877, Entropy = 0.271 bits # # Lowest score = -9, Highest score = 22 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9 R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9 N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9 D 0 -1 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -8 -5 -2 3 3 -1 -9 C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9 Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -5 -2 2 3 0 -9 E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9 G 2 -3 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9 H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -9 I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9 L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 -1 2 -4 -3 -1 -9 K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9 M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -2 2 -2 -2 -1 -9 F -4 -5 -4 -6 -5 -5 -6 -6 -2 1 3 -6 0 11 -5 -4 -3 1 9 -1 -5 -6 -3 -9 P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -6 -6 -1 -1 0 -1 -9 S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9 T 1 -1 1 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 3 -6 -3 0 0 0 0 -9 W -7 3 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -7 -5 -9 Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -2 9 -6 -3 -3 0 13 -3 -4 -5 -2 -9 V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9 B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 0 -9 Z 0 0 1 3 -6 3 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9 X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -2 -1 0 -1 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM30000066400000000000000000000051521216526722600212610ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -5.06, Entropy = 2.57 bits # # Lowest score = -17, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17 R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17 N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17 D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17 C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17 Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17 E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17 G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17 H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17 I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17 L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17 K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17 M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17 F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17 P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17 S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17 T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17 W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17 Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17 V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17 B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17 Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17 X -3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -17 * -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM300000066400000000000000000000040241216526722600213360ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 300 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.835, Entropy = 0.254 bits # # Lowest score = -9, Highest score = 22 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -1 0 0 -2 0 0 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9 R -1 7 0 -1 -4 2 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9 N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -2 -2 2 1 0 -9 D 0 -1 2 4 -6 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -9 C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9 Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9 E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 -1 -9 G 2 -2 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9 H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -3 -2 -2 -3 -2 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9 L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -4 -3 -1 -9 K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9 M -1 0 -2 -3 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 -1 -9 F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 3 -6 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9 P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 -1 -9 S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9 W -6 3 -5 -7 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9 Y -4 -5 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -3 -4 -5 -2 -9 V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -3 5 -2 -2 0 -9 B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9 Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 -1 -9 X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 -1 0 0 -4 -2 0 0 -1 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM310000066400000000000000000000040241216526722600213370ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 310 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.779, Entropy = 0.238 bits # # Lowest score = -9, Highest score = 22 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9 R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -9 N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -9 D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -2 -6 -1 0 0 -7 -5 -2 3 3 -1 -9 C -2 -4 -4 -5 15 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9 Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9 E 0 -1 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -9 G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9 H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 1 -2 -1 0 -5 -1 4 -2 -2 -1 -9 L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -3 -3 -1 -9 K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -9 M -1 0 -2 -2 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 -1 -9 F -4 -5 -4 -6 -4 -5 -6 -5 -2 1 3 -5 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9 P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9 W -6 3 -4 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9 Y -4 -4 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -2 -4 -4 -2 -9 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9 B 0 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9 Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -9 X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 0 0 0 -4 -2 0 0 0 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM320000066400000000000000000000040241216526722600213400ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 320 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.741, Entropy = 0.224 bits # # Lowest score = -8, Highest score = 22 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8 R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -8 N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -8 D 1 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -8 C -2 -4 -4 -5 15 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8 Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 0 0 -5 -4 -2 2 3 0 -8 E 0 -1 2 3 -5 2 4 1 1 -2 -3 0 -2 -5 0 0 0 -7 -5 -2 3 3 0 -8 G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -8 H -1 2 2 1 -4 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 0 -8 L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -2 -2 0 2 -3 -3 -1 -8 K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -8 M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 1 -2 -1 -1 -4 -2 2 -2 -2 0 -8 F -4 -5 -4 -6 -4 -5 -5 -5 -2 1 3 -5 1 11 -5 -3 -3 1 9 -1 -5 -5 -2 -8 P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8 S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8 T 1 -1 0 0 -2 0 0 0 -1 0 -2 0 -1 -3 1 1 2 -5 -3 0 0 0 0 -8 W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -6 -6 -4 -8 Y -4 -4 -2 -5 1 -4 -5 -5 0 -1 0 -5 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8 B 0 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -3 -2 2 2 0 -8 Z 0 0 1 3 -5 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -8 X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM330000066400000000000000000000040241216526722600213410ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 330 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.693, Entropy = 0.210 bits # # Lowest score = -8, Highest score = 22 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8 R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -4 0 0 -1 3 -4 -2 0 0 -1 -8 N 0 0 2 2 -4 1 2 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8 D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8 C -2 -4 -4 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8 Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8 E 0 -1 2 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 2 3 0 -8 G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8 H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 4 -2 -2 0 -8 L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -3 -1 -2 0 2 -3 -2 -1 -8 K -1 4 1 0 -5 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 1 -1 -8 M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8 F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -5 -3 -3 1 9 -1 -4 -5 -2 -8 P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8 S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8 T 1 -1 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8 W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -5 -6 -4 -8 Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8 V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8 B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8 Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8 X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM340000066400000000000000000000040241216526722600213420ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 340 substitution matrix, scale = ln(2)/4 = 0.173287 # # Expected score = -0.680, Entropy = 0.198 bits # # Lowest score = -8, Highest score = 22 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8 R -1 6 0 -1 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 0 -1 -8 N 0 0 1 2 -3 1 1 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8 D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8 C -2 -4 -3 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8 Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8 E 0 0 1 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8 G 1 -2 1 1 -3 -1 1 4 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8 H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 0 -1 -2 0 -2 1 2 0 -8 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 3 -2 -2 0 -8 L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -2 -1 -2 0 2 -3 -2 -1 -8 K -1 4 1 0 -5 1 0 -1 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 1 0 -8 M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8 F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -4 -3 -3 1 9 -1 -4 -5 -2 -8 P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -4 5 1 1 -5 -5 -1 0 0 0 -8 S 1 0 1 0 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8 T 1 0 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8 W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 1 -5 -3 -5 22 1 -6 -5 -6 -4 -8 Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8 V 0 -2 -1 -2 -2 -2 -1 -1 -2 3 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8 B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8 Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8 X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM350000066400000000000000000000051551216526722600213510ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 350 substitution matrix, scale = ln(2)/5 = 0.138629 # # Expected score = -0.701, Entropy = 0.186 bits # # Lowest score = -10, Highest score = 27 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 2 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10 R -1 7 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 -1 4 -5 -3 0 1 -1 -10 N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10 D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -3 -6 0 1 0 -8 -5 -2 3 3 -1 -10 C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -10 1 -2 -5 -6 -3 -10 Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -5 -2 2 3 0 -10 E 1 0 2 4 -6 3 4 1 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -10 G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -10 H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -10 I 0 -2 -2 -2 -3 -2 -2 -2 -2 5 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10 L -2 -3 -3 -4 -7 -2 -4 -4 -2 4 8 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -10 K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -10 M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 0 -10 F -4 -5 -4 -6 -5 -5 -6 -6 -2 2 3 -6 1 13 -5 -4 -3 1 11 -1 -5 -6 -2 -10 P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -7 -6 -1 0 0 0 -10 S 1 0 1 1 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -10 T 1 -1 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -10 W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 27 1 -7 -6 -7 -5 -10 Y -4 -5 -3 -5 1 -5 -5 -6 0 0 0 -5 -2 11 -6 -3 -3 1 14 -2 -4 -5 -2 -10 V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 5 -2 -2 0 -10 B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -10 Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 3 0 -10 X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -5 -2 0 0 0 -1 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM360000066400000000000000000000040241216526722600213440ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 360 substitution matrix, scale = ln(2)/5 = 0.138629 # # Expected score = -0.697, Entropy = 0.175 bits # # Lowest score = -9, Highest score = 27 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9 R -1 6 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 -1 -9 N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -9 D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -9 C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9 Q 0 2 1 2 -6 3 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9 E 1 0 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9 G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -9 H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -9 L -2 -3 -3 -4 -7 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -9 K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9 M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 0 -9 F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 3 -6 1 12 -5 -4 -3 2 11 -1 -5 -5 -2 -9 P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 0 1 0 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9 W -7 4 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -4 2 -6 -3 -6 27 1 -7 -6 -7 -4 -9 Y -4 -5 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9 B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9 Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -9 X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM370000066400000000000000000000040241216526722600213450ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 370 substitution matrix, scale = ln(2)/5 = 0.138629 # # Expected score = -0.649, Entropy = 0.165 bits # # Lowest score = -9, Highest score = 27 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9 R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 -1 -9 N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 1 0 -9 D 1 0 2 4 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9 C -2 -4 -4 -5 18 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9 Q 0 2 1 2 -6 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9 E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9 G 2 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 1 -8 -6 -1 1 0 -1 -9 H -1 2 2 1 -4 3 1 -2 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9 L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -1 -2 0 3 -3 -3 -1 -9 K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 -1 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -9 F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 3 -6 1 12 -5 -4 -3 2 11 0 -5 -5 -2 -9 P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9 W -7 3 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 27 1 -7 -6 -6 -4 -9 Y -4 -4 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9 V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -9 B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9 Z 0 1 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 0 -9 X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM380000066400000000000000000000040241216526722600213460ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 380 substitution matrix, scale = ln(2)/5 = 0.138629 # # Expected score = -0.612, Entropy = 0.156 bits # # Lowest score = -9, Highest score = 26 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 1 0 0 -9 R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9 N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9 C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9 Q 0 2 1 2 -5 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 3 3 0 -9 G 2 -2 1 1 -3 -1 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9 H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9 L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -1 -2 0 3 -3 -3 -1 -9 K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -5 0 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -9 F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 3 -5 1 12 -5 -4 -3 2 10 0 -5 -5 -2 -9 P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9 W -6 3 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 26 1 -6 -6 -6 -4 -9 Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -2 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9 V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -2 0 -9 B 1 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9 Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -9 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM390000066400000000000000000000040241216526722600213470ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 390 substitution matrix, scale = ln(2)/5 = 0.138629 # # Expected score = -0.581, Entropy = 0.147 bits # # Lowest score = -9, Highest score = 26 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -4 0 1 0 0 -9 R -1 6 1 0 -4 1 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9 N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -4 -3 -1 2 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -7 -5 -2 3 3 0 -9 C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9 Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 3 0 -9 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -1 2 3 0 -9 G 1 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -9 H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9 L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -9 K -1 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9 F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 3 -5 1 12 -5 -3 -3 2 10 0 -5 -5 -2 -9 P 1 0 0 0 -3 0 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9 W -6 3 -4 -7 -9 -5 -7 -7 -3 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -6 -6 -4 -9 Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -1 