debian/0000755000000000000000000000000011534350252007166 5ustar debian/copyright0000644000000000000000000000252711534345226011134 0ustar Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 Maintainer: Lincoln D. Stein . Source: http://search.cpan.org/dist/Boulder/ Name: Boulder Files: * Copyright: 1997-2000, Lincoln D. Stein 1997-1999, Cold Spring Harbor Laboratory, Cold Spring Harbor NY 1999, Luca I.G. Toldo License: Artistic or GPL-1+ Files: debian/* Copyright: 2001, 2002, Christopher L Cheney 2002, Aurelien Jarno 2003, Emanuele Rocca 2004, Daniel Ruoso 2006, 2008, 2011, Russ Allbery 2008, gregor herrmann License: Artistic or GPL-1+ License: Artistic This program is free software; you can redistribute it and/or modify it under the terms of the Artistic License, which comes with Perl. . On Debian systems, the complete text of the Artistic License can be found in /usr/share/common-licenses/Artistic. License: GPL-1+ 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 1, or (at your option) any later version. . On Debian systems, the complete text of version 1 of the GNU General Public License can be found in /usr/share/common-licenses/GPL-1. debian/rules0000755000000000000000000000003611534345503010250 0ustar #!/usr/bin/make -f %: dh $@ debian/docs0000644000000000000000000000001611534342265010043 0ustar README docs/* debian/watch0000644000000000000000000000015111447517764010234 0ustar version=3 http://search.cpan.org/dist/Boulder/ .*/Boulder-v?(\d[\d.]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip) debian/patches/0000755000000000000000000000000011534350237010620 5ustar debian/patches/examples.patch0000644000000000000000000000215111447517763013472 0ustar Author: Russ Allbery --- a/eg/genbank.pl +++ b/eg/genbank.pl @@ -1,7 +1,7 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # This requires LWP to be installed. -use lib '.','..'; +#use lib '.','..'; use Boulder::Genbank; $gb = new Boulder::Genbank(-accessor=>'Entrez',-param=>[qw/M57939 M28274 L36028/]); --- a/eg/genbank2.pl +++ b/eg/genbank2.pl @@ -1,7 +1,7 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # This requires LWP to be installed. -use lib '.','..'; +#use lib '.','..'; use Boulder::Genbank; $gb = new Boulder::Genbank(-accessor=>'Entrez',-param=>[qw/M57939/]); --- a/eg/genbank3.pl +++ b/eg/genbank3.pl @@ -1,7 +1,7 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # This requires LWP to be installed. -use lib '.','..'; +#use lib '.','..'; use Boulder::Genbank; use Boulder::Stream; --- a/eg/quickblast.pl +++ b/eg/quickblast.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl # do a quick BLAST search a la fasta use Getopt::Long; --- a/eg/test.pl +++ b/eg/test.pl @@ -1,6 +1,6 @@ -#!/usr/local/bin/perl +#!/usr/bin/perl -use lib '.','..'; +#use lib '.','..'; use Stone; debian/patches/fix_pod.patch0000644000000000000000000001050711534347213013274 0ustar Author: Russ Allbery Description: Fix various POD formatting and spelling errors. --- libboulder-perl.orig/Boulder/XML.pm +++ libboulder-perl/Boulder/XML.pm @@ -101,7 +101,7 @@ =item $stream = Boulder::XML->new(*IN,*OUT); -=item $stream = Boulder::XML->new(-in=>*IN,-out=>*OUT,-tag=>$tag,-delim=>$delim,-strip=>$strip) +=item $stream = Boulder::XML->new(-in=>*IN, -out=>*OUT, -tag=>$tag, -delim=>$delim, -strip=>$strip) new() creates a new Boulder::XML stream that can be read from or written to. All arguments are optional. @@ -127,7 +127,7 @@ =item $fh = Boulder::XML->newFh(*IN,*OUT); -=item $fh = Boulder::XML->newFh(-in=>*IN,-out=>*OUT,-tag=>$tag,-delim=>$delim,-strip=>$strip) +=item $fh = Boulder::XML->newFh(-in=>*IN, -out=>*OUT, -tag=>$tag, -delim=>$delim, -strip=>$strip) The newFh() constructor creates a tied filehandle that can read and write Boulder::XML streams. Invoking <> on the filehandle will --- libboulder-perl.orig/Boulder/Genbank.pm +++ libboulder-perl/Boulder/Genbank.pm @@ -339,13 +339,13 @@ The names "-type" and "-types" can be used interchangeably. +=back + =head2 $seqObj = $entry->bioSeq; Returns a L object from the Bioperl project. Dies with an error message unless the Bio::Seq module is installed. -=back - =head1 OUTPUT TAGS The tags returned by the parsing operation are taken from the NCBI --- libboulder-perl.orig/Boulder/Medline.pm +++ libboulder-perl/Boulder/Medline.pm @@ -119,46 +119,46 @@ These are tags that appear at the top level of the parsed Medline entry. -=over 4 + ABSTRACT + ABSTRACT AUTHOR + ADDRESS + AUTHOR + CALL NUMBER + CAS REGISTRY/EC NUMBER + CLASS UPDATE DATE + COMMENTS + COUNTRY + DATE OF ENTRY + DATE OF PUBLICATION + ENGLISH ABSTRACT INDICATOR + ENTRY MONTH + GENE SYMBOL + ID NUMBER + INDEXING PRIORITY + ISSN + ISSUE/PART/SUPPLEMENT + JOURNAL SUBSET + JOURNAL TITLE CODE + LANGUAGE + LAST REVISION DATE + MACHINE-READABLE IDENTIFIER + MeSH HEADING + NO-AUTHOR INDICATOR + NOT FOR PUBLICATION + NUMBER OF REFERENCES + PAGINATION + PERSONAL NAME AS SUBJECT + PUBLICATION TYPE + RECORD ORIGINATOR + SECONDARY SOURCE ID + SPECIAL LIST INDICATOR + TITLE + TITLE ABBREVIATION + TRANSLITERATED/VERNACULAR TITLE + UNIQUE IDENTIFIER + VOLUME ISSUE -ABSTRACT -ABSTRACT AUTHOR -ADDRESS -AUTHOR -CALL NUMBER -CAS REGISTRY/EC NUMBER -CLASS UPDATE DATE -COMMENTS -COUNTRY -DATE OF ENTRY -DATE OF PUBLICATION -ENGLISH ABSTRACT INDICATOR -ENTRY MONTH -GENE SYMBOL -ID NUMBER -INDEXING PRIORITY -ISSN -ISSUE/PART/SUPPLEMENT -JOURNAL SUBSET -JOURNAL TITLE CODE -LANGUAGE -LAST REVISION DATE -MACHINE-READABLE IDENTIFIER -MeSH HEADING -NO-AUTHOR INDICATOR -NOT FOR PUBLICATION -NUMBER OF REFERENCES -PAGINATION -PERSONAL NAME AS SUBJECT -PUBLICATION TYPE -RECORD ORIGINATOR -SECONDARY SOURCE ID -SPECIAL LIST INDICATOR -TITLE -TITLE ABBREVIATION -TRANSLITERATED/VERNACULAR TITLE -UNIQUE IDENTIFIER -VOLUME ISSUE +=over 4 =item Identifier --- libboulder-perl.orig/Stone/Cursor.pm +++ libboulder-perl/Stone/Cursor.pm @@ -25,6 +25,8 @@ =head2 CLASS METHODS +=over 4 + =item Boulder::Cursor->new($stone) Return a new Boulder::Cursor over the specified L object. This @@ -34,8 +36,12 @@ my $cursor = $stone->cursor; +=back + =head2 OBJECT METHODS +=over 4 + =item $cursor->each() Iterate over the attached B. Each iteration will return a @@ -59,6 +65,8 @@ This resets the cursor back to the beginning of the associated B. +=back + =head1 AUTHOR Lincoln D. Stein . --- libboulder-perl.orig/Stone/GB_Sequence.pm +++ libboulder-perl/Stone/GB_Sequence.pm @@ -87,13 +87,13 @@ The names "-type" and "-types" can be used interchangeably. +=back + =head2 $seqObj = $entry->bioSeq; Returns a L object from the Bioperl project. Dies with an error message unless the Bio::Seq module is installed. -=back - =head1 AUTHOR Lincoln D. Stein . --- libboulder-perl.orig/Boulder.pod +++ libboulder-perl/Boulder.pod @@ -110,7 +110,7 @@ =head2 Hierarchical Records -The simple boulder format can be extended to accomodate nested +The simple boulder format can be extended to accommodate nested relations and other intresting structures. Nested records can be created in this way: debian/patches/series0000644000000000000000000000003511447517763012047 0ustar examples.patch fix_pod.patch debian/compat0000644000000000000000000000000211534344051010364 0ustar 8 debian/changelog0000644000000000000000000000706111534350162011044 0ustar libboulder-perl (1.30-4) unstable; urgency=low * Team upload. [ gregor herrmann ] * Split out changes to upstream code into separate patches; add quilt framework. * debian/watch: use dist-based URL. * debian/control: Changed: Switched Vcs-Browser field to ViewSVN (source stanza). * debian/control: Added: ${misc:Depends} to Depends: field. [ Nathan Handler ] * debian/watch: Update to ignore development releases. [ Russ Allbery ] * Remove myself from Uploaders. * Update