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9 V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -1 0 -9 B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9 Z 0 1 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM40000066400000000000000000000051521216526722600212620ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -4.27, Entropy = 2.26 bits # # Lowest score = -15, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 6 -6 -3 -3 -6 -3 -2 -1 -6 -4 -5 -6 -4 -7 -1 0 0 -12 -7 -2 -3 -2 -3 -15 R -6 8 -5 -9 -7 -1 -8 -8 -1 -5 -8 1 -3 -8 -3 -2 -5 -1 -9 -7 -6 -3 -5 -15 N -3 -5 7 2 -9 -3 -1 -2 1 -4 -6 0 -7 -8 -5 0 -1 -7 -4 -7 6 -2 -3 -15 D -3 -9 2 7 -12 -2 3 -3 -3 -6 -11 -4 -9 -13 -7 -3 -4 -13 -10 -7 6 2 -5 -15 C -6 -7 -9 -12 9 -12 -12 -8 -7 -5 -13 -12 -12 -11 -7 -2 -7 -14 -3 -5 -11 -12 -8 -15 Q -3 -1 -3 -2 -12 8 2 -6 1 -7 -4 -2 -3 -11 -2 -4 -5 -11 -10 -6 -2 6 -4 -15 E -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 -6 -12 -5 -4 -5 -15 -8 -6 2 6 -4 -15 G -1 -8 -2 -3 -8 -6 -3 6 -8 -9 -9 -6 -7 -8 -5 -1 -5 -13 -12 -5 -2 -4 -4 -15 H -6 -1 1 -3 -7 1 -4 -8 9 -8 -5 -5 -9 -5 -3 -5 -6 -6 -3 -6 -1 0 -4 -15 I -4 -5 -4 -6 -5 -7 -5 -9 -8 8 -1 -5 0 -2 -7 -6 -2 -12 -5 2 -5 -5 -4 -15 L -5 -8 -6 -11 -13 -4 -8 -9 -5 -1 7 -7 1 -2 -6 -7 -6 -5 -6 -2 -8 -6 -5 -15 K -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 -1 -12 -6 -3 -2 -10 -8 -8 -2 -3 -4 -15 M -4 -3 -7 -9 -12 -3 -6 -7 -9 0 1 -1 11 -3 -7 -5 -3 -11 -10 -1 -8 -4 -4 -15 F -7 -8 -8 -13 -11 -11 -12 -8 -5 -2 -2 -12 -3 9 -9 -6 -8 -4 2 -7 -9 -12 -7 -15 P -1 -3 -5 -7 -7 -2 -5 -5 -3 -7 -6 -6 -7 -9 8 -1 -3 -12 -12 -5 -6 -3 -4 -15 S 0 -2 0 -3 -2 -4 -4 -1 -5 -6 -7 -3 -5 -6 -1 6 1 -4 -6 -5 -1 -4 -2 -15 T 0 -5 -1 -4 -7 -5 -5 -5 -6 -2 -6 -2 -3 -8 -3 1 7 -11 -6 -2 -2 -5 -3 -15 W -12 -1 -7 -13 -14 -11 -15 -13 -6 -12 -5 -10 -11 -4 -12 -4 -11 13 -4 -14 -9 -13 -9 -15 Y -7 -9 -4 -10 -3 -10 -8 -12 -3 -5 -6 -8 -10 2 -12 -6 -6 -4 10 -6 -6 -8 -7 -15 V -2 -7 -7 -7 -5 -6 -6 -5 -6 2 -2 -8 -1 -7 -5 -5 -2 -14 -6 7 -7 -6 -4 -15 B -3 -6 6 6 -11 -2 2 -2 -1 -5 -8 -2 -8 -9 -6 -1 -2 -9 -6 -7 6 1 -4 -15 Z -2 -3 -2 2 -12 6 6 -4 0 -5 -6 -3 -4 -12 -3 -4 -5 -13 -8 -6 1 6 -4 -15 X -3 -5 -3 -5 -8 -4 -4 -4 -4 -4 -5 -4 -4 -7 -4 -2 -3 -9 -7 -4 -4 -4 -4 -15 * -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM400000066400000000000000000000040241216526722600213370ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 400 substitution matrix, scale = ln(2)/5 = 0.138629 # # Expected score = -0.521, Entropy = 0.139 bits # # Lowest score = -8, Highest score = 26 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 1 0 0 -8 R -1 5 1 0 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 1 0 -8 N 0 1 1 2 -3 1 2 1 1 -1 -3 1 -1 -3 0 1 0 -4 -3 -1 2 1 0 -8 D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -2 2 2 0 -8 C -2 -4 -3 -5 17 -5 -5 -3 -3 -2 -6 -5 -5 -4 -2 0 -2 -8 1 -2 -4 -5 -3 -8 Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 2 0 -8 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8 G 1 -2 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -8 H -1 2 1 1 -3 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -8 I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -8 L -2 -3 -3 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -8 K -1 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -8 M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 5 1 -1 -1 0 -4 -1 2 -2 -1 0 -8 F -3 -4 -3 -5 -4 -4 -5 -5 -2 2 3 -5 1 11 -4 -3 -3 2 10 0 -4 -5 -2 -8 P 1 0 0 0 -2 0 0 0 0 -1 -2 0 -1 -4 5 1 1 -6 -5 -1 0 0 0 -8 S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -8 W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -5 -6 -4 -8 Y -3 -4 -3 -4 1 -4 -4 -5 0 0 0 -4 -1 10 -5 -3 -3 1 13 -2 -3 -4 -2 -8 V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -8 B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 2 0 -8 Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -8 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM410000066400000000000000000000051551216526722600213460ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 410 substitution matrix, scale = ln(2)/6 = 0.115525 # # Expected score = -0.617, Entropy = 0.131 bits # # Lowest score = -10, Highest score = 31 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10 R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10 N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 1 -5 -3 -1 2 2 0 -10 D 1 0 2 3 -6 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10 C -2 -4 -4 -6 20 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10 Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10 E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10 G 2 -2 1 1 -4 0 1 5 -1 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 0 -10 H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10 I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10 L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 8 -3 5 4 -3 -3 -1 -2 1 3 -3 -3 -1 -10 K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10 M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -10 F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 14 -5 -4 -3 2 12 0 -5 -5 -2 -10 P 1 0 0 0 -3 1 0 0 0 -2 -3 0 -2 -5 6 1 1 -7 -5 -1 0 0 0 -10 S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10 T 1 0 1 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -10 W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -7 -3 -6 31 2 -7 -6 -7 -4 -10 Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -2 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10 V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10 B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10 Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -10 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM420000066400000000000000000000051551216526722600213470ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 420 substitution matrix, scale = ln(2)/6 = 0.115525 # # Expected score = -0.599, Entropy = 0.124 bits # # Lowest score = -10, Highest score = 31 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10 R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10 N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 2 0 -10 D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10 C -2 -4 -4 -5 20 -6 -6 -3 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10 Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10 E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10 G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 0 1 1 -8 -6 -1 1 0 0 -10 H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10 I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10 L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 7 -3 5 4 -2 -3 -1 -2 1 3 -3 -3 -1 -10 K 0 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10 M -1 0 -1 -2 -6 -1 -2 -2 -2 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -10 F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -10 P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -10 S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10 W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -7 -4 -10 Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10 V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10 B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10 Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -7 -5 -2 2 3 0 -10 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM430000066400000000000000000000040241216526722600213420ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 430 substitution matrix, scale = ln(2)/6 = 0.115525 # # Expected score = -0.543, Entropy = 0.117 bits # # Lowest score = -9, Highest score = 31 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -9 R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9 N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9 C -2 -4 -4 -5 20 -6 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9 Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 3 0 -9 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -9 G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9 H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9 L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -9 K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9 F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9 P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9 W -7 4 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -6 -4 -9 Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -9 V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -9 B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9 Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -5 -1 2 3 0 -9 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM440000066400000000000000000000040241216526722600213430ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 440 substitution matrix, scale = ln(2)/6 = 0.115525 # # Expected score = -0.529, Entropy = 0.111 bits # # Lowest score = -9, Highest score = 30 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -6 -4 0 1 0 0 -9 R -1 5 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9 N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -2 2 2 0 -9 C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9 Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9 G 2 -2 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9 H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9 L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -2 -1 -9 K 0 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9 F -4 -5 -4 -6 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9 P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9 W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 30 2 -6 -6 -6 -4 -9 Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -4 -2 -9 V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -9 B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9 Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM450000066400000000000000000000040241216526722600213440ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 450 substitution matrix, scale = ln(2)/6 = 0.115525 # # Expected score = -0.476, Entropy = 0.105 bits # # Lowest score = -9, Highest score = 30 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 1 -1 0 -2 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9 R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9 N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -4 -3 -1 1 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9 C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -2 0 -2 -9 1 -2 -4 -5 -2 -9 Q 0 2 1 2 -5 3 2 0 3 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9 G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9 H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -9 I 0 -2 -1 -2 -2 -1 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9 L -2 -3 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9 K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -2 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9 F -3 -4 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -3 -3 2 12 0 -4 -5 -2 -9 P 1 0 0 0 -2 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9 W -6 4 -4 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9 Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 14 -2 -4 -4 -2 -9 V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9 B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9 Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9 X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM460000066400000000000000000000040251216526722600213460ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 460 substitution matrix, scale = ln(2)/6 = 0.115525 # # Expected score = -0.429, Entropy = 0.0994 bits # # Lowest score = -9, Highest score = 30 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9 R -1 5 1 0 -4 1 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9 N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -3 0 1 0 -4 -3 -1 1 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9 C -2 -4 -3 -5 19 -5 -5 -3 -3 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9 Q 0 1 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 1 2 0 -9 E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9 G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -7 -5 -1 1 0 0 -9 H 0 2 1 1 -3 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9 I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -9 L -1 -2 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -1 1 3 -3 -2 -1 -9 K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9 F -3 -4 -3 -5 -3 -4 -5 -5 -2 2 3 -5 1 12 -4 -3 -3 2 11 0 -4 -5 -2 -9 P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 0 0 -9 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9 W -6 4 -4 -7 -9 -5 -7 -7 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9 Y -3 -4 -3 -4 2 -4 -4 -5 0 0 1 -4 -1 11 -5 -3 -3 2 14 -2 -4 -4 -2 -9 V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9 B 1 0 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9 Z 0 1 1 2 -5 2 2 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9 X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM470000066400000000000000000000051571216526722600213560ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 470 substitution matrix, scale = ln(2)/7 = 0.0990210 # # Expected score = -0.520, Entropy = 0.0942 bits # # Lowest score = -10, Highest score = 35 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 1 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10 R -1 6 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10 N 1 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10 D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10 C -2 -4 -4 -5 22 -6 -5 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -10 2 -2 -5 -6 -3 -10 Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -10 G 2 -1 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 1 1 1 -8 -6 -1 1 1 0 -10 H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10 I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10 L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 8 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10 K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10 M -1 0 -1 -2 -6 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10 F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10 P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -4 -3 -1 1 0 0 -10 T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10 W -7 4 -5 -8 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -4 -6 35 2 -7 -6 -7 -4 -10 Y -4 -5 -3 -5 2 -4 -5 -6 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10 V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -10 B 1 0 2 3 -5 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10 Z 0 1 1 3 -6 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -7 -5 -1 2 3 0 -10 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM480000066400000000000000000000051571216526722600213570ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 480 substitution matrix, scale = ln(2)/7 = 0.0990210 # # Expected score = -0.494, Entropy = 0.0893 bits # # Lowest score = -10, Highest score = 35 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 1 1 -2 0 1 2 0 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10 R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -10 N 1 1 1 2 -4 1 2 1 1 -1 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10 D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -1 2 2 0 -10 C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -10 2 -2 -4 -5 -3 -10 Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -8 -5 -1 2 3 0 -10 G 2 -1 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -10 H 0 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10 I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10 L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10 K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10 M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10 F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10 P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10 T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10 W -7 4 -5 -7 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -3 -6 35 2 -7 -6 -6 -4 -10 Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10 V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 3 -1 -1 0 -10 B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10 Z 0 1 1 2 -5 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -6 -5 -1 2 2 0 -10 X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM490000066400000000000000000000040261216526722600213520ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 490 substitution matrix, scale = ln(2)/7 = 0.0990210 # # Expected score = -0.431, Entropy = 0.0847 bits # # Lowest score = -9, Highest score = 34 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 2 0 0 -1 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9 R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9 N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9 C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 2 -2 -4 -5 -2 -9 Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9 E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9 G 2 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9 H 0 2 1 1 -4 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -9 I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9 L -1 -3 -2 -3 -6 -2 -3 -3 -2 4 7 -2 5 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9 K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9 F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -9 P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 4 1 1 -6 -5 -1 0 1 0 -9 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9 W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9 Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -2 -4 -4 -2 -9 V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9 B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9 Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9 X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM50000066400000000000000000000051521216526722600212630ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 50 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -3.70, Entropy = 2.00 bits # # Lowest score = -13, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -5 -2 -2 -5 -3 -1 -1 -5 -3 -5 -5 -4 -7 0 0 0 -11 -6 -1 -2 -2 -2 -13 R -5 8 -4 -7 -6 0 -7 -7 0 -4 -7 1 -3 -8 -3 -2 -5 -1 -8 -6 -5 -2 -4 -13 N -2 -4 7 2 -8 -2 -1 -2 1 -4 -6 0 -6 -7 -4 1 -1 -7 -3 -6 5 -1 -2 -13 D -2 -7 2 7 -11 -1 3 -2 -2 -6 -10 -3 -8 -12 -6 -2 -3 -12 -9 -6 6 2 -4 -13 C -5 -6 -8 -11 9 -11 -11 -7 -6 -5 -12 -11 -11 -10 -6 -2 -6 -13 -3 -5 -9 -11 -7 -13 Q -3 0 -2 -1 -11 8 2 -5 2 -6 -4 -2 -3 -10 -2 -4 -4 -10 -9 -5 -2 6 -3 -13 E -1 -7 -1 3 -11 2 7 -3 -3 -4 -7 -3 -5 -11 -4 -3 -4 -13 -7 -5 2 6 -3 -13 G -1 -7 -2 -2 -7 -5 -3 6 -7 -8 -9 -6 -7 -8 -4 -1 -4 -12 -11 -4 -2 -4 -4 -13 H -5 0 1 -2 -6 2 -3 -7 9 -7 -5 -4 -8 -5 -3 -4 -5 -6 -2 -5 0 0 -4 -13 I -3 -4 -4 -6 -5 -6 -4 -8 -7 8 0 -5 0 -1 -7 -5 -1 -11 -5 3 -5 -5 -3 -13 L -5 -7 -6 -10 -12 -4 -7 -9 -5 0 6 -6 2 -1 -6 -7 -5 -5 -5 -1 -7 -5 -5 -13 K -5 1 0 -3 -11 -2 -3 -6 -4 -5 -6 6 -1 -11 -5 -3 -2 -9 -8 -7 -1 -2 -4 -13 M -4 -3 -6 -8 -11 -3 -5 -7 -8 0 2 -1 10 -3 -6 -4 -3 -10 -8 0 -7 -4 -4 -13 F -7 -8 -7 -12 -10 -10 -11 -8 -5 -1 -1 -11 -3 9 -8 -5 -7 -3 3 -6 -9 -11 -6 -13 P 0 -3 -4 -6 -6 -2 -4 -4 -3 -7 -6 -5 -6 -8 8 -1 -3 -11 -11 -4 -5 -3 -4 -13 S 0 -2 1 -2 -2 -4 -3 -1 -4 -5 -7 -3 -4 -5 -1 6 1 -4 -5 -4 -1 -3 -2 -13 T 0 -5 -1 -3 -6 -4 -4 -4 -5 -1 -5 -2 -3 -7 -3 1 6 -10 -5 -2 -2 -4 -2 -13 W -11 -1 -7 -12 -13 -10 -13 -12 -6 -11 -5 -9 -10 -3 -11 -4 -10 13 -4 -12 -8 -11 -9 -13 Y -6 -8 -3 -9 -3 -9 -7 -11 -2 -5 -5 -8 -8 3 -11 -5 -5 -4 9 -6 -5 -8 -6 -13 V -1 -6 -6 -6 -5 -5 -5 -4 -5 3 -1 -7 0 -6 -4 -4 -2 -12 -6 7 -6 -5 -3 -13 B -2 -5 5 6 -9 -2 2 -2 0 -5 -7 -1 -7 -9 -5 -1 -2 -8 -5 -6 5 1 -3 -13 Z -2 -2 -1 2 -11 6 6 -4 0 -5 -5 -2 -4 -11 -3 -3 -4 -11 -8 -5 1 6 -3 -13 X -2 -4 -2 -4 -7 -3 -3 -4 -4 -3 -5 -4 -4 -6 -4 -2 -2 -9 -6 -3 -3 -3 -4 -13 * -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM500000066400000000000000000000040261216526722600213420ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 500 substitution matrix, scale = ln(2)/7 = 0.0990210 # # Expected score = -0.401, Entropy = 0.0803 bits # # Lowest score = -9, Highest score = 34 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9 R -1 5 1 0 -4 2 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9 N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9 D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9 C -2 -4 -3 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9 Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9 E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -1 -5 0 1 0 -7 -5 -1 2 2 0 -9 G 1 -1 1 1 -3 0 1 4 -1 -2 -3 0 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9 H 0 2 1 1 -4 2 1 -1 4 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9 I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9 L -1 -2 -2 -3 -6 -2 -3 -3 -2 4 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9 K 0 4 1 1 -5 1 1 0 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9 M -1 0 -1 -2 -5 -1 -1 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -1 -1 0 -9 F -3 -4 -4 -5 -3 -4 -5 -5 -2 2 4 -5 1 13 -4 -3 -3 3 13 0 -4 -5 -2 -9 P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 1 0 -9 S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9 T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9 W -6 4 -5 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9 Y -3 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -1 -4 -4 -2 -9 V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -1 3 -1 -1 0 -9 B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -1 -4 0 1 0 -6 -4 -1 2 2 0 -9 Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9 X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9 * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM60000066400000000000000000000051521216526722600212640ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 60 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -3.21, Entropy = 1.79 bits # # Lowest score = -12, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -5 -2 -2 -5 -3 -1 0 -5 -3 -4 -5 -3 -6 0 1 1 -10 -6 -1 -2 -2 -2 -12 R -5 8 -3 -6 -6 0 -6 -7 0 -4 -6 2 -2 -7 -2 -2 -4 0 -8 -5 -5 -2 -4 -12 N -2 -3 6 2 -7 -2 0 -1 1 -4 -5 0 -6 -6 -4 1 -1 -6 -3 -5 5 -1 -2 -12 D -2 -6 2 7 -10 -1 3 -2 -2 -5 -9 -2 -7 -11 -5 -2 -3 -11 -8 -6 5 2 -3 -12 C -5 -6 -7 -10 9 -10 -10 -7 -6 -4 -11 -10 -10 -9 -6 -1 -5 -12 -2 -4 -9 -10 -6 -12 Q -3 0 -2 -1 -10 7 2 -5 2 -5 -3 -1 -2 -9 -1 -3 -4 -9 -8 -5 -1 6 -3 -12 E -1 -6 0 3 -10 2 7 -2 -3 -4 -7 -3 -5 -10 -3 -2 -4 -12 -7 -4 2 5 -3 -12 G 0 -7 -1 -2 -7 -5 -2 6 -6 -7 -8 -5 -6 -7 -4 0 -3 -11 -10 -4 -2 -3 -3 -12 H -5 0 1 -2 -6 2 -3 -6 8 -6 -4 -4 -7 -4 -2 -4 -5 -5 -2 -5 0 0 -3 -12 I -3 -4 -4 -5 -4 -5 -4 -7 -6 7 0 -4 1 -1 -6 -4 -1 -10 -4 3 -4 -4 -3 -12 L -4 -6 -5 -9 -11 -3 -7 -8 -4 0 6 -6 2 -1 -5 -6 -5 -4 -5 -1 -7 -5 -4 -12 K -5 2 0 -2 -10 -1 -3 -5 -4 -4 -6 6 0 -10 -4 -2 -2 -8 -7 -6 -1 -2 -3 -12 M -3 -2 -6 -7 -10 -2 -5 -6 -7 1 2 0 10 -2 -6 -4 -2 -9 -7 0 -6 -4 -3 -12 F -6 -7 -6 -11 -9 -9 -10 -7 -4 -1 -1 -10 -2 8 -7 -5 -6 -3 3 -5 -8 -10 -5 -12 P 0 -2 -4 -5 -6 -1 -3 -4 -2 -6 -5 -4 -6 -7 7 0 -2 -10 -10 -4 -4 -2 -3 -12 S 1 -2 1 -2 -1 -3 -2 0 -4 -4 -6 -2 -4 -5 0 5 1 -4 -5 -4 0 -3 -2 -12 T 1 -4 -1 -3 -5 -4 -4 -3 -5 -1 -5 -2 -2 -6 -2 1 6 -9 -5 -1 -2 -4 -2 -12 W -10 0 -6 -11 -12 -9 -12 -11 -5 -10 -4 -8 -9 -3 -10 -4 -9 13 -3 -11 -8 -11 -8 -12 Y -6 -8 -3 -8 -2 -8 -7 -10 -2 -4 -5 -7 -7 3 -10 -5 -5 -3 9 -5 -5 -7 -5 -12 V -1 -5 -5 -6 -4 -5 -4 -4 -5 3 -1 -6 0 -5 -4 -4 -1 -11 -5 6 -5 -5 -3 -12 B -2 -5 5 5 -9 -1 2 -2 0 -4 -7 -1 -6 -8 -4 0 -2 -8 -5 -5 5 1 -3 -12 Z -2 -2 -1 2 -10 6 5 -3 0 -4 -5 -2 -4 -10 -2 -3 -4 -11 -7 -5 1 5 -3 -12 X -2 -4 -2 -3 -6 -3 -3 -3 -3 -3 -4 -3 -3 -5 -3 -2 -2 -8 -5 -3 -3 -3 -3 -12 * -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM70000066400000000000000000000051521216526722600212650ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -2.77, Entropy = 1.60 bits # # Lowest score = -11, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -4 -2 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -6 0 1 1 -9 -5 -1 -1 -1 -2 -11 R -4 8 -3 -6 -5 0 -5 -6 0 -3 -6 2 -2 -7 -2 -1 -4 0 -7 -5 -4 -2 -3 -11 N -2 -3 6 3 -7 -1 0 -1 1 -3 -5 0 -5 -6 -3 1 0 -6 -3 -5 5 -1 -2 -11 D -1 -6 3 6 -9 0 3 -1 -1 -5 -8 -2 -7 -10 -4 -1 -2 -10 -7 -5 5 2 -3 -11 C -4 -5 -7 -9 9 -9 -9 -6 -5 -4 -10 -9 -9 -8 -5 -1 -5 -11 -2 -4 -8 -9 -6 -11 Q -2 0 -1 0 -9 7 2 -4 2 -5 -3 -1 -2 -9 -1 -3 -3 -8 -8 -4 -1 5 -2 -11 E -1 -5 0 3 -9 2 6 -2 -2 -4 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -3 -11 G 0 -6 -1 -1 -6 -4 -2 6 -6 -6 -7 -5 -6 -7 -3 0 -3 -10 -9 -3 -1 -3 -3 -11 H -4 0 1 -1 -5 2 -2 -6 8 -6 -4 -3 -6 -4 -2 -3 -4 -5 -1 -4 0 1 -3 -11 I -2 -3 -3 -5 -4 -5 -4 -6 -6 7 1 -4 1 0 -5 -4 -1 -9 -4 3 -4 -4 -3 -11 L -4 -6 -5 -8 -10 -3 -6 -7 -4 1 6 -5 2 -1 -5 -6 -4 -4 -4 0 -6 -4 -4 -11 K -4 2 0 -2 -9 -1 -2 -5 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -7 -6 -1 -2 -3 -11 M -3 -2 -5 -7 -9 -2 -4 -6 -6 1 2 0 10 -2 -5 -3 -2 -8 -7 0 -6 -3 -3 -11 F -6 -7 -6 -10 -8 -9 -9 -7 -4 0 -1 -9 -2 8 -7 -4 -6 -2 4 -5 -7 -9 -5 -11 P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -5 -4 -5 -7 7 0 -2 -9 -9 -3 -4 -2 -3 -11 S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -6 -2 -3 -4 0 5 2 -3 -5 -3 0 -2 -1 -11 T 1 -4 0 -2 -5 -3 -3 -3 -4 -1 -4 -1 -2 -6 -2 2 6 -8 -4 -1 -1 -3 -2 -11 W -9 0 -6 -10 -11 -8 -11 -10 -5 -9 -4 -7 -8 -2 -9 -3 -8 13 -3 -10 -7 -10 -7 -11 Y -5 -7 -3 -7 -2 -8 -6 -9 -1 -4 -4 -7 -7 4 -9 -5 -4 -3 9 -5 -4 -7 -5 -11 V -1 -5 -5 -5 -4 -4 -4 -3 -4 3 0 -6 0 -5 -3 -3 -1 -10 -5 6 -5 -4 -2 -11 B -1 -4 5 5 -8 -1 2 -1 0 -4 -6 -1 -6 -7 -4 0 -1 -7 -4 -5 5 1 -2 -11 Z -1 -2 -1 2 -9 5 5 -3 1 -4 -4 -2 -3 -9 -2 -2 -3 -10 -7 -4 1 5 -3 -11 X -2 -3 -2 -3 -6 -2 -3 -3 -3 -3 -4 -3 -3 -5 -3 -1 -2 -7 -5 -2 -2 -3 -3 -11 * -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM80000066400000000000000000000051521216526722600212660ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 80 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -2.55, Entropy = 1.44 bits # # Lowest score = -11, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -4 -1 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -5 0 1 1 -8 -5 0 -1 -1 -1 -11 R -4 7 -2 -5 -5 0 -4 -6 0 -3 -5 2 -2 -6 -2 -1 -3 0 -7 -5 -3 -1 -3 -11 N -1 -2 5 3 -6 -1 0 -1 2 -3 -5 0 -4 -5 -3 1 0 -5 -3 -4 4 0 -1 -11 D -1 -5 3 6 -9 0 4 -1 -1 -4 -7 -2 -6 -9 -4 -1 -2 -10 -7 -5 5 2 -3 -11 C -4 -5 -6 -9 9 -9 -9 -6 -5 -4 -9 -9 -8 -8 -5 -1 -4 -10 -2 -3 -7 -9 -5 -11 Q -2 0 -1 0 -9 7 2 -4 2 -4 -3 -1 -2 -8 -1 -3 -3 -8 -7 -4 0 5 -2 -11 E -1 -4 0 4 -9 2 6 -2 -2 -3 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -2 -11 G 0 -6 -1 -1 -6 -4 -2 6 -5 -6 -7 -4 -5 -6 -3 0 -2 -10 -8 -3 -1 -2 -3 -11 H -4 0 2 -1 -5 2 -2 -5 8 -5 -4 -3 -5 -3 -2 -3 -4 -4 -1 -4 0 1 -2 -11 I -2 -3 -3 -4 -4 -4 -3 -6 -5 7 1 -4 1 0 -5 -4 -1 -8 -3 3 -4 -4 -2 -11 L -4 -5 -5 -7 -9 -3 -6 -7 -4 1 6 -5 2 0 -4 -5 -4 -3 -4 0 -6 -4 -3 -11 K -4 2 0 -2 -9 -1 -2 -4 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -6 -5 -1 -1 -3 -11 M -3 -2 -4 -6 -8 -2 -4 -5 -5 1 2 0 9 -2 -5 -3 -2 -7 -6 1 -5 -3 -2 -11 F -5 -6 -5 -9 -8 -8 -9 -6 -3 0 0 -9 -2 8 -7 -4 -5 -2 4 -4 -7 -8 -5 -11 P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -4 -4 -5 -7 7 0 -2 -9 -8 -3 -3 -2 -2 -11 S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -5 -2 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -11 T 1 -3 0 -2 -4 -3 -3 -2 -4 -1 -4 -1 -2 -5 -2 2 5 -8 -4 -1 -1 -3 -1 -11 W -8 0 -5 -10 -10 -8 -11 -10 -4 -8 -3 -7 -7 -2 -9 -3 -8 13 -2 -10 -7 -9 -7 -11 Y -5 -7 -3 -7 -2 -7 -6 -8 -1 -3 -4 -6 -6 4 -8 -4 -4 -2 9 -5 -4 -6 -4 -11 V 0 -5 -4 -5 -3 -4 -4 -3 -4 3 0 -5 1 -4 -3 -3 -1 -10 -5 6 -4 -4 -2 -11 B -1 -3 4 5 -7 0 2 -1 0 -4 -6 -1 -5 -7 -3 0 -1 -7 -4 -4 5 2 -2 -11 Z -1 -1 0 2 -9 5 5 -2 1 -4 -4 -1 -3 -8 -2 -2 -3 -9 -6 -4 2 5 -2 -11 X -1 -3 -1 -3 -5 -2 -2 -3 -2 -2 -3 -3 -2 -5 -2 -1 -1 -7 -4 -2 -2 -2 -3 -11 * -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1 JAligner-1.0/src/jaligner/matrix/matrices/PAM90000066400000000000000000000051521216526722600212670ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 90 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -2.26, Entropy = 1.30 bits # # Lowest score = -10, Highest score = 13 # A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -4 -1 -1 -3 -2 0 0 -4 -2 -3 -3 -2 -5 0 1 1 -8 -5 0 -1 -1 -1 -10 R -4 7 -2 -5 -5 0 -4 -5 1 -3 -5 2 -2 -6 -1 -1 -3 0 -6 -4 -3 -1 -2 -10 N -1 -2 5 3 -6 -1 0 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -4 4 0 -1 -10 D -1 -5 3 6 -8 0 4 -1 -1 -4 -7 -2 -5 -8 -4 -1 -2 -9 -6 -4 5 3 -2 -10 C -3 -5 -6 -8 9 -8 -8 -5 -5 -3 -9 -8 -8 -7 -5 -1 -4 -10 -1 -3 -7 -8 -5 -10 Q -2 0 -1 0 -8 6 2 -3 2 -4 -3 -1 -2 -7 -1 -2 -3 -7 -6 -4 0 5 -2 -10 E 0 -4 0 4 -8 2 6 -1 -1 -3 -5 -2 -4 -8 -2 -2 -2 -10 -6 -3 2 5 -2 -10 G 0 -5 -1 -1 -5 -3 -1 5 -5 -5 -6 -4 -5 -6 -3 0 -2 -9 -8 -3 -1 -2 -2 -10 H -4 1 2 -1 -5 2 -1 -5 8 -5 -3 -2 -5 -3 -2 -3 -3 -4 -1 -4 1 1 -2 -10 I -2 -3 -3 -4 -3 -4 -3 -5 -5 6 1 -3 1 0 -4 -3 0 -8 -3 3 -3 -3 -2 -10 L -3 -5 -4 -7 -9 -3 -5 -6 -3 1 6 -5 2 0 -4 -5 -3 -3 -3 0 -5 -4 -3 -10 K -3 2 1 -2 -8 -1 -2 -4 -2 -3 -5 5 0 -8 -3 -1 -1 -6 -6 -5 0 -1 -2 -10 M -2 -2 -4 -5 -8 -2 -4 -5 -5 1 2 0 9 -1 -4 -3 -2 -7 -6 1 -5 -3 -2 -10 F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -8 -1 8 -6 -4 -5 -2 4 -4 -6 -8 -4 -10 P 0 -1 -2 -4 -5 -1 -2 -3 -2 -4 -4 -3 -4 -6 7 0 -1 -8 -8 -3 -3 -2 -2 -10 S 1 -1 1 -1 -1 -2 -2 0 -3 -3 -5 -1 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -10 T 1 -3 0 -2 -4 -3 -2 -2 -3 0 -3 -1 -2 -5 -1 2 5 -7 -4 -1 -1 -2 -1 -10 W -8 0 -5 -9 -10 -7 -10 -9 -4 -8 -3 -6 -7 -2 -8 -3 -7 13 -2 -9 -7 -8 -6 -10 Y -5 -6 -2 -6 -1 -6 -6 -8 -1 -3 -3 -6 -6 4 -8 -4 -4 -2 9 -4 -4 -6 -4 -10 V 0 -4 -4 -4 -3 -4 -3 -3 -4 3 0 -5 1 -4 -3 -3 -1 -9 -4 6 -4 -3 -2 -10 B -1 -3 4 5 -7 0 2 -1 1 -3 -5 0 -5 -6 -3 0 -1 -7 -4 -4 4 2 -2 -10 Z -1 -1 0 3 -8 5 5 -2 1 -3 -4 -1 -3 -8 -2 -2 -2 -8 -6 -3 2 5 -2 -10 X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 JAligner-1.0/src/jaligner/matrix/package.html000066400000000000000000000002441216526722600212250ustar00rootroot00000000000000 Scoring matrices package. @author Ahmed Moustafa JAligner-1.0/src/jaligner/package.html000066400000000000000000000003201216526722600177140ustar00rootroot00000000000000 Core classes for the implementation of Smith-Waterman-Gotoh algorithm @author Ahmed Moustafa JAligner-1.0/src/jaligner/test/000077500000000000000000000000001216526722600164175ustar00rootroot00000000000000JAligner-1.0/src/jaligner/test/NeedlemanWunschGotohTester.java000066400000000000000000000120331216526722600245310ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.test; import jaligner.Alignment; import jaligner.NeedlemanWunschGotoh; import jaligner.Sequence; import jaligner.formats.Format; import jaligner.formats.Pair; import jaligner.matrix.Matrix; import jaligner.matrix.MatrixLoader; import java.util.ArrayList; import java.util.Iterator; import java.util.List; import java.util.Random; /** * Testing the scores of the alignments of {@link jaligner.NeedlemanWunschGotoh}. * * @author Bram Minnaert */ public class NeedlemanWunschGotohTester { public static void main(String[] args) { int numberOfTests = Integer.parseInt(args[0]); int sequencesSize = Integer.parseInt(args[1]); Random random = new Random(); Format format = new Pair(); try { List matrices = new ArrayList(); for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) { matrices.add(i.next()); } int countOfMatrices = matrices.size(); int i = 1; while (i <= numberOfTests) { System.gc(); String s1 = RandomSequenceGenerator.generate(sequencesSize); String s2 = RandomSequenceGenerator.generate(sequencesSize); int o = random.nextInt(50); int e = random.nextInt(10); if (s1.length() > 0 && s2.length() > 0 && o >= e) { Matrix matrix = (Matrix) MatrixLoader .load((String) matrices.get(random .nextInt(countOfMatrices))); Sequence seq1 = new Sequence(s1); Sequence seq2 = new Sequence(s2); Alignment alignment1 = NeedlemanWunschGotoh.align(seq1, seq2, matrix, o, e); if (!alignment1.checkScore()) { System.err.println("Invalid alignment found:"); System.err.println("Sequence 1 = " + s1); System.err.println("Sequence 2 = " + s2); System.err.println(format.format(alignment1)); System.err.println(alignment1.getSummary()); System.err .println("The score of the alignment above is: " + alignment1.calculateScore()); System.exit(1); } Alignment alignment2 = NeedlemanWunschGotoh.align(seq2, seq1, matrix, o, e); if (!alignment1.checkScore()) { System.err.println("Invalid alignment found:"); System.err.println("Sequence 1 = " + s2); System.err.println("Sequence 2 = " + s1); System.err.println(format.format(alignment2)); System.err.println(alignment2.getSummary()); System.err .println("The score of the alignment above is: " + alignment2.calculateScore()); System.exit(1); } if (alignment1.getScore() != alignment2.getScore()) { System.err.println("Not symmetric alignment:"); System.err.println("Alignment #1: "); System.err.println("Sequence 1 = " + s1); System.err.println("Sequence 2 = " + s2); System.err.println(format.format(alignment1)); System.err.println(alignment1.getSummary()); System.err.println(); System.err.println("Alignment #2: "); System.err.println("Sequence 1 = " + s2); System.err.println("Sequence 2 = " + s1); System.err.println(format.format(alignment2)); System.err.println(alignment2.getSummary()); System.exit(1); } } System.out.println("Processed " + i + "/" + numberOfTests); i++; } } catch (Exception e) { e.printStackTrace(); System.exit(1); } } }JAligner-1.0/src/jaligner/test/NeedlemanWunschTester.java000066400000000000000000000117201216526722600235320ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.test; import jaligner.Alignment; import jaligner.NeedlemanWunsch; import jaligner.Sequence; import jaligner.formats.Format; import jaligner.formats.Pair; import jaligner.matrix.Matrix; import jaligner.matrix.MatrixLoader; import java.util.ArrayList; import java.util.Iterator; import java.util.List; import java.util.Random; /** * Testing the scores of the alignments of {@link jaligner.NeedlemanWunsch}. * * @author Ahmed Moustafa */ public class NeedlemanWunschTester { public static void main(String[] args) { int numberOfTests = Integer.parseInt(args[0]); int sequencesSize = Integer.parseInt(args[1]); Random random = new Random(); Format format = new Pair(); try { List matrices = new ArrayList(); for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) { matrices.add(i.next()); } int countOfMatrices = matrices.size(); int i = 1; while (i <= numberOfTests) { System.gc(); String s1 = RandomSequenceGenerator.generate(sequencesSize); String s2 = RandomSequenceGenerator.generate(sequencesSize); float gap = random.nextInt(1000); if (s1.length() > 0 && s2.length() > 0) { Matrix matrix = (Matrix) MatrixLoader .load((String) matrices.get(random .nextInt(countOfMatrices))); Sequence seq1 = new Sequence(s1); Sequence seq2 = new Sequence(s2); Alignment alignment1 = NeedlemanWunsch.align(seq1, seq2, matrix, gap); if (!alignment1.checkScore()) { System.out.println("Invalid alignment found:"); System.out.println("Sequence 1 = " + s1); System.out.println("Sequence 2 = " + s2); System.out.println(format.format(alignment1)); System.out.println(alignment1.getSummary()); System.out .println("The score of the alignment above is: " + alignment1.calculateScore()); System.exit(1); } Alignment alignment2 = NeedlemanWunsch.align(seq2, seq1, matrix, gap); if (!alignment1.checkScore()) { System.out.println("Invalid alignment found:"); System.out.println("Sequence 1 = " + s2); System.out.println("Sequence 2 = " + s1); System.out.println(format.format(alignment2)); System.out.println(alignment2.getSummary()); System.out .println("The score of the alignment above is: " + alignment2.calculateScore()); System.exit(1); } if (alignment1.getScore() != alignment2.getScore()) { System.out.println("Not symmetric alignment:"); System.out.println("Alignment #1: "); System.out.println("Sequence 1 = " + s1); System.out.println("Sequence 2 = " + s2); System.out.println(format.format(alignment1)); System.out.println(alignment1.getSummary()); System.out.println(); System.out.println("Alignment #2: "); System.out.println("Sequence 1 = " + s2); System.out.println("Sequence 2 = " + s1); System.out.println(format.format(alignment2)); System.out.println(alignment2.getSummary()); System.exit(1); } } System.out.println("Processed " + i + "/" + numberOfTests); i++; } } catch (Exception e) { e.printStackTrace(); System.exit(1); } } }JAligner-1.0/src/jaligner/test/RandomSequenceGenerator.java000066400000000000000000000041401216526722600240410ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.test; import java.util.Random; /** * This class contains a random generator for protein sequences. * * @author Bram Minnaert */ public class RandomSequenceGenerator { /** * All possible characters */ private static final char[] CHARS = { 'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V' }; /** * Number of possible characters */ private static final int NUMBER_OF_CHARS = CHARS.length; /** * Random generator */ private static Random random = new Random(); /** * Returns random sequence * * @param length * Size of the sequence * @return Random sequence */ public static String generate(int length) { StringBuffer buffer = new StringBuffer(); char randomChar; int randomInt; for (int i = 0; i < length; i++) { randomInt = random.nextInt(NUMBER_OF_CHARS); randomChar = CHARS[randomInt]; buffer.append(randomChar); } return buffer.toString(); } /** * Displays 10 random protein sequences with length 50. * * @param args * no args */ public static void main(String[] args) { for (int i = 0; i < 10; i++) { System.out.println("S" + i + " = " + generate(50)); } } }JAligner-1.0/src/jaligner/test/SmithWatermanGotohTester.java000066400000000000000000000120211216526722600242310ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.test; import jaligner.Alignment; import jaligner.Sequence; import jaligner.SmithWatermanGotoh; import jaligner.formats.Format; import jaligner.formats.Pair; import jaligner.matrix.Matrix; import jaligner.matrix.MatrixLoader; import java.util.ArrayList; import java.util.Iterator; import java.util.List; import java.util.Random; /** * Testing the scores of the alignments of {@link jaligner.SmithWatermanGotoh}. * * @author Bram Minnaert */ public class SmithWatermanGotohTester { public static void main(String[] args) { int numberOfTests = Integer.parseInt(args[0]); int sequencesSize = Integer.parseInt(args[1]); Random random = new Random(); Format format = new Pair(); try { List matrices = new ArrayList(); for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) { matrices.add(i.next()); } int countOfMatrices = matrices.size(); int i = 1; while (i <= numberOfTests) { System.gc(); String s1 = RandomSequenceGenerator.generate(sequencesSize); String s2 = RandomSequenceGenerator.generate(sequencesSize); int o = random.nextInt(50); int e = random.nextInt(10); if (s1.length() > 0 && s2.length() > 0 && o >= e) { Matrix matrix = (Matrix) MatrixLoader .load((String) matrices.get(random .nextInt(countOfMatrices))); Sequence seq1 = new Sequence(s1); Sequence seq2 = new Sequence(s2); Alignment alignment1 = SmithWatermanGotoh.align(seq1, seq2, matrix, o, e); if (!alignment1.checkScore()) { System.err.println("Invalid alignment found:"); System.err.println("Sequence 1 = " + s1); System.err.println("Sequence 2 = " + s2); System.err.println(format.format(alignment1)); System.err.println(alignment1.getSummary()); System.err .println("The score of the alignment above is: " + alignment1.calculateScore()); System.exit(1); } Alignment alignment2 = SmithWatermanGotoh.align(seq2, seq1, matrix, o, e); if (!alignment1.checkScore()) { System.err.println("Invalid alignment found:"); System.err.println("Sequence 1 = " + s2); System.err.println("Sequence 2 = " + s1); System.err.println(format.format(alignment2)); System.err.println(alignment2.getSummary()); System.err .println("The score of the alignment above is: " + alignment2.calculateScore()); System.exit(1); } if (alignment1.getScore() != alignment2.getScore()) { System.err.println("Not symmetric alignment:"); System.err.println("Alignment #1: "); System.err.println("Sequence 1 = " + s1); System.err.println("Sequence 2 = " + s2); System.err.println(format.format(alignment1)); System.err.println(alignment1.getSummary()); System.err.println(); System.err.println("Alignment #2: "); System.err.println("Sequence 1 = " + s2); System.err.println("Sequence 2 = " + s1); System.err.println(format.format(alignment2)); System.err.println(alignment2.getSummary()); System.exit(1); } } System.out.println("Processed " + i + "/" + numberOfTests); i++; } } catch (Exception e) { e.printStackTrace(); System.exit(1); } } }JAligner-1.0/src/jaligner/test/package.html000066400000000000000000000002321216526722600206750ustar00rootroot00000000000000 Testing package. @author Bram Minnaert JAligner-1.0/src/jaligner/ui/000077500000000000000000000000001216526722600160555ustar00rootroot00000000000000JAligner-1.0/src/jaligner/ui/AlignCommandLine.java000066400000000000000000000056251216526722600220710ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui; import jaligner.Alignment; import jaligner.Sequence; import jaligner.SmithWatermanGotoh; import jaligner.formats.Pair; import jaligner.matrix.Matrix; import jaligner.matrix.MatrixLoader; import jaligner.util.Commons; import jaligner.util.SequenceParser; import java.io.File; import java.util.logging.Level; import java.util.logging.Logger; /** * Command line interface for JAligner. * * @author Ahmed Moustafa */ public class AlignCommandLine { private static final Logger logger = Logger.getLogger(AlignCommandLine.class.getName()); /** * @param args The command line arguments */ public static void main(String[] args) { logger.info( Commons.getJAlignerInfo() ); if (args.length == 0) { new AlignWindow().setVisible(true); } else { if (args.length == 5) { try { String f1 = args[0]; // file name of sequence #1 String f2 = args[1]; // file name of sequence #2 String m = args[2]; // scoring matrix id or file name user-defined scoring matrix float o = Float.parseFloat(args[3]); // open gap penalty float e = Float.parseFloat(args[4]); // extend gap penalty Sequence s1 = SequenceParser.parse(new File(f1)); Sequence s2 = SequenceParser.parse(new File(f2)); Matrix matrix = MatrixLoader.load(m); Alignment alignment = SmithWatermanGotoh.align (s1, s2, matrix, o, e); System.out.println (alignment.getSummary()); System.out.println (new Pair().format(alignment)); } catch (Exception e) { logger.log(Level.SEVERE, "Failed processing the command line: " + e.getMessage(), e); System.exit(1); } } else { logger.severe( "Invalid number of arguments: " + args.length ); printUsage(); System.exit(1); } } } /** * Prints the syntax for using JAligner */ private static void printUsage( ) { StringBuffer buffer = new StringBuffer(); buffer.append ( "\n" ); buffer.append ( "Usage:\n" ); buffer.append ( "------\n" ); buffer.append ( "[1] java -jar jaligner.jar \n" ); buffer.append ( "[2] java -jar jaligner.jar\n" ); buffer.append ( "\n" ) ; logger.info(buffer.toString()); } }JAligner-1.0/src/jaligner/ui/AlignWindow.form000066400000000000000000001526701216526722600211770ustar00rootroot00000000000000
JAligner-1.0/src/jaligner/ui/AlignWindow.java000066400000000000000000002106601216526722600211470ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui; import jaligner.Alignment; import jaligner.Sequence; import jaligner.SmithWatermanGotoh; import jaligner.example.SmithWatermanGotohExample; import jaligner.formats.CLUSTAL; import jaligner.formats.FASTA; import jaligner.formats.FormatFactory; import jaligner.formats.Pair; import jaligner.matrix.Matrix; import jaligner.matrix.MatrixLoader; import jaligner.ui.clipboard.ClipboardListener; import jaligner.ui.clipboard.ClipboardPoller; import jaligner.ui.filechooser.FileChooserFactory; import jaligner.ui.filechooser.NamedInputStream; import jaligner.ui.images.ToolbarIcons; import jaligner.ui.logging.DocumentHandler; import jaligner.ui.util.TextComponentUtil; import jaligner.ui.util.TextComponentUtilException; import jaligner.util.Commons; import jaligner.util.SequenceParser; import java.awt.Color; import java.awt.Component; import java.awt.Cursor; import java.awt.Image; import java.awt.event.ActionEvent; import java.awt.event.MouseEvent; import java.net.URL; import java.text.DecimalFormat; import java.util.Collection; import java.util.Enumeration; import java.util.HashMap; import java.util.Iterator; import java.util.logging.Level; import java.util.logging.Logger; import javax.swing.AbstractAction; import javax.swing.AbstractButton; import javax.swing.Action; import javax.swing.JComboBox; import javax.swing.JFormattedTextField; import javax.swing.JOptionPane; import javax.swing.JTextArea; import javax.swing.KeyStroke; import javax.swing.event.CaretEvent; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; import javax.swing.text.JTextComponent; /** * Graphical user inteface for JAligner. * * @author Ahmed Moustafa */ public class AlignWindow extends javax.swing.JFrame implements ClipboardListener, DocumentListener { /** * */ private static final long serialVersionUID = 3257844376876364850L; /** * Window width */ private static final int WINDOW_WIDTH = 800; /** * Window height */ private static final int WINDOW_HEIGHT = 600; /** * Default open gap penalty */ private static final float DEFAULT_OPEN_GAP_PENALTY = 10f; /** * Default extend gap penalty */ private static final float DEFAULT_EXTEND_GAP_PENALTY = 0.5f; /** * Default scoring matrix */ private static final String DEFAULT_SCORING_MATRIX = "BLOSUM62"; /** * Logger */ private static final Logger logger = Logger.getLogger(AlignWindow.class.getName()); /** * Clipboard poller thread */ private ClipboardPoller clipboardPoller = null; /** * Loaded scoring matrices */ private HashMap matrices = new HashMap(); /** * Current text component */ private JTextComponent currentTextComponent = null; // The actions public Action nextFocusAction = new AbstractAction("Move Focus Forwards") { /** * */ private static final long serialVersionUID = 3763091972940183858L; public void actionPerformed(ActionEvent evt) { ((Component)evt.getSource()).transferFocus(); } }; public Action prevFocusAction = new AbstractAction("Move Focus Backwards") { /** * */ private static final long serialVersionUID = 3257844402628997943L; public void actionPerformed(ActionEvent evt) { ((Component)evt.getSource()).transferFocusBackward(); } }; /** * Constructor */ public AlignWindow() { initComponents(); logger.addHandler(new DocumentHandler(jTextPaneConsole)); try { // Set the icon for the frame URL url = getClass().getResource( ToolbarIcons.GIFS_HOME + "jaligner.gif"); if (url != null) { Image image = java.awt.Toolkit.getDefaultToolkit().getImage(url); setIconImage(image); } else { logger.warning("Image URL is NULL"); } } catch (Exception e) { logger.log(Level.WARNING, "Failed setting the frame image: " + e.getMessage(), e); } jMenuItemFileOpen.setVisible(false); jFormattedTextFieldGapOpen.setValue(new Float(DEFAULT_OPEN_GAP_PENALTY)); jFormattedTextFieldGapExtend.setValue(new Float(DEFAULT_EXTEND_GAP_PENALTY)); Collection matrices = null; try { matrices = MatrixLoader.list(false); } catch (Exception e) { logger.log(Level.WARNING, "Failed getting list of scoring matrices: " + e.getMessage(), e); } if (matrices != null) { populateComboBox(jComboBoxScoringMatrix, matrices, DEFAULT_SCORING_MATRIX); } FormatFactory.getInstance().registerFormat(new CLUSTAL()); FormatFactory.getInstance().registerFormat(new Pair()); FormatFactory.getInstance().registerFormat(new FASTA()); Collection formats = FormatFactory.getInstance().getFormats(); String[] outputFormats = new String[formats.size()]; Iterator i = formats.iterator(); for (int j = 0; i.hasNext(); j++) { outputFormats[j] = i.next(); } populateComboBox(jComboBoxOutputFormat, outputFormats, null); jTextAreaSequence1.getDocument().addDocumentListener(this); jTextAreaSequence2.getDocument().addDocumentListener(this); jTextAreaAlignment.getDocument().addDocumentListener(this); // Add actions jTextAreaSequence1.getInputMap().put(KeyStroke.getKeyStroke("TAB"), nextFocusAction.getClass().getName()); jTextAreaSequence1.getActionMap().put(nextFocusAction.getClass().getName(), nextFocusAction); jTextAreaSequence1.getInputMap().put(KeyStroke.getKeyStroke("shift TAB"), prevFocusAction.getClass().getName()); jTextAreaSequence1.getActionMap().put(prevFocusAction.getClass().getName(), prevFocusAction); jTextAreaSequence2.getInputMap().put(KeyStroke.getKeyStroke("TAB"), nextFocusAction.getClass().getName()); jTextAreaSequence2.getActionMap().put(nextFocusAction.getClass().getName(), nextFocusAction); jTextAreaSequence2.getInputMap().put(KeyStroke.getKeyStroke("shift TAB"), prevFocusAction.getClass().getName()); jTextAreaSequence2.getActionMap().put(prevFocusAction.getClass().getName(), prevFocusAction); // Add radio buttons to group buttonGroupSequences.add(jRadioButtonSequence1); buttonGroupSequences.add(jRadioButtonSequence2); buttonGroupSequences.add(jRadioButtonAlignment); buttonGroupSequences.add(jRadioButtonConsole); // Split the space jSplitPaneBody.setResizeWeight(.9D); jSplitPaneIO.setResizeWeight(.5D); jSplitPaneSequences.setResizeWeight(.5D); // Set the focus on the text area for sequence #1 jTextAreaSequence1.requestFocus(); // Start the clipboard checker clipboardPoller = new ClipboardPoller(this); clipboardPoller.start(); // Hide the print menu item in under the File menu jMenuItemFilePrint.setVisible(false); // Set the frame size this.setSize(WINDOW_WIDTH, WINDOW_HEIGHT); } // //GEN-BEGIN:initComponents private void initComponents() { jPopup = new javax.swing.JPopupMenu(); jPopupOpen = new javax.swing.JMenuItem(); jPopupSave = new javax.swing.JMenuItem(); jPopupSeparator1 = new javax.swing.JSeparator(); jPopupCut = new javax.swing.JMenuItem(); jPopupCopy = new javax.swing.JMenuItem(); jPopupPaste = new javax.swing.JMenuItem(); jPopupDelete = new javax.swing.JMenuItem(); jPopupSeparator2 = new javax.swing.JSeparator(); jPopupPrint = new javax.swing.JMenuItem(); jPopupSeparator3 = new javax.swing.JSeparator(); jPopupSelectAll = new javax.swing.JMenuItem(); buttonGroupSequences = new javax.swing.ButtonGroup(); jToolBar = new javax.swing.JToolBar(); jButtonOpen = new javax.swing.JButton(); jButtonSave = new javax.swing.JButton(); jButtonCut = new javax.swing.JButton(); jButtonCopy = new javax.swing.JButton(); jButtonPaste = new javax.swing.JButton(); jButtonDelete = new javax.swing.JButton(); jButtonPrint = new javax.swing.JButton(); jButtonExit = new javax.swing.JButton(); jSplitPaneBody = new javax.swing.JSplitPane(); jSplitPaneIO = new javax.swing.JSplitPane(); jSplitPaneSequences = new javax.swing.JSplitPane(); jPanelSequence1 = new javax.swing.JPanel(); jScrollPaneSequence1 = new javax.swing.JScrollPane(); jTextAreaSequence1 = new javax.swing.JTextArea(); jRadioButtonSequence1 = new javax.swing.JRadioButton(); jPanelSequence2 = new javax.swing.JPanel(); jScrollPaneSequence2 = new javax.swing.JScrollPane(); jTextAreaSequence2 = new javax.swing.JTextArea(); jRadioButtonSequence2 = new javax.swing.JRadioButton(); jPanelAlignment = new javax.swing.JPanel(); jRadioButtonAlignment = new javax.swing.JRadioButton(); jScrollPaneAlignment = new javax.swing.JScrollPane(); jTextAreaAlignment = new javax.swing.JTextArea(); jPanelConsole = new javax.swing.JPanel(); jRadioButtonConsole = new javax.swing.JRadioButton(); jScrollPaneConsole = new javax.swing.JScrollPane(); jTextPaneConsole = new javax.swing.JTextPane(); jPanelControls = new javax.swing.JPanel(); jPanelScoringMatrix = new javax.swing.JPanel(); jLabelScoringMatrix = new javax.swing.JLabel(); jComboBoxScoringMatrix = new javax.swing.JComboBox(); jPanelGapOpen = new javax.swing.JPanel(); jLabelOpenGapPenalty = new javax.swing.JLabel(); jFormattedTextFieldGapOpen = new JFormattedTextField(new DecimalFormat("##0.0##")); jPanelGapExtend = new javax.swing.JPanel(); jLabelExtendGapPenalty = new javax.swing.JLabel(); jFormattedTextFieldGapExtend = new JFormattedTextField(new DecimalFormat("##0.0##")); jPanelOutputFormat = new javax.swing.JPanel(); jLabelOutputFormat = new javax.swing.JLabel(); jComboBoxOutputFormat = new javax.swing.JComboBox(); jPanelGo = new javax.swing.JPanel(); jButtonGo = new javax.swing.JButton(); jMenuBar = new javax.swing.JMenuBar(); jMenuFile = new javax.swing.JMenu(); jMenuItemFileOpen = new javax.swing.JMenuItem(); jMenuItemFileLoadSequence1 = new javax.swing.JMenuItem(); jMenuItemFileLoadSequence2 = new javax.swing.JMenuItem(); jMenuItemFileLoadMatrix = new javax.swing.JMenuItem(); jSeparatorFile = new javax.swing.JSeparator(); jMenuItemFileExit = new javax.swing.JMenuItem(); jMenuItemFilePrint = new javax.swing.JMenuItem(); jMenuEdit = new javax.swing.JMenu(); jMenuItemEditCut = new javax.swing.JMenuItem(); jMenuItemEditCopy = new javax.swing.JMenuItem(); jMenuItemEditPaste = new javax.swing.JMenuItem(); jMenuItemEditDelete = new javax.swing.JMenuItem(); jMenuItemEditSelectAll = new javax.swing.JMenuItem(); jMenuTools = new javax.swing.JMenu(); jMenuItemToolsRunExample = new javax.swing.JMenuItem(); jMenuHelp = new javax.swing.JMenu(); jMenuItemAbout = new javax.swing.JMenuItem(); jPopupOpen.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O, java.awt.event.InputEvent.CTRL_MASK)); jPopupOpen.setIcon(ToolbarIcons.OPEN); jPopupOpen.setMnemonic('O'); jPopupOpen.setText("Open..."); jPopupOpen.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupOpenActionPerformed(evt); } }); jPopup.add(jPopupOpen); jPopupSave.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S, java.awt.event.InputEvent.CTRL_MASK)); jPopupSave.setIcon(ToolbarIcons.SAVE); jPopupSave.setMnemonic('S'); jPopupSave.setText("Save..."); jPopupSave.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupSaveActionPerformed(evt); } }); jPopup.add(jPopupSave); jPopup.add(jPopupSeparator1); jPopupCut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.CTRL_MASK)); jPopupCut.setIcon(ToolbarIcons.CUT); jPopupCut.setMnemonic('t'); jPopupCut.setText("Cut"); jPopupCut.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupCutActionPerformed(evt); } }); jPopup.add(jPopupCut); jPopupCopy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK)); jPopupCopy.setIcon(ToolbarIcons.COPY); jPopupCopy.setMnemonic('C'); jPopupCopy.setText("Copy"); jPopupCopy.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupCopyActionPerformed(evt); } }); jPopup.add(jPopupCopy); jPopupPaste.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK)); jPopupPaste.setIcon(ToolbarIcons.PASTE); jPopupPaste.setMnemonic('P'); jPopupPaste.setText("Paste"); jPopupPaste.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupPasteActionPerformed(evt); } }); jPopup.add(jPopupPaste); jPopupDelete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0)); jPopupDelete.setIcon(ToolbarIcons.DELETE); jPopupDelete.setMnemonic('D'); jPopupDelete.setText("Delete"); jPopupDelete.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupDeleteActionPerformed(evt); } }); jPopup.add(jPopupDelete); jPopup.add(jPopupSeparator2); jPopupPrint.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_P, java.awt.event.InputEvent.CTRL_MASK)); jPopupPrint.setIcon(ToolbarIcons.PRINT); jPopupPrint.setMnemonic('D'); jPopupPrint.setText("Print"); jPopupPrint.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupPrintActionPerformed(evt); } }); jPopup.add(jPopupPrint); jPopup.add(jPopupSeparator3); jPopupSelectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK)); jPopupSelectAll.setMnemonic('A'); jPopupSelectAll.setText("Select All"); jPopupSelectAll.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jPopupSelectAllActionPerformed(evt); } }); jPopup.add(jPopupSelectAll); setDefaultCloseOperation(javax.swing.WindowConstants.DO_NOTHING_ON_CLOSE); setTitle("JAligner - biological pairwise sequence alignment "); setName("AlignWindow"); // NOI18N addWindowListener(new java.awt.event.WindowAdapter() { public void windowClosing(java.awt.event.WindowEvent evt) { exitForm(evt); } }); jButtonOpen.setIcon(ToolbarIcons.OPEN); jButtonOpen.setToolTipText("Open..."); jButtonOpen.setFocusable(false); jButtonOpen.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonOpen.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonOpenActionPerformed(evt); } }); jToolBar.add(jButtonOpen); jButtonSave.setIcon(ToolbarIcons.SAVE); jButtonSave.setToolTipText("Save..."); jButtonSave.setFocusable(false); jButtonSave.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonSave.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonSaveActionPerformed(evt); } }); jToolBar.add(jButtonSave); jButtonCut.setIcon(ToolbarIcons.CUT); jButtonCut.setToolTipText("Cut"); jButtonCut.setFocusable(false); jButtonCut.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonCut.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonCutActionPerformed(evt); } }); jToolBar.add(jButtonCut); jButtonCopy.setIcon(ToolbarIcons.COPY); jButtonCopy.setToolTipText("Copy"); jButtonCopy.setFocusable(false); jButtonCopy.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonCopy.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonCopyActionPerformed(evt); } }); jToolBar.add(jButtonCopy); jButtonPaste.setIcon(ToolbarIcons.PASTE); jButtonPaste.setToolTipText("Paste"); jButtonPaste.setFocusable(false); jButtonPaste.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonPaste.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonPasteActionPerformed(evt); } }); jToolBar.add(jButtonPaste); jButtonDelete.setIcon(ToolbarIcons.DELETE); jButtonDelete.setToolTipText("Delete"); jButtonDelete.setFocusable(false); jButtonDelete.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonDelete.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonDeleteActionPerformed(evt); } }); jToolBar.add(jButtonDelete); jButtonPrint.setIcon(ToolbarIcons.PRINT); jButtonPrint.setToolTipText("Print"); jButtonPrint.setFocusable(false); jButtonPrint.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonPrint.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonPrintActionPerformed(evt); } }); jToolBar.add(jButtonPrint); jButtonExit.setIcon(ToolbarIcons.CLOSE); jButtonExit.setToolTipText("Exit"); jButtonExit.setFocusable(false); jButtonExit.setPreferredSize(new java.awt.Dimension(24, 24)); jButtonExit.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonExitActionPerformed(evt); } }); jToolBar.add(jButtonExit); getContentPane().add(jToolBar, java.awt.BorderLayout.NORTH); jSplitPaneBody.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT); jSplitPaneBody.setOneTouchExpandable(true); jSplitPaneIO.setOneTouchExpandable(true); jSplitPaneSequences.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT); jSplitPaneSequences.setOneTouchExpandable(true); jPanelSequence1.setLayout(new java.awt.BorderLayout()); jScrollPaneSequence1.setPreferredSize(new java.awt.Dimension(400, 50)); jTextAreaSequence1.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N jTextAreaSequence1.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { jTextAreaSequence1MouseClicked(evt); } }); jTextAreaSequence1.addCaretListener(new javax.swing.event.CaretListener() { public void caretUpdate(javax.swing.event.CaretEvent evt) { jTextAreaSequence1CaretUpdate(evt); } }); jTextAreaSequence1.addFocusListener(new java.awt.event.FocusAdapter() { public void focusGained(java.awt.event.FocusEvent evt) { jTextAreaSequence1FocusGained(evt); } }); jScrollPaneSequence1.setViewportView(jTextAreaSequence1); jPanelSequence1.add(jScrollPaneSequence1, java.awt.BorderLayout.CENTER); jRadioButtonSequence1.setMnemonic('1'); jRadioButtonSequence1.setText("Sequence #1"); jRadioButtonSequence1.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jRadioButtonSequence1ActionPerformed(evt); } }); jPanelSequence1.add(jRadioButtonSequence1, java.awt.BorderLayout.NORTH); jSplitPaneSequences.setTopComponent(jPanelSequence1); jPanelSequence2.setLayout(new java.awt.BorderLayout()); jScrollPaneSequence2.setPreferredSize(new java.awt.Dimension(400, 50)); jTextAreaSequence2.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N jTextAreaSequence2.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { jTextAreaSequence2MouseClicked(evt); } }); jTextAreaSequence2.addCaretListener(new javax.swing.event.CaretListener() { public void caretUpdate(javax.swing.event.CaretEvent evt) { jTextAreaSequence2CaretUpdate(evt); } }); jTextAreaSequence2.addFocusListener(new java.awt.event.FocusAdapter() { public void focusGained(java.awt.event.FocusEvent evt) { jTextAreaSequence2FocusGained(evt); } }); jScrollPaneSequence2.setViewportView(jTextAreaSequence2); jPanelSequence2.add(jScrollPaneSequence2, java.awt.BorderLayout.CENTER); jRadioButtonSequence2.setMnemonic('2'); jRadioButtonSequence2.setText("Sequence #2"); jRadioButtonSequence2.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jRadioButtonSequence2ActionPerformed(evt); } }); jPanelSequence2.add(jRadioButtonSequence2, java.awt.BorderLayout.NORTH); jSplitPaneSequences.setBottomComponent(jPanelSequence2); jSplitPaneIO.setLeftComponent(jSplitPaneSequences); jPanelAlignment.setLayout(new java.awt.BorderLayout()); jRadioButtonAlignment.setMnemonic('A'); jRadioButtonAlignment.setText("Alignment"); jRadioButtonAlignment.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jRadioButtonAlignmentActionPerformed(evt); } }); jPanelAlignment.add(jRadioButtonAlignment, java.awt.BorderLayout.NORTH); jScrollPaneAlignment.setPreferredSize(new java.awt.Dimension(400, 50)); jTextAreaAlignment.setEditable(false); jTextAreaAlignment.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N jTextAreaAlignment.setTabSize(0); jTextAreaAlignment.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { jTextAreaAlignmentMouseClicked(evt); } }); jTextAreaAlignment.addCaretListener(new javax.swing.event.CaretListener() { public void caretUpdate(javax.swing.event.CaretEvent evt) { jTextAreaAlignmentCaretUpdate(evt); } }); jTextAreaAlignment.addFocusListener(new java.awt.event.FocusAdapter() { public void focusGained(java.awt.event.FocusEvent evt) { jTextAreaAlignmentFocusGained(evt); } }); jScrollPaneAlignment.setViewportView(jTextAreaAlignment); jPanelAlignment.add(jScrollPaneAlignment, java.awt.BorderLayout.CENTER); jSplitPaneIO.setRightComponent(jPanelAlignment); jSplitPaneBody.setTopComponent(jSplitPaneIO); jPanelConsole.setLayout(new java.awt.BorderLayout()); jRadioButtonConsole.setMnemonic('C'); jRadioButtonConsole.setText("Console"); jRadioButtonConsole.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jRadioButtonConsoleActionPerformed(evt); } }); jPanelConsole.add(jRadioButtonConsole, java.awt.BorderLayout.NORTH); jScrollPaneConsole.setPreferredSize(new java.awt.Dimension(400, 50)); jTextPaneConsole.setEditable(false); jTextPaneConsole.setFont(new java.awt.Font("Courier", 0, 12)); // NOI18N jTextPaneConsole.addMouseListener(new java.awt.event.MouseAdapter() { public void mouseClicked(java.awt.event.MouseEvent evt) { jTextPaneConsoleMouseClicked(evt); } }); jTextPaneConsole.addCaretListener(new javax.swing.event.CaretListener() { public void caretUpdate(javax.swing.event.CaretEvent evt) { jTextPaneConsoleCaretUpdate(evt); } }); jTextPaneConsole.addFocusListener(new java.awt.event.FocusAdapter() { public void focusGained(java.awt.event.FocusEvent evt) { jTextPaneConsoleFocusGained(evt); } }); jScrollPaneConsole.setViewportView(jTextPaneConsole); jPanelConsole.add(jScrollPaneConsole, java.awt.BorderLayout.CENTER); jSplitPaneBody.setBottomComponent(jPanelConsole); getContentPane().add(jSplitPaneBody, java.awt.BorderLayout.CENTER); jPanelControls.setAutoscrolls(true); jPanelControls.setLayout(new java.awt.GridLayout(1, 0)); jLabelScoringMatrix.setDisplayedMnemonic('M'); jLabelScoringMatrix.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); jLabelScoringMatrix.setLabelFor(jComboBoxScoringMatrix); jLabelScoringMatrix.setText("Matrix"); jPanelScoringMatrix.add(jLabelScoringMatrix); jComboBoxScoringMatrix.setToolTipText("Scoring matrix"); jComboBoxScoringMatrix.setPrototypeDisplayValue("BLOSUMXXX"); jPanelScoringMatrix.add(jComboBoxScoringMatrix); jPanelControls.add(jPanelScoringMatrix); jLabelOpenGapPenalty.setDisplayedMnemonic('O'); jLabelOpenGapPenalty.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); jLabelOpenGapPenalty.setLabelFor(jFormattedTextFieldGapOpen); jLabelOpenGapPenalty.setText("Open"); jPanelGapOpen.add(jLabelOpenGapPenalty); jFormattedTextFieldGapOpen.setColumns(3); jFormattedTextFieldGapOpen.setToolTipText("Gap open penalty"); jPanelGapOpen.add(jFormattedTextFieldGapOpen); jPanelControls.add(jPanelGapOpen); jLabelExtendGapPenalty.setDisplayedMnemonic('E'); jLabelExtendGapPenalty.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); jLabelExtendGapPenalty.setLabelFor(jFormattedTextFieldGapExtend); jLabelExtendGapPenalty.setText("Extend"); jPanelGapExtend.add(jLabelExtendGapPenalty); jFormattedTextFieldGapExtend.setColumns(3); jFormattedTextFieldGapExtend.setToolTipText("Gap extend penalty"); jPanelGapExtend.add(jFormattedTextFieldGapExtend); jPanelControls.add(jPanelGapExtend); jLabelOutputFormat.setDisplayedMnemonic('F'); jLabelOutputFormat.setLabelFor(jComboBoxOutputFormat); jLabelOutputFormat.setText("Format"); jPanelOutputFormat.add(jLabelOutputFormat); jComboBoxOutputFormat.setToolTipText("Alignment output format"); jPanelOutputFormat.add(jComboBoxOutputFormat); jPanelControls.add(jPanelOutputFormat); jButtonGo.setMnemonic('G'); jButtonGo.setText("Go"); jButtonGo.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jButtonGoActionPerformed(evt); } }); jPanelGo.add(jButtonGo); jPanelControls.add(jPanelGo); getContentPane().add(jPanelControls, java.awt.BorderLayout.SOUTH); jMenuFile.setMnemonic('F'); jMenuFile.setText("File"); jMenuItemFileOpen.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemFileOpen.setIcon(ToolbarIcons.OPEN); jMenuItemFileOpen.setMnemonic('O'); jMenuItemFileOpen.setText("Open..."); jMenuItemFileOpen.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemFileOpenActionPerformed(evt); } }); jMenuFile.add(jMenuItemFileOpen); jMenuItemFileLoadSequence1.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_1, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemFileLoadSequence1.setIcon(ToolbarIcons.OPEN); jMenuItemFileLoadSequence1.setMnemonic('1'); jMenuItemFileLoadSequence1.setText("Load sequence #1..."); jMenuItemFileLoadSequence1.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemFileLoadSequence1ActionPerformed(evt); } }); jMenuFile.add(jMenuItemFileLoadSequence1); jMenuItemFileLoadSequence2.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_2, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemFileLoadSequence2.setIcon(ToolbarIcons.OPEN); jMenuItemFileLoadSequence2.setMnemonic('2'); jMenuItemFileLoadSequence2.setText("Load sequence #2..."); jMenuItemFileLoadSequence2.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemFileLoadSequence2ActionPerformed(evt); } }); jMenuFile.add(jMenuItemFileLoadSequence2); jMenuItemFileLoadMatrix.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_M, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemFileLoadMatrix.setIcon(ToolbarIcons.OPEN); jMenuItemFileLoadMatrix.setMnemonic('M'); jMenuItemFileLoadMatrix.setText("Load scoring matrix..."); jMenuItemFileLoadMatrix.setToolTipText("Load user-defined scoring matrix from file system"); jMenuItemFileLoadMatrix.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemFileLoadMatrixActionPerformed(evt); } }); jMenuFile.add(jMenuItemFileLoadMatrix); jMenuFile.add(jSeparatorFile); jMenuItemFileExit.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.ALT_MASK)); jMenuItemFileExit.setIcon(ToolbarIcons.CLOSE); jMenuItemFileExit.setMnemonic('X'); jMenuItemFileExit.setText("Exit"); jMenuItemFileExit.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemFileExitActionPerformed(evt); } }); jMenuFile.add(jMenuItemFileExit); jMenuItemFilePrint.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_P, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemFilePrint.setIcon(ToolbarIcons.PRINT); jMenuItemFilePrint.setText("Print..."); jMenuItemFilePrint.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemFilePrintActionPerformed(evt); } }); jMenuFile.add(jMenuItemFilePrint); jMenuBar.add(jMenuFile); jMenuEdit.setMnemonic('E'); jMenuEdit.setText("Edit"); jMenuItemEditCut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemEditCut.setIcon(ToolbarIcons.CUT); jMenuItemEditCut.setMnemonic('t'); jMenuItemEditCut.setText("Cut"); jMenuItemEditCut.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemEditCutActionPerformed(evt); } }); jMenuEdit.add(jMenuItemEditCut); jMenuItemEditCopy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemEditCopy.setIcon(ToolbarIcons.COPY); jMenuItemEditCopy.setMnemonic('C'); jMenuItemEditCopy.setText("Copy"); jMenuItemEditCopy.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemEditCopyActionPerformed(evt); } }); jMenuEdit.add(jMenuItemEditCopy); jMenuItemEditPaste.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemEditPaste.setIcon(ToolbarIcons.PASTE); jMenuItemEditPaste.setMnemonic('P'); jMenuItemEditPaste.setText("Paste"); jMenuItemEditPaste.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemEditPasteActionPerformed(evt); } }); jMenuEdit.add(jMenuItemEditPaste); jMenuItemEditDelete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0)); jMenuItemEditDelete.setIcon(ToolbarIcons.DELETE); jMenuItemEditDelete.setMnemonic('D'); jMenuItemEditDelete.setText("Delete"); jMenuItemEditDelete.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemEditDeleteActionPerformed(evt); } }); jMenuEdit.add(jMenuItemEditDelete); jMenuItemEditSelectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK)); jMenuItemEditSelectAll.setMnemonic('A'); jMenuItemEditSelectAll.setText("Select All"); jMenuItemEditSelectAll.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemEditSelectAllActionPerformed(evt); } }); jMenuEdit.add(jMenuItemEditSelectAll); jMenuBar.add(jMenuEdit); jMenuTools.setMnemonic('T'); jMenuTools.setText("Tools"); jMenuItemToolsRunExample.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F5, 0)); jMenuItemToolsRunExample.setMnemonic('E'); jMenuItemToolsRunExample.setText("Example"); jMenuItemToolsRunExample.setToolTipText("Aligns P53 human and P53 mouse"); jMenuItemToolsRunExample.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemToolsRunExampleActionPerformed(evt); } }); jMenuTools.add(jMenuItemToolsRunExample); jMenuBar.add(jMenuTools); jMenuHelp.setMnemonic('H'); jMenuHelp.setText("Help"); jMenuItemAbout.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0)); jMenuItemAbout.setIcon(ToolbarIcons.ABOUT); jMenuItemAbout.setMnemonic('A'); jMenuItemAbout.setText("About..."); jMenuItemAbout.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { jMenuItemAboutActionPerformed(evt); } }); jMenuHelp.add(jMenuItemAbout); jMenuBar.add(jMenuHelp); setJMenuBar(jMenuBar); pack(); }// //GEN-END:initComponents private void jPopupPrintActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupPrintActionPerformed print(); }//GEN-LAST:event_jPopupPrintActionPerformed private void jMenuItemToolsRunExampleActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemToolsRunExampleActionPerformed try { logger.info("Running the example..."); jTextAreaSequence1.setText(SmithWatermanGotohExample.loadP53Human()); jTextAreaSequence2.setText(SmithWatermanGotohExample.loadP53Mouse()); align(); jTextAreaAlignment.requestFocus(); logger.info("Finished running the example..."); } catch (Exception e) { logger.log(Level.SEVERE, "Failed running the example: " + e.getMessage(), e); } }//GEN-LAST:event_jMenuItemToolsRunExampleActionPerformed private void jMenuItemFilePrintActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFilePrintActionPerformed print(); }//GEN-LAST:event_jMenuItemFilePrintActionPerformed private void jButtonPrintActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonPrintActionPerformed print(); }//GEN-LAST:event_jButtonPrintActionPerformed private void jTextPaneConsoleCaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextPaneConsoleCaretUpdate handleCaretUpdateEvent(evt); }//GEN-LAST:event_jTextPaneConsoleCaretUpdate private void jTextPaneConsoleMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextPaneConsoleMouseClicked jTextPaneConsole.requestFocus(); if (evt.getButton() == MouseEvent.BUTTON3) { jPopup.show(evt.getComponent(), evt.getX(), evt.getY()); } }//GEN-LAST:event_jTextPaneConsoleMouseClicked private void jTextPaneConsoleFocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextPaneConsoleFocusGained currentTextComponent = jTextPaneConsole; jRadioButtonConsole.setSelected(true); handleMoveToTextComponent(); }//GEN-LAST:event_jTextPaneConsoleFocusGained private void jRadioButtonConsoleActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonConsoleActionPerformed jTextPaneConsole.requestFocus(); }//GEN-LAST:event_jRadioButtonConsoleActionPerformed private void jTextAreaAlignmentFocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentFocusGained currentTextComponent = jTextAreaAlignment; jRadioButtonAlignment.setSelected(true); handleMoveToTextComponent(); }//GEN-LAST:event_jTextAreaAlignmentFocusGained private void jTextAreaSequence2FocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaSequence2FocusGained currentTextComponent = jTextAreaSequence2; jRadioButtonSequence2.setSelected(true); handleMoveToTextComponent(); }//GEN-LAST:event_jTextAreaSequence2FocusGained private void jTextAreaSequence1FocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaSequence1FocusGained currentTextComponent = jTextAreaSequence1; jRadioButtonSequence1.setSelected(true); handleMoveToTextComponent(); }//GEN-LAST:event_jTextAreaSequence1FocusGained private void jRadioButtonAlignmentActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonAlignmentActionPerformed jTextAreaAlignment.requestFocus(); }//GEN-LAST:event_jRadioButtonAlignmentActionPerformed private void jRadioButtonSequence2ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonSequence2ActionPerformed jTextAreaSequence2.requestFocus(); }//GEN-LAST:event_jRadioButtonSequence2ActionPerformed private void jRadioButtonSequence1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButtonSequence1ActionPerformed jTextAreaSequence1.requestFocus(); }//GEN-LAST:event_jRadioButtonSequence1ActionPerformed private void jMenuItemEditCopyActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditCopyActionPerformed copy(); }//GEN-LAST:event_jMenuItemEditCopyActionPerformed private void jMenuItemEditDeleteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditDeleteActionPerformed delete(); }//GEN-LAST:event_jMenuItemEditDeleteActionPerformed private void jMenuItemEditPasteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditPasteActionPerformed paste(); }//GEN-LAST:event_jMenuItemEditPasteActionPerformed private void jMenuItemFileOpenActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileOpenActionPerformed loadFileToTextArea("", currentTextComponent); }//GEN-LAST:event_jMenuItemFileOpenActionPerformed private void jMenuItemEditCutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditCutActionPerformed cut(); }//GEN-LAST:event_jMenuItemEditCutActionPerformed private void jMenuItemEditSelectAllActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditSelectAllActionPerformed selectAll(); }//GEN-LAST:event_jMenuItemEditSelectAllActionPerformed private void jTextAreaSequence2MouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextAreaSequence2MouseClicked jTextAreaSequence2.requestFocus(); if (evt.getButton() == MouseEvent.BUTTON3) { jPopup.show(evt.getComponent(), evt.getX(), evt.getY()); } }//GEN-LAST:event_jTextAreaSequence2MouseClicked private void jTextAreaSequence2CaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextAreaSequence2CaretUpdate handleCaretUpdateEvent(evt); }//GEN-LAST:event_jTextAreaSequence2CaretUpdate private void jButtonExitActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonExitActionPerformed exitForm(null); }//GEN-LAST:event_jButtonExitActionPerformed private void jButtonGoActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonGoActionPerformed align(); }//GEN-LAST:event_jButtonGoActionPerformed private void jMenuItemFileLoadSequence2ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadSequence2ActionPerformed loadFileToTextArea("sequence #2", jTextAreaSequence2); }//GEN-LAST:event_jMenuItemFileLoadSequence2ActionPerformed private void jMenuItemFileLoadSequence1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadSequence1ActionPerformed loadFileToTextArea("sequence #1", jTextAreaSequence1); }//GEN-LAST:event_jMenuItemFileLoadSequence1ActionPerformed private void jMenuItemFileLoadMatrixActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadMatrixActionPerformed NamedInputStream selectedInputStream = null; try { logger.info("Loading scoring matrix..."); selectedInputStream = FileChooserFactory.getFileChooser().open(); if (selectedInputStream != null) { Matrix matrix = MatrixLoader.load(selectedInputStream); // Put the loaded matrix in the matrices hashmap matrices.put(selectedInputStream.getName(), matrix); boolean found = false; int index = 0; int count = jComboBoxScoringMatrix.getItemCount(); while (index < count && !found) { if (((String)jComboBoxScoringMatrix.getItemAt(index)).equalsIgnoreCase(selectedInputStream.getName())) { found = true; } else { index++; } } if (!found) { // Add the loaded matrix to the scoring matrices dropdown menu jComboBoxScoringMatrix.addItem(selectedInputStream.getName()); index = jComboBoxScoringMatrix.getItemCount()-1; } // Set the selected item to the new loaded matrix jComboBoxScoringMatrix.setSelectedIndex(index); logger.info("Finished loading scoring matrix"); } else { logger.info("Canceled loading scoring matrix"); } } catch (Exception e) { String message = "Failed loading scoring matrix: " + e.getMessage(); logger.log(Level.SEVERE, message, e); showErrorMessage(message); } finally { if (selectedInputStream != null) { try { selectedInputStream.getInputStream().close(); } catch(Exception e) { logger.log(Level.WARNING, "Failed closing input stream: " + e.getMessage(), e); } } } }//GEN-LAST:event_jMenuItemFileLoadMatrixActionPerformed private void jTextAreaAlignmentMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentMouseClicked jTextAreaAlignment.requestFocus(); if (evt.getButton() == MouseEvent.BUTTON3) { jPopup.show(evt.getComponent(), evt.getX(), evt.getY()); } }//GEN-LAST:event_jTextAreaAlignmentMouseClicked private void jPopupSaveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupSaveActionPerformed saveTextAreaToFile((JTextArea) jPopup.getInvoker()); }//GEN-LAST:event_jPopupSaveActionPerformed private void jButtonSaveActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonSaveActionPerformed saveTextAreaToFile(currentTextComponent); }//GEN-LAST:event_jButtonSaveActionPerformed private void jTextAreaAlignmentCaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentCaretUpdate handleCaretUpdateEvent(evt); }//GEN-LAST:event_jTextAreaAlignmentCaretUpdate private void jPopupOpenActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupOpenActionPerformed loadFileToTextArea("", (JTextArea) jPopup.getInvoker()); }//GEN-LAST:event_jPopupOpenActionPerformed private void jPopupSelectAllActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupSelectAllActionPerformed selectAll(); }//GEN-LAST:event_jPopupSelectAllActionPerformed private void jPopupDeleteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupDeleteActionPerformed delete(); }//GEN-LAST:event_jPopupDeleteActionPerformed private void jPopupPasteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupPasteActionPerformed paste(); }//GEN-LAST:event_jPopupPasteActionPerformed private void jPopupCopyActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupCopyActionPerformed copy(); }//GEN-LAST:event_jPopupCopyActionPerformed private void jPopupCutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jPopupCutActionPerformed cut(); }//GEN-LAST:event_jPopupCutActionPerformed private void jTextAreaSequence1CaretUpdate(javax.swing.event.CaretEvent evt) {//GEN-FIRST:event_jTextAreaSequence1CaretUpdate handleCaretUpdateEvent(evt); }//GEN-LAST:event_jTextAreaSequence1CaretUpdate private void jButtonDeleteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonDeleteActionPerformed delete(); }//GEN-LAST:event_jButtonDeleteActionPerformed private void jButtonPasteActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonPasteActionPerformed paste(); }//GEN-LAST:event_jButtonPasteActionPerformed private void jButtonCopyActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonCopyActionPerformed copy(); }//GEN-LAST:event_jButtonCopyActionPerformed private void jButtonCutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonCutActionPerformed cut(); }//GEN-LAST:event_jButtonCutActionPerformed private void jButtonOpenActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonOpenActionPerformed loadFileToTextArea("", currentTextComponent); }//GEN-LAST:event_jButtonOpenActionPerformed private void jTextAreaSequence1MouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_jTextAreaSequence1MouseClicked jTextAreaSequence1.requestFocus(); if (evt.getButton() == MouseEvent.BUTTON3) { jPopup.show(evt.getComponent(), evt.getX(), evt.getY()); } }//GEN-LAST:event_jTextAreaSequence1MouseClicked private void jMenuItemAboutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemAboutActionPerformed String message = "JAligner" + Commons.getLineSeparator() + Commons.getLineSeparator() + "open-source Java implementation" + Commons.getLineSeparator() + "of the Smith-Waterman algorithm" + Commons.getLineSeparator() + "for biological sequence alignment." + Commons.getLineSeparator() + Commons.getLineSeparator() + "Build: " + Commons.getCurrentRelease() + Commons.getLineSeparator() + Commons.getLineSeparator() + "By: Ahmed Moustafa" + Commons.getLineSeparator() + Commons.getLineSeparator() + "https://github.com/ahmedmoustafa/JAligner"; JOptionPane.showMessageDialog(this, message, "About JAligner", JOptionPane.INFORMATION_MESSAGE); }//GEN-LAST:event_jMenuItemAboutActionPerformed private void jMenuItemFileExitActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileExitActionPerformed exitForm(null); }//GEN-LAST:event_jMenuItemFileExitActionPerformed /** Exit the Application */ private void exitForm(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_exitForm logger.info("Quitting..."); if (JOptionPane.showConfirmDialog(this, "Are you sure you want to exit JAligner?", "JAligner - confirmation", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) { logger.info("Thank you for using JAligner!"); System.exit(0); } else { logger.info("Canceled quitting"); currentTextComponent.requestFocus(); } }//GEN-LAST:event_exitForm // Variables declaration - do not modify//GEN-BEGIN:variables private javax.swing.ButtonGroup buttonGroupSequences; private javax.swing.JButton jButtonCopy; private javax.swing.JButton jButtonCut; private javax.swing.JButton jButtonDelete; private javax.swing.JButton jButtonExit; private javax.swing.JButton jButtonGo; private javax.swing.JButton jButtonOpen; private javax.swing.JButton jButtonPaste; private javax.swing.JButton jButtonPrint; private javax.swing.JButton jButtonSave; private javax.swing.JComboBox jComboBoxOutputFormat; private javax.swing.JComboBox jComboBoxScoringMatrix; private javax.swing.JFormattedTextField jFormattedTextFieldGapExtend; private javax.swing.JFormattedTextField jFormattedTextFieldGapOpen; private javax.swing.JLabel jLabelExtendGapPenalty; private javax.swing.JLabel jLabelOpenGapPenalty; private javax.swing.JLabel jLabelOutputFormat; private javax.swing.JLabel jLabelScoringMatrix; private javax.swing.JMenuBar jMenuBar; private javax.swing.JMenu jMenuEdit; private javax.swing.JMenu jMenuFile; private javax.swing.JMenu jMenuHelp; private javax.swing.JMenuItem jMenuItemAbout; private javax.swing.JMenuItem jMenuItemEditCopy; private javax.swing.JMenuItem jMenuItemEditCut; private javax.swing.JMenuItem jMenuItemEditDelete; private javax.swing.JMenuItem jMenuItemEditPaste; private javax.swing.JMenuItem jMenuItemEditSelectAll; private javax.swing.JMenuItem jMenuItemFileExit; private javax.swing.JMenuItem jMenuItemFileLoadMatrix; private javax.swing.JMenuItem jMenuItemFileLoadSequence1; private javax.swing.JMenuItem jMenuItemFileLoadSequence2; private javax.swing.JMenuItem jMenuItemFileOpen; private javax.swing.JMenuItem jMenuItemFilePrint; private javax.swing.JMenuItem jMenuItemToolsRunExample; private javax.swing.JMenu jMenuTools; private javax.swing.JPanel jPanelAlignment; private javax.swing.JPanel jPanelConsole; private javax.swing.JPanel jPanelControls; private javax.swing.JPanel jPanelGapExtend; private javax.swing.JPanel jPanelGapOpen; private javax.swing.JPanel jPanelGo; private javax.swing.JPanel jPanelOutputFormat; private javax.swing.JPanel jPanelScoringMatrix; private javax.swing.JPanel jPanelSequence1; private javax.swing.JPanel jPanelSequence2; private javax.swing.JPopupMenu jPopup; private javax.swing.JMenuItem jPopupCopy; private javax.swing.JMenuItem jPopupCut; private javax.swing.JMenuItem jPopupDelete; private javax.swing.JMenuItem jPopupOpen; private javax.swing.JMenuItem jPopupPaste; private javax.swing.JMenuItem jPopupPrint; private javax.swing.JMenuItem jPopupSave; private javax.swing.JMenuItem jPopupSelectAll; private javax.swing.JSeparator jPopupSeparator1; private javax.swing.JSeparator jPopupSeparator2; private javax.swing.JSeparator jPopupSeparator3; private javax.swing.JRadioButton jRadioButtonAlignment; private javax.swing.JRadioButton jRadioButtonConsole; private javax.swing.JRadioButton jRadioButtonSequence1; private javax.swing.JRadioButton jRadioButtonSequence2; private javax.swing.JScrollPane jScrollPaneAlignment; private javax.swing.JScrollPane jScrollPaneConsole; private javax.swing.JScrollPane jScrollPaneSequence1; private javax.swing.JScrollPane jScrollPaneSequence2; private javax.swing.JSeparator jSeparatorFile; private javax.swing.JSplitPane jSplitPaneBody; private javax.swing.JSplitPane jSplitPaneIO; private javax.swing.JSplitPane jSplitPaneSequences; private javax.swing.JTextArea jTextAreaAlignment; private javax.swing.JTextArea jTextAreaSequence1; private javax.swing.JTextArea jTextAreaSequence2; private javax.swing.JTextPane jTextPaneConsole; private javax.swing.JToolBar jToolBar; // End of variables declaration//GEN-END:variables /** * Populates a combobox with an array of strings and selects the default * @param combobox combobox to be populated * @param items array of strings to be added to the combobox * @param selected the default selected item */ private void populateComboBox(JComboBox combobox, String[] items, String selected) { for (int i = 0; i < items.length; i++) { combobox.addItem(items[i]); if (items[i].equals(selected)) { combobox.setSelectedIndex(i); } } } /** * Populates a combobox with an array of strings and selects the default * @param combobox combobox to be populated * @param items array of strings to be added to the combobox * @param selected the default selected item */ private void populateComboBox(JComboBox combobox, Collection items, String selected) { String item; Iterator i = items.iterator(); int index = 0; while (i.hasNext()) { item = (String) i.next(); combobox.addItem(item); if (item.equals(selected)) { combobox.setSelectedIndex(index); } index++; } } /** * Displays an error message * @param message the error message to be displayed */ private void showErrorMessage(String message) { JOptionPane.showMessageDialog(this, message, "JAligner - error message", JOptionPane.ERROR_MESSAGE); } /** * Loads the contents of a selected file into a text component. * @param id * @param textComponent */ private void loadFileToTextArea(String id, JTextComponent textComponent) { logger.info("Loading " + id + "..."); try { if (TextComponentUtil.open(textComponent)) { textComponent.requestFocus(); textComponent.setCaretPosition(0); logger.info("Finished loading " + id); } else { logger.info("Canceled loading " + id); } } catch (Exception e) { String message = "Failed loading " + id + ": " + e.getMessage(); logger.log(Level.SEVERE, message, e); showErrorMessage(message); } } /** * Saves a text component to a file. * @param textComponent */ private void saveTextAreaToFile(JTextComponent textComponent) { try { logger.info("Saving..."); if (TextComponentUtil.save(textComponent)) { logger.info("Finished saving"); } else { logger.info("Canceled saving"); } } catch (Exception e) { String message = "Failed saving: " + e.getMessage(); logger.log(Level.SEVERE, message, e); showErrorMessage(message); } } /** * * */ private void cut() { TextComponentUtil.cut(currentTextComponent); } /** * * */ private void copy() { TextComponentUtil.copy(currentTextComponent); } /** * * */ private void paste() { TextComponentUtil.paste(currentTextComponent); } /** * * */ private void delete() { TextComponentUtil.delete(currentTextComponent); } /** * * */ private void selectAll() { TextComponentUtil.selectAll(currentTextComponent); } /** * Prints the contents of a text component * */ private void print() { try { logger.info("Printing..."); TextComponentUtil.print(currentTextComponent); logger.info("Finished printing."); } catch (TextComponentUtilException textComponentUtilException) { logger.log(Level.SEVERE, "Failed printing: " + textComponentUtilException.getMessage(), textComponentUtilException); } } /** * Implements insertUpdate of {@link DocumentListener} */ public void insertUpdate(DocumentEvent e) { if (e.getDocument() == currentTextComponent.getDocument()) { setSaveControlsEnabled(true); setSelectAllControlsEnabled(true); setPrintControlsEnabled(true); } } /** * Implements removeUpdate of {@link DocumentListener} */ public void removeUpdate(DocumentEvent e) { if (e.getDocument() == currentTextComponent.getDocument()) { if (e.getDocument().getLength() == 0) { setSaveControlsEnabled(false); setSelectAllControlsEnabled(false); setPrintControlsEnabled(false); } } } /** * Implements changedUpdate of {@link DocumentListener} */ public void changedUpdate(DocumentEvent e) {} /** * Implements the notify method of the interface {@link ClipboardListener} */ public void clipboardCheck(String clipboardContents) { setPasteControlsEnabled(clipboardContents != null && currentTextComponent != null && currentTextComponent.isEditable()); } /** * Sets the status of the open controls * @param enabled */ private void setOpenControlsEnabled(boolean enabled) { jMenuItemFileOpen.setEnabled(enabled); jButtonOpen.setEnabled(enabled); jPopupOpen.setEnabled(enabled); } /** * Sets the status of the save controls * @param enabled */ private void setSaveControlsEnabled(boolean enabled) { jButtonSave.setEnabled(enabled); jPopupSave.setEnabled(enabled); } /** * Sets the status of the cut controls * @param enabled */ private void setCutControlsEnabled(boolean enabled) { jMenuItemEditCut.setEnabled(enabled); jButtonCut.setEnabled(enabled); jPopupCut.setEnabled(enabled); } /** * Sets the status of the copy controls * @param enabled */ private void setCopyControlsEnabled(boolean enabled) { jMenuItemEditCopy.setEnabled(enabled); jButtonCopy.setEnabled(enabled); jPopupCopy.setEnabled(enabled); } /** * Sets the status of the paste controls * @param enabled */ private void setPasteControlsEnabled(boolean enabled) { jMenuItemEditPaste.setEnabled(enabled); jButtonPaste.setEnabled(enabled); jPopupPaste.setEnabled(enabled); } /** * Sets the status of the delete controls * @param enabled */ private void setDeleteControlsEnabled(boolean enabled) { jMenuItemEditDelete.setEnabled(enabled); jButtonDelete.setEnabled(enabled); jPopupDelete.setEnabled(enabled); } /** * Sets the status of the select all controls * @param enabled */ private void setSelectAllControlsEnabled(boolean enabled) { jMenuItemEditSelectAll.setEnabled(enabled); jPopupSelectAll.setEnabled(enabled); } /** * Sets the status of the print controls * @param enabled */ private void setPrintControlsEnabled(boolean enabled) { jButtonPrint.setEnabled(enabled); jPopupPrint.setEnabled(enabled); } /** * * @param event */ private void handleCaretUpdateEvent(CaretEvent event) { if (event.getSource() == currentTextComponent) { boolean enabled = event.getDot() != event.getMark(); // Read controls setCopyControlsEnabled(enabled); // Write controls enabled &= currentTextComponent.isEditable(); setCutControlsEnabled(enabled); setDeleteControlsEnabled(enabled); } } /** * * */ private void handleMoveToTextComponent( ) { boolean enabled; enabled = currentTextComponent.getSelectedText() != null; setCopyControlsEnabled(enabled); if (currentTextComponent.isEditable()) { setOpenControlsEnabled(true); setCutControlsEnabled(enabled); setDeleteControlsEnabled(enabled); } else { setPasteControlsEnabled(false); setOpenControlsEnabled(false); setCutControlsEnabled(false); setDeleteControlsEnabled(false); } enabled = currentTextComponent.getText().length() > 0; setSaveControlsEnabled(enabled); setSelectAllControlsEnabled(enabled); setPrintControlsEnabled(enabled); // Adjust background of the radio buttons Enumeration buttons = buttonGroupSequences.getElements(); AbstractButton button = null; while (buttons.hasMoreElements()) { button = (AbstractButton) buttons.nextElement(); if (button.isSelected()) { button.setForeground(Color.blue); } else { button.setForeground(Color.black); } } } /** * * */ private void align() { jTextAreaAlignment.setText(""); String matrixId = (String) jComboBoxScoringMatrix.getSelectedItem(); float open = ((Number)jFormattedTextFieldGapOpen.getValue()).floatValue(); float extend = ((Number)jFormattedTextFieldGapExtend.getValue()).floatValue(); Sequence sequence1 = null; try { logger.info("Processing sequence #1..."); sequence1 = SequenceParser.parse(jTextAreaSequence1.getText()); logger.info("Finished processing sequence #1"); } catch (Exception e) { String message = "Failed parsing sequence #1: " + e.getMessage(); logger.log(Level.SEVERE, message, e); showErrorMessage(message); jTextAreaSequence1.requestFocus(); return; } Sequence sequence2 = null; try { logger.info("Processing sequence #2..."); sequence2 = SequenceParser.parse(jTextAreaSequence2.getText()); logger.info("Finished processing sequence #2"); } catch (Exception e) { String message = "Failed parsing sequence #2: " + e.getMessage(); logger.log(Level.SEVERE, message, e); showErrorMessage(message); jTextAreaSequence2.requestFocus(); return; } logger.info("Aliging..."); try { setCursor(new Cursor(Cursor.WAIT_CURSOR)); long start = System.currentTimeMillis(); Matrix matrix = null; if (!matrices.containsKey(matrixId)) { matrix = MatrixLoader.load(matrixId); matrices.put(matrixId, matrix); } else { matrix = (Matrix) matrices.get(matrixId); } Alignment alignment = SmithWatermanGotoh.align(sequence1, sequence2, matrix, open, extend); long end = System.currentTimeMillis(); logger.info("Finished aligning in " + (end - start) + " milliseconds"); StringBuffer buffer = new StringBuffer(); buffer.append(alignment.getSummary()); buffer.append(Commons.getLineSeparator()); String formatId = (String) jComboBoxOutputFormat.getSelectedItem(); String formattedAlignment = FormatFactory.getInstance().getFormat(formatId).format(alignment); buffer.append(formattedAlignment); jTextAreaAlignment.setText(""); jTextAreaAlignment.append(buffer.toString()); jTextAreaAlignment.setCaretPosition(0); } catch (Error error) { String message = "Failed aligning: " + error.getMessage(); logger.log(Level.SEVERE, message, error); showErrorMessage(message); } catch (Exception exception) { String message = "Failed aligning: " + exception.getMessage(); logger.log(Level.SEVERE, message, exception); showErrorMessage(message); } finally { setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); } } /** * * @param args */ public static void main(String[] args) { logger.info( Commons.getJAlignerInfo() ); new AlignWindow().setVisible(true); } }JAligner-1.0/src/jaligner/ui/clipboard/000077500000000000000000000000001216526722600200145ustar00rootroot00000000000000JAligner-1.0/src/jaligner/ui/clipboard/ClipboardHandler.java000066400000000000000000000022471216526722600240610ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.clipboard; /** * Abstract class to handle setting and getting "text" contents of * the system clipboard. * * @author Ahmed Moustafa */ public interface ClipboardHandler { /** * Returns the contents of the system of the clipboard * * @return String */ public String getContents(); /** * Sets the contents of the system of the clipboard * * @param s the clipboard contents to set */ public void setContents(String s); }JAligner-1.0/src/jaligner/ui/clipboard/ClipboardHandlerAWT.java000066400000000000000000000040751216526722600244360ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.clipboard; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.StringSelection; import java.awt.datatransfer.Transferable; import java.util.logging.Level; import java.util.logging.Logger; /** * Sets and gets the contents of the system clipboard. * * @author Ahmed Moustafa */ public class ClipboardHandlerAWT implements ClipboardHandler { private static Logger logger = Logger.getLogger(ClipboardHandlerAWT.class.getName()); /** * Gets the contents of the system clipboard * * @return The text contents of the system clipboard */ public String getContents() { String contents = null; Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); Transferable data = c.getContents(null); if (data != null && data.isDataFlavorSupported(DataFlavor.stringFlavor)) { try { contents = ((String)(data.getTransferData(DataFlavor.stringFlavor))); } catch (Exception e) { logger.log(Level.WARNING, "Failed getting tranfer data: " + e.getMessage(), e); } } return contents; } /** * Sets the contents of the system clipboard * * @param s the clipboard contents to set */ public void setContents(String s) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); c.setContents(new StringSelection(s), null); } }JAligner-1.0/src/jaligner/ui/clipboard/ClipboardHandlerFactory.java000066400000000000000000000030171216526722600254050ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.clipboard; import jaligner.util.Commons; /** * A factory for {@link jaligner.ui.clipboard.ClipboardHandler}. * * @author Ahmed Moustafa */ public class ClipboardHandlerFactory { /** * Instance of a concrete {@link ClipboardHandlerFactory}. */ private static ClipboardHandler instance = null; /** * Constructor */ private ClipboardHandlerFactory ( ) { super(); } /** * Returns an instance of a concrete {@link ClipboardHandler}. * @return Concrete {@link ClipboardHandler}. */ public static ClipboardHandler getClipboardHandler( ) { if (instance == null) { if (Commons.isJnlp()) { instance = new ClipboardHandlerJNLP(); } else { instance = new ClipboardHandlerAWT(); } } return instance; } }JAligner-1.0/src/jaligner/ui/clipboard/ClipboardHandlerJNLP.java000066400000000000000000000044021216526722600245400ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.clipboard; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.StringSelection; import java.awt.datatransfer.Transferable; import java.util.logging.Level; import java.util.logging.Logger; import javax.jnlp.ClipboardService; import javax.jnlp.ServiceManager; /** * Sets and gets the contents of the system clipboard. * * @author Ahmed Moustafa */ public class ClipboardHandlerJNLP implements ClipboardHandler { private static Logger logger = Logger.getLogger(ClipboardHandlerJNLP.class.getName()); /** * Gets the contents of the system clipboard * * @return The text system clipboad contents */ public String getContents() { String contents = null; try { ClipboardService cs = (ClipboardService)ServiceManager.lookup(ClipboardService.class.getName()); Transferable data = cs.getContents(); if (data != null && data.isDataFlavorSupported(DataFlavor.stringFlavor)) { contents = ((String)(data.getTransferData(DataFlavor.stringFlavor))); } } catch (Exception e) { logger.log(Level.WARNING, "Failed getting the clipboard contents: " + e.getMessage(), e ); } return contents; } /** * Sets the contents of the system clipboard * * @param s clipboard contents to set */ public void setContents(String s) { try { ClipboardService cs = (ClipboardService)ServiceManager.lookup(ClipboardService.class.getName()); cs.setContents(new StringSelection(s)); } catch (Exception e) { logger.log(Level.WARNING, "Failed setting the clipboard contents: " + e.getMessage(), e ); } } }JAligner-1.0/src/jaligner/ui/clipboard/ClipboardListener.java000066400000000000000000000020771216526722600242720ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.clipboard; /** * Listener interface to get notified with the clipboard contents. * * @author Ahmed Moustafa */ public interface ClipboardListener { /** * Notifies the listener with the current contents of the clipboard. * @param contents The current contents of the clipboard */ public void clipboardCheck (String contents); }JAligner-1.0/src/jaligner/ui/clipboard/ClipboardPoller.java000066400000000000000000000043341216526722600237400ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.clipboard; import java.util.logging.Level; import java.util.logging.Logger; /** * Checks the system clipboard to notifies a listener with current contents. * * @author Ahmed Moustafa */ public class ClipboardPoller extends Thread { /** * Sleeping interval */ private static final int SLEEPING_TIME_IN_MILLISECONDS = 1500; /** * Clipboard listener {@link ClipboardListener} */ private ClipboardListener listener = null; /** * Running flag */ private boolean running = false; /** * Logger */ private Logger logger = null; /** * Constructor * @param listener */ public ClipboardPoller(ClipboardListener listener) { logger = Logger.getLogger(this.getClass().getName()); this.listener = listener; } /** * Runs the thread */ public void run() { logger.info("Started"); while (running) { String contents = ClipboardHandlerFactory.getClipboardHandler().getContents(); listener.clipboardCheck(contents); try { Thread.sleep(SLEEPING_TIME_IN_MILLISECONDS); } catch (Exception e){ logger.log(Level.SEVERE, "Failed sleeping: " + e.getMessage(), e); running = false; } } logger.info("Stopped"); } /** * Starts the thread */ public void start() { logger.info("Starting..."); if (!running) { if (listener != null) { running = true; } else { logger.warning("No listener"); } } else { logger.warning("Already started"); } super.start(); } }JAligner-1.0/src/jaligner/ui/clipboard/package.html000066400000000000000000000002571216526722600223010ustar00rootroot00000000000000 Clipboard handling for JNLP and AWT. @author Ahmed Moustafa JAligner-1.0/src/jaligner/ui/filechooser/000077500000000000000000000000001216526722600203575ustar00rootroot00000000000000JAligner-1.0/src/jaligner/ui/filechooser/FileChooser.java000066400000000000000000000035111216526722600234240ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.filechooser; import java.io.InputStream; /** * Opens and saves files. * * @author Ahmed Moustafa */ public abstract class FileChooser { /** * Buffer size while reading from or write to a file (4 KB) */ public static final int BUFFER_SIZE = 4096; private String userDir = null; /** * Shows a dialog to select a file * * @return InputStream * @throws FileChooserException */ public abstract NamedInputStream open() throws FileChooserException; /** * Saves an input stream to a file * * @param is * @param fileName * @return boolean * @throws FileChooserException */ public abstract boolean save(InputStream is, String fileName) throws FileChooserException; /** * Gets the current user working directory * @return current working directory */ public String getUserDirectory ( ) { if (userDir == null) { userDir = System.getProperty("user.home"); } return userDir; } /** * Sets the user working directory * @param userDir The user directory to set */ public void setUserDirectory (String userDir) { this.userDir = userDir; } }JAligner-1.0/src/jaligner/ui/filechooser/FileChooserException.java000066400000000000000000000020601216526722600253010ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.filechooser; /** * File chooser exception * * @author Ahmed Moustafa */ public class FileChooserException extends Exception { /** * */ private static final long serialVersionUID = 3258408434931086648L; /** * @param message */ public FileChooserException(String message) { super(message); } } JAligner-1.0/src/jaligner/ui/filechooser/FileChooserFactory.java000066400000000000000000000027311216526722600247570ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.filechooser; import jaligner.util.Commons; /** * A factory for {@link jaligner.ui.filechooser.FileChooser}. * * @author Ahmed Moustafa */ public class FileChooserFactory { /** * Instance of a concrete {@link FileChooser}. */ private static FileChooser instance = null; /** * Constructor */ private FileChooserFactory ( ) { super(); } /** * Returns an instance of a concrete {@link FileChooser}. * @return Concrete {@link FileChooser}. */ public static FileChooser getFileChooser( ) { if (instance == null) { if (Commons.isJnlp()) { instance = new FileChooserJNLP(); } else { instance = new FileChooserTrusted(); } } return instance; } }JAligner-1.0/src/jaligner/ui/filechooser/FileChooserJNLP.java000066400000000000000000000050431216526722600241120ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.filechooser; import java.io.InputStream; import java.util.logging.Logger; import javax.jnlp.FileContents; import javax.jnlp.FileOpenService; import javax.jnlp.FileSaveService; import javax.jnlp.ServiceManager; /** * Opens and saves files. * * @author Ahmed Moustafa */ public class FileChooserJNLP extends FileChooser { private static final Logger logger = Logger.getLogger(FileChooserJNLP.class.getName()); /** * Shows a dialog to select a file. * * @return InputStream * @throws FileChooserException */ public NamedInputStream open() throws FileChooserException { try { FileOpenService fos = (FileOpenService) ServiceManager.lookup(FileOpenService.class.getName()); FileContents fc = null; if ((fc = fos.openFileDialog(getUserDirectory(), null)) != null) { logger.info("Loaded: " + fc.getName()); return new NamedInputStream(fc.getName(), fc.getInputStream()); } else { return null; } } catch (Exception e) { String message = "Failed open: " + e.getMessage(); logger.warning(message); throw new FileChooserException(message); } } /** * Saves an input stream to a file. * * @param is * @param fileName * @return Boolean * @throws FileChooserException */ public boolean save(InputStream is, String fileName) throws FileChooserException { try { FileSaveService fss = (FileSaveService) ServiceManager.lookup(FileSaveService.class.getName()); FileContents fc = fss.saveFileDialog(getUserDirectory(), null, is, fileName); if (fc != null) { logger.info("Saved: " + fc.getName()); return true; } else { return false; } } catch (Exception e) { String message = "Failed save: " + e.getMessage(); logger.warning(message); throw new FileChooserException(message); } } }JAligner-1.0/src/jaligner/ui/filechooser/FileChooserTrusted.java000066400000000000000000000061701216526722600250030ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.filechooser; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.InputStream; import java.util.logging.Logger; import javax.swing.JFileChooser; /** * Opens and saves files. * * @author Ahmed Moustafa */ public class FileChooserTrusted extends FileChooser { private static final Logger logger = Logger.getLogger(FileChooserJNLP.class.getName()); /** * Shows a dialog to select a file. * @return input stream * @throws FileChooserException * @see NamedInputStream */ public NamedInputStream open() throws FileChooserException { try { JFileChooser chooser = new JFileChooser( ); chooser.setCurrentDirectory(new File(getUserDirectory())); int returnVal = chooser.showOpenDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { setUserDirectory(chooser.getCurrentDirectory().toString()); logger.info("Loaded: " + chooser.getSelectedFile().getName()); return new NamedInputStream(chooser.getSelectedFile().getName(), new FileInputStream(chooser.getSelectedFile())); } else { return null; } } catch (Exception e) { String message = "Failed open: " + e.getMessage(); logger.warning(message); throw new FileChooserException(message); } } /** * Saves an input stream to a file. * * @param is * @param fileName * @return boolean * @throws FileChooserException */ public boolean save(InputStream is, String fileName) throws FileChooserException { try { JFileChooser chooser = new JFileChooser( ); chooser.setCurrentDirectory(new File(getUserDirectory())); if (fileName != null) { chooser.setSelectedFile(new File(fileName)); } int returnVal = chooser.showSaveDialog(null); if (returnVal == JFileChooser.APPROVE_OPTION) { setUserDirectory(chooser.getCurrentDirectory().toString()); File file = chooser.getSelectedFile(); logger.info("Saved: " + file.getName()); FileOutputStream fos = new FileOutputStream(file); byte[] buffer = new byte[BUFFER_SIZE]; int len; while ((len = is.read(buffer)) != -1) { fos.write(buffer, 0, len); } fos.close(); is.close(); return true; } else { return false; } } catch (Exception e) { String message = "Failed save: " + e.getMessage(); logger.warning(message); throw new FileChooserException(message); } } }JAligner-1.0/src/jaligner/ui/filechooser/NamedInputStream.java000066400000000000000000000031231216526722600244410ustar00rootroot00000000000000/* * This program inputStream free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program inputStream distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.filechooser; import java.io.InputStream; import java.io.Serializable; /** * * @author Ahmed Moustafa */ public class NamedInputStream extends Object implements Serializable { /** * */ private static final long serialVersionUID = 3256441404384686387L; /** * Name. */ private String name = null; /** * Input stream. */ private InputStream inputStream = null; /** * */ public NamedInputStream(String name, InputStream inputStream) { this.name = name; this.inputStream = inputStream; } /** * @return Returns the inputStream. */ public InputStream getInputStream() { return this.inputStream; } /** * @return Returns the name. */ public String getName() { return this.name; } }JAligner-1.0/src/jaligner/ui/filechooser/package.html000066400000000000000000000002441216526722600226400ustar00rootroot00000000000000 File loading and storing. @author Ahmed Moustafa JAligner-1.0/src/jaligner/ui/images/000077500000000000000000000000001216526722600173225ustar00rootroot00000000000000JAligner-1.0/src/jaligner/ui/images/ToolbarIcons.java000066400000000000000000000044651216526722600225740ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.images; import javax.swing.ImageIcon; /** * Toolbar icons * * @author Ahmed Moustafa */ public abstract class ToolbarIcons { /** * Path to the gifs folder */ public static final String GIFS_HOME = "/jaligner/ui/images/gifs/"; /** * Open icon */ public static final ImageIcon OPEN = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "open.gif")); /** * Save icon */ public static final ImageIcon SAVE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "save.gif")); /** * Cut icon */ public static final ImageIcon CUT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "cut.gif")); /** * Copy icon */ public static final ImageIcon COPY = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "copy.gif")); /** * Paste icon */ public static final ImageIcon PASTE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "paste.gif")); /** * Delete icon */ public static final ImageIcon DELETE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "delete.gif")); /** * Close icon */ public static final ImageIcon CLOSE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "close.gif")); /** * About icon */ public static final ImageIcon ABOUT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "about.gif")); /** * Print icon */ public static final ImageIcon PRINT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "print.gif")); }JAligner-1.0/src/jaligner/ui/images/gifs/000077500000000000000000000000001216526722600202525ustar00rootroot00000000000000JAligner-1.0/src/jaligner/ui/images/gifs/jaligner.gif000066400000000000000000000001651216526722600225360ustar00rootroot00000000000000GIF89a!,FNTzlyXFȲJ&Iڶ7Yr!7O1!||ҩ(;JAligner-1.0/src/jaligner/ui/images/package.html000066400000000000000000000002461216526722600216050ustar00rootroot00000000000000 Images used in the toolbar. @author Ahmed Moustafa JAligner-1.0/src/jaligner/ui/logging/000077500000000000000000000000001216526722600175035ustar00rootroot00000000000000JAligner-1.0/src/jaligner/ui/logging/DocumentHandler.java000066400000000000000000000065011216526722600234240ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.logging; import java.awt.Color; import java.util.logging.ErrorManager; import java.util.logging.Handler; import java.util.logging.Level; import java.util.logging.LogRecord; import javax.swing.JTextPane; import javax.swing.text.Style; import javax.swing.text.StyleConstants; import javax.swing.text.StyledDocument; /** * Logging handler of {@link javax.swing.JTextPane}. * * @author Ahmed Moustafa */ public class DocumentHandler extends Handler { /** * Maximum document size */ private static final int MAXIMUM_DOCUMENT_SIZE = 524288; // 0.5 MB private JTextPane textPane = null; private Style infoStyle = null; private Style severStyle = null; /** * Constructor * @param textPane */ public DocumentHandler(JTextPane textPane) { this.textPane = textPane; setFormatter(new RecordFormatter()); StyledDocument document = (StyledDocument) this.textPane.getDocument(); infoStyle = document.addStyle("INFO", null); StyleConstants.setFontFamily(infoStyle,"Monospaced"); StyleConstants.setBackground(infoStyle, Color.white); StyleConstants.setForeground(infoStyle, Color.blue); severStyle = document.addStyle("SEVER", null); StyleConstants.setFontFamily(severStyle,"Monospaced"); StyleConstants.setBackground(severStyle, Color.white); StyleConstants.setForeground(severStyle, Color.red); } /** * */ public void close() { } /** * */ public void flush() { } /** * */ public void publish(LogRecord record) { if (!isLoggable(record)) { return; } String message; try { message = getFormatter().format(record); } catch (Exception exception) { reportError(null, exception, ErrorManager.FORMAT_FAILURE); return; } synchronized(textPane) { if (textPane.getDocument().getLength() >= MAXIMUM_DOCUMENT_SIZE) { // Delete the contents of the text pane. textPane.setText(""); } try { if (record.getLevel() == Level.SEVERE) { textPane.getDocument().insertString(textPane.getDocument().getLength(), message, severStyle); } else { textPane.getDocument().insertString(textPane.getDocument().getLength(), message, infoStyle); } textPane.setCaretPosition(textPane.getDocument().getLength()); } catch (Exception ex) { reportError(null, ex, ErrorManager.WRITE_FAILURE); } } } }JAligner-1.0/src/jaligner/ui/logging/RecordFormatter.java000066400000000000000000000033651216526722600234570ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.logging; import java.util.Date; import java.util.logging.Formatter; import java.util.logging.Handler; import java.util.logging.LogRecord; /** * Logging record formatter * * @author Ahmed Moustafa */ public class RecordFormatter extends Formatter { /** * This method is called for every log records * * @param record */ public String format(LogRecord record) { StringBuffer buffer = new StringBuffer( ); buffer.append ( new Date().toString() ); buffer.append ( " " ); buffer.append ( record.getLevel() ); buffer.append ( "\t" ); buffer.append ( record.getMessage() ); buffer.append ( "\n" ); return buffer.toString(); } /** * This method is called just after the handler using this * formatter is created * * @param handler */ public String getHead(Handler handler) { return ""; } /** * This method is called just after the handler using this * formatter is closed * * @param handler */ public String getTail(Handler handler) { return "\n"; } }JAligner-1.0/src/jaligner/ui/logging/package.html000066400000000000000000000002331216526722600217620ustar00rootroot00000000000000 Logging package. @author Ahmed Moustafa JAligner-1.0/src/jaligner/ui/package.html000066400000000000000000000002651216526722600203410ustar00rootroot00000000000000 Command line and graphical user interface. @author Ahmed Moustafa JAligner-1.0/src/jaligner/ui/util/000077500000000000000000000000001216526722600170325ustar00rootroot00000000000000JAligner-1.0/src/jaligner/ui/util/PrintJobMointor.java000066400000000000000000000051441216526722600230000ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.util; import java.util.logging.Level; import java.util.logging.Logger; import javax.print.DocPrintJob; import javax.print.event.PrintJobAdapter; import javax.print.event.PrintJobEvent; /** * Mointor for print job. * * @author Ahmed Moustafa */ public class PrintJobMointor { /** * Logger */ private static final Logger logger = Logger.getLogger(TextComponentUtil.class.getName()); // True iff it is safe to close the print job's input stream private boolean done = false; PrintJobMointor(DocPrintJob job) { // Add a listener to the print job job.addPrintJobListener(new PrintJobAdapter() { public void printJobCanceled(PrintJobEvent printJobEvent) { logger.info("Print job canceled"); allDone(); } public void printJobCompleted(PrintJobEvent printJobEvent) { logger.info("Print job completed"); allDone(); } public void printJobFailed(PrintJobEvent printJobEvent) { logger.info("Print job failed"); allDone(); } public void printJobNoMoreEvents(PrintJobEvent printJobEvent) { allDone(); } void allDone() { synchronized (PrintJobMointor.this) { done = true; PrintJobMointor.this.notify(); } } }); } /** * Waits for print job * */ public synchronized void waitForPrintJob() { try { logger.info("Waiting for print job..."); while (!done) { wait(); } logger.info("Finished waiting for print"); } catch (InterruptedException e) { logger.log(Level.SEVERE, "Failed waiting for print job: " + e.getMessage(), e); } } } JAligner-1.0/src/jaligner/ui/util/TextComponentUtil.java000066400000000000000000000225621216526722600233510ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.util; import jaligner.ui.clipboard.ClipboardHandlerFactory; import jaligner.ui.filechooser.FileChooserFactory; import jaligner.ui.filechooser.NamedInputStream; import jaligner.util.Commons; import java.io.BufferedReader; import java.io.ByteArrayInputStream; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.util.logging.Level; import java.util.logging.Logger; import javax.print.Doc; import javax.print.DocFlavor; import javax.print.DocPrintJob; import javax.print.PrintService; import javax.print.PrintServiceLookup; import javax.print.ServiceUI; import javax.print.SimpleDoc; import javax.print.attribute.HashDocAttributeSet; import javax.print.attribute.HashPrintRequestAttributeSet; import javax.print.attribute.PrintRequestAttributeSet; import javax.print.attribute.standard.DocumentName; import javax.print.attribute.standard.JobName; import javax.swing.text.Document; import javax.swing.text.JTextComponent; /** * Text component (e.g. {@link javax.swing.JTextArea}or * {@link javax.swing.JTextPane}) editing helper class. * * @author Ahmed Moustafa */ public class TextComponentUtil { /** * Empty string */ private static final String EMPTY = ""; /** * Logger */ private static final Logger logger = Logger .getLogger(TextComponentUtil.class.getName()); /** * Copies the selected text to the system clipboad and then deletes it from * the text component. * * @param textComponent */ public static void cut(JTextComponent textComponent) { copy(textComponent); delete(textComponent); } /** * Copies the selected text to the system clipboard. * * @param textComponent */ public static void copy(JTextComponent textComponent) { ClipboardHandlerFactory.getClipboardHandler().setContents( textComponent.getSelectedText()); } /** * Copies the text contents of the system clipboard to the text component. * * @param textComponent */ public static void paste(JTextComponent textComponent) { String contents = ClipboardHandlerFactory.getClipboardHandler() .getContents(); if (contents != null) { StringBuffer buffer = new StringBuffer(); char c; for (int i = 0, n = contents.length(); i < n; i++) { c = contents.charAt(i); // Not to copy a null character if (c != 0) { buffer.append(c); } } textComponent.replaceSelection(buffer.toString()); } if (!textComponent.hasFocus()) { textComponent.requestFocus(); } } /** * Deletes the selected text in a text component. * * @param textComponent */ public static void delete(JTextComponent textComponent) { textComponent.replaceSelection(EMPTY); } /** * Selects all contents of a text component. * * @param textComponent */ public static void selectAll(JTextComponent textComponent) { if (!textComponent.hasFocus()) { textComponent.requestFocus(); } textComponent.selectAll(); } /** * Opens a file and puts the contents of the file in a text component. * * @param textComponent * @throws TextComponentUtilException */ public static boolean open(JTextComponent textComponent) throws TextComponentUtilException { InputStream is = null; BufferedReader reader = null; try { NamedInputStream selectedInputStream = FileChooserFactory .getFileChooser().open(); if (selectedInputStream != null) { is = selectedInputStream.getInputStream(); textComponent.setText(EMPTY); reader = new BufferedReader(new InputStreamReader(is)); String line; Document document = textComponent.getDocument(); while ((line = reader.readLine()) != null) { document.insertString(document.getLength(), line + Commons.getLineSeparator(), null); } if (!textComponent.hasFocus()) { textComponent.requestFocus(); } return true; } else { return false; } } catch (Exception e) { throw new TextComponentUtilException(e.getMessage()); } finally { if (is != null) { try { is.close(); } catch (Exception e) { logger.log(Level.WARNING, "Failed closing input stream: " + e.getMessage(), e); } } if (reader != null) { try { reader.close(); } catch (Exception e) { logger.log(Level.WARNING, "Failed closing reader: " + e.getMessage(), e); } } } } /** * Saves the contents of a text component to a file. * * @param textComponent * @param fileName * @return true if a file has been chosen or false otherwise * @throws TextComponentUtilException */ public static boolean save(JTextComponent textComponent, String fileName) throws TextComponentUtilException { InputStream is = null; try { is = new ByteArrayInputStream(textComponent.getText().getBytes()); return FileChooserFactory.getFileChooser().save(is, fileName); } catch (Exception e) { throw new TextComponentUtilException(e.getMessage()); } finally { try { is.close(); } catch (Exception e) { logger.log(Level.WARNING, "Failed closing input stream: " + e.getMessage(), e); } } } /** * Saves the contents of a text component to a file. * * @param textComponent * @return true if a file has been chosen or false otherwise * @throws TextComponentUtilException */ public static boolean save(JTextComponent textComponent) throws TextComponentUtilException { return save(textComponent, null); } /** * Prints the contents of a text component. * * @param textComponent */ public static void print(JTextComponent textComponent) throws TextComponentUtilException { InputStream is = null; try { PrintService[] printServices = PrintServiceLookup .lookupPrintServices(DocFlavor.INPUT_STREAM.AUTOSENSE, null); if (printServices.length > 0) { PrintRequestAttributeSet printRequestAttributeSet = new HashPrintRequestAttributeSet(); printRequestAttributeSet.add(new JobName("JAligner", null)); PrintService service = ServiceUI.printDialog(null, 50, 50, printServices, PrintServiceLookup .lookupDefaultPrintService(), DocFlavor.INPUT_STREAM.AUTOSENSE, printRequestAttributeSet); if (service != null) { DocPrintJob printJob = service.createPrintJob(); PrintJobMointor printJobMointor = new PrintJobMointor( printJob); is = new ByteArrayInputStream(textComponent.getText() .getBytes()); DocumentName documentName = new DocumentName("JAligner", null); HashDocAttributeSet docAttributeSet = new HashDocAttributeSet(); docAttributeSet.add(documentName); Doc doc = new SimpleDoc(is, DocFlavor.INPUT_STREAM.AUTOSENSE, docAttributeSet); printJob.print(doc, printRequestAttributeSet); printJobMointor.waitForPrintJob(); } } else { throw new TextComponentUtilException("No print service found!"); } } catch (Exception e) { throw new TextComponentUtilException(e.getMessage()); } finally { if (is != null) { try { is.close(); } catch (IOException e) { logger.log(Level.WARNING, "Failed closing input stream: " + e.getMessage(), e); } } } } }JAligner-1.0/src/jaligner/ui/util/TextComponentUtilException.java000066400000000000000000000020331216526722600252170ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.ui.util; /** * * @author Ahmed Moustafa */ public class TextComponentUtilException extends Exception { /** * */ private static final long serialVersionUID = 4050763797251567922L; /** * @param message */ public TextComponentUtilException(String message) { super(message); } } JAligner-1.0/src/jaligner/ui/util/package.html000066400000000000000000000002531216526722600213130ustar00rootroot00000000000000 Text component utilites package. @author Ahmed Moustafa JAligner-1.0/src/jaligner/util/000077500000000000000000000000001216526722600164155ustar00rootroot00000000000000JAligner-1.0/src/jaligner/util/Commons.java000066400000000000000000000116041216526722600206750ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.util; import java.net.JarURLConnection; import java.net.URL; import java.util.jar.Attributes; import java.util.jar.JarFile; import java.util.jar.Manifest; import java.util.logging.Level; import java.util.logging.Logger; /** * Global constants/variables/settings * * @author Ahmed Moustafa */ public abstract class Commons { /** * Tab */ public static final String TAB = "\t"; /** * Logger */ private static final Logger logger = Logger.getLogger(Commons.class .getName()); /** * Build timestamp attribute in the manifest in the jar */ private static final String BUILD_TIMESTAMP = "Created-At"; /** * */ private static final String currentRelease = getManifestBuildTimestamp(); /** * Default home directory */ private static final String DEFAULT_USER_DIRECTORY = "."; /** * Default file separator */ private static final String DEFAULT_FILE_SEPARATOR = "/"; /** * Default line separator */ private static final String DEFAULT_LINE_SEPARATOR = "\r\n"; /** * User home directory */ private static String userDirectory = DEFAULT_USER_DIRECTORY; static { try { userDirectory = System.getProperty("user.dir"); } catch (Exception e) { logger.log(Level.WARNING, "Failed getting user current directory: " + e.getMessage(), e); } } /** * Line separator */ private static String fileSeparator = DEFAULT_FILE_SEPARATOR; static { try { fileSeparator = System.getProperty("file.separator"); } catch (Exception e) { logger.log(Level.WARNING, "Failed getting system file separator: " + e.getMessage(), e); } } /** * Line separator */ private static String lineSeparator = DEFAULT_LINE_SEPARATOR; static { try { lineSeparator = System.getProperty("line.separator"); } catch (Exception e) { logger.log(Level.WARNING, "Failed getting system line separator: " + e.getMessage(), e); } } /** * JNLP enabled */ private static boolean jnlp = false; static { try { jnlp = "true".equalsIgnoreCase(System.getProperty("jnlp.enabled")); } catch (Exception e) { logger.log(Level.WARNING, "Failed getting jnlp enabled property: " + e.getMessage(), e); } setJnlp(jnlp); } /** * Returns system file separator. * * @return file separator */ public static String getFileSeparator() { return fileSeparator; } /** * Returns system line separator. * * @return line separator */ public static String getLineSeparator() { return lineSeparator; } /** * Returns user's current directory. * * @return user's current directory */ public static String getUserDirectory() { return userDirectory; } /** * Sets the JNLP flag to true of false * * @param jnlp * true or false */ public static void setJnlp(boolean jnlp) { Commons.jnlp = jnlp; } /** * Returns true if jnlp is enabled * * @return true if jnlp is enabled, otherwise returns false */ public static boolean isJnlp() { return jnlp; } /** * Gets the build teimstamp from the jar manifest * * @return build timestamp */ private static String getManifestBuildTimestamp() { JarURLConnection connection = null; JarFile jarFile = null; URL url = Commons.class.getClassLoader().getResource("jaligner"); try { // Get jar connection connection = (JarURLConnection) url.openConnection(); // Get the jar file jarFile = connection.getJarFile(); // Get the manifest Manifest manifest = jarFile.getManifest(); // Get the manifest entries Attributes attributes = manifest.getMainAttributes(); Attributes.Name name = new Attributes.Name(BUILD_TIMESTAMP); return attributes.getValue(name); } catch (Exception e) { String message = "Failed getting the current release info: " + e.getMessage(); logger.log(Level.WARNING, message); } return null; } /** * Returns the current release version of JAligner * * @return current release */ public static String getCurrentRelease() { return currentRelease; } /** * Returns information about JAligner * * @return information about JAligner */ public static String getJAlignerInfo() { return "JAligner - Build: " + getCurrentRelease() + " - By: Ahmed Moustafa"; } }JAligner-1.0/src/jaligner/util/SequenceParser.java000066400000000000000000000134601216526722600222110ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.util; import jaligner.Sequence; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; import java.io.InputStreamReader; import java.util.StringTokenizer; import java.util.logging.Level; import java.util.logging.Logger; /** * SequenceParser to sequences from different formats. *
* The supported formats are: *
    *
  • Plain sequence
    • , and *
  • FASTA
    • *
* * @author Ahmed Moustafa */ public class SequenceParser { /** * Logger */ private static final Logger logger = Logger.getLogger(SequenceParser.class.getName()); /** * Returns a parsed Sequence from a string. * @param sequence string to parse * @return parsed sequence * @throws SequenceParserException * @see Sequence */ public static Sequence parse (String sequence) throws SequenceParserException { if (sequence == null) { throw new SequenceParserException ( "Null sequence" ); } if (sequence.trim().length() == 0) { throw new SequenceParserException ( "Empty sequence" ); } sequence = sequence.replaceAll("\r\n", "\n"); String sequenceName = null; String sequenceDescription = null; if (sequence.startsWith(">")) { // FASTA format int index = sequence.indexOf("\n"); if (index == -1) { throw new SequenceParserException ( "Invalid sequence format" ); } String first = sequence.substring(1, index); sequence = sequence.substring(index); index = 0; for (int i = 0; i < first.length() && first.charAt(i) != ' ' && first.charAt(i) != '\t'; i++, index++) { // Skip white spaces } sequenceName = first.substring(0, index); StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|"); while (stringTokenizer.hasMoreTokens()) { sequenceName = stringTokenizer.nextToken(); } sequenceDescription = index + 1 > first.length() ? "" : first.substring(index + 1); } else { // Plain format ... nothing to do here } Sequence s = new Sequence(prepare(sequence), sequenceName, sequenceDescription, Sequence.PROTEIN); return s; } /** * Returns a Sequence parsed and loaded from a file * @param file to parse * @return parsed sequence * @throws SequenceParserException * @see Sequence */ public static Sequence parse (File file) throws SequenceParserException { String sequenceName = null; String sequenceDescription = null; BufferedReader reader = null; try { reader = new BufferedReader(new InputStreamReader(new FileInputStream(file))); StringBuffer buffer = new StringBuffer(); // Read & parse the first line String line = reader.readLine(); if (line.startsWith(">")) { // FASTA sequence line = line.substring(1).trim(); int index = 0; for (int i = 0; i < line.length() && line.charAt(i) != ' ' && line.charAt(i) != '\t'; i++, index++) { // Skip white spaces } sequenceName = line.substring(0, index); StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|"); while (stringTokenizer.hasMoreTokens()) { sequenceName = stringTokenizer.nextToken(); } sequenceDescription = index + 1 > line.length() ? "" : line.substring(index + 1); } else { // Plain sequence buffer.append(prepare(line)); } // Read the remaining the file (the actual sequence) while ((line = reader.readLine()) != null) { buffer.append(prepare(line)); } reader.close(); Sequence s = new Sequence(buffer.toString(), sequenceName, sequenceDescription, Sequence.PROTEIN); return s; } catch (Exception e) { throw new SequenceParserException(e.getMessage()); } finally { if (reader != null) { try { reader.close(); } catch (Exception silent) { logger.log(Level.WARNING, "Failed closing reader: " + silent.getMessage(), silent); } } } } /** * Removes whitespaces from a sequence and validates other characters. * @param sequence sequence to be prepared * @return prepared array of characters * @throws SequenceParserException */ private static String prepare (String sequence) throws SequenceParserException { StringBuffer buffer = new StringBuffer(); String copy = sequence.trim().toUpperCase(); for (int i = 0, n = copy.length(); i < n; i++) { switch ( copy.charAt(i) ) { // skip whitespaces case 9: case 10: case 13: case 32: break; // add a valid character case 'A': case 'B': case 'C': case 'D': case 'E': case 'F': case 'G': case 'H': case 'I': case 'K': case 'L': case 'M': case 'N': case 'P': case 'Q': case 'R': case 'S': case 'T': case 'U': case 'V': case 'W': case 'Y': case 'Z': case 'X': case '-': case '*': buffer.append(copy.charAt(i)); break; // throw an exception for anything else default: throw new SequenceParserException( "Invalid sequence character: '" + copy.charAt(i) + "'"); } } return buffer.toString(); } }JAligner-1.0/src/jaligner/util/SequenceParserException.java000066400000000000000000000020451216526722600240650ustar00rootroot00000000000000/* * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package jaligner.util; /** * * @author Ahmed Moustafa */ public class SequenceParserException extends Exception { /** * */ private static final long serialVersionUID = 3258417248288191543L; /** * @param message */ public SequenceParserException(String message) { super(message); } }JAligner-1.0/src/jaligner/util/package.html000066400000000000000000000002741216526722600207010ustar00rootroot00000000000000 Utility classes for helping core and GUI classes. @author Ahmed Moustafa