debhelper compatibility level to V8. - Use debhelper rule minimization. * Update copyright to the DEP-5 format and add more copyright holders. * Switch to source format 3.0 (quilt) and remove quilt dependencies. * Update standards version to 3.9.1. * Remove unnecessary Priority and Section fields in the binary stanza. * Fix additional spelling and formatting errors in the POD documentation. * Merge Build-Depends-Indep into Build-Depends. For a package that builds only arch-all binary packages, there's no point in separating these. -- Russ Allbery Fri, 04 Mar 2011 21:56:02 -0800 libboulder-perl (1.30-3) unstable; urgency=low [ gregor herrmann ] * debian/control: Added: Vcs-Svn field (source stanza); Vcs-Browser field (source stanza); Homepage field (source stanza). Removed: XS- Vcs-Svn fields. * debian/rules: delete /usr/lib/perl5 only if it exists. (Closes: #467701) [ Joachim Breitner ] * Removed myself from uploaders. [ Russ Allbery ] * Update standards version to 3.7.3 (no changes required). * Update debhelper compatibility level to V5 (no changes required). -- Russ Allbery Mon, 03 Mar 2008 21:06:44 -0800 libboulder-perl (1.30-2) unstable; urgency=low * Add some whitespace to the prototypes in the Boulder::XML documentation so that nroff can determine where to split lines. * Install the upstream documentation and examples. * Clean up and simplify debian/rules. * Run tests as part of the package build. * Remove the empty /usr/lib/perl5 directory. * Update to debhelper compatibility level V4. * Update to standards version 3.6.2 (no changes required). * Add a watch file. -- Russ Allbery Mon, 16 Jan 2006 21:13:00 -0800 libboulder-perl (1.30-1) unstable; urgency=low * New upstream version * New Maintainer (Closes: #217111) -- Daniel Ruoso Fri, 9 Jan 2004 15:08:36 -0300 libboulder-perl (1.27-2) unstable; urgency=low * Maintainer field set to QA group. * Clarification about the licence added to debian/copyright. Closes: #157550 * "Upstream Author(s)" replaced with "Upstream Author" in debian/copyright. * debian/control: Section changed to perl. * Updated Standard Versions to 3.6.1 -- Emanuele Rocca Mon, 17 Nov 2003 17:13:39 +0100 libboulder-perl (1.27-1.1) unstable; urgency=low * Non-Maintainer Upload (BSP 2002-11). * Changed Build-Depends to Build-Depends-Indep (closes: bug#170048). * Now Build the .deb in binary-indep target (closes: bug#157465). -- Aurelien Jarno Sat, 23 Nov 2002 13:19:48 +0100 libboulder-perl (1.27-1) unstable; urgency=high * New Upstream. -- Christopher L Cheney Sun, 10 Feb 2002 02:00:00 -0600 libboulder-perl (1.24-1) unstable; urgency=low * New Upstream. -- Christopher L Cheney Fri, 10 Aug 2001 23:00:00 -0500 libboulder-perl (1.20-1) unstable; urgency=low * Initial Release. -- Christopher L Cheney Tue, 6 Mar 2001 10:00:00 -0600 debian/control0000644000000000000000000000213711534347370010603 0ustar Source: libboulder-perl Section: perl Priority: optional Build-Depends: debhelper (>= 8), libxml-parser-perl, perl Maintainer: Debian Perl Group Uploaders: Daniel Ruoso Standards-Version: 3.9.1 Homepage: http://search.cpan.org/dist/Boulder/ Vcs-Svn: svn://svn.debian.org/pkg-perl/trunk/libboulder-perl/ Vcs-Browser: http://svn.debian.org/viewsvn/pkg-perl/trunk/libboulder-perl/ Package: libboulder-perl Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, libxml-parser-perl Description: Perl module for hierarchical tag/value structures Boulder provides a simple stream-oriented format for transmitting data objects between one or more processes. It does not provide for the serialization of Perl objects the way FreezeThaw or Data::Dumper do, but it does provide the advantage of being language independent. . In addition to a stream-oriented interface, Boulder comes with a simple record-oriented database-oriented interface, Boulder::Store, which provides query and search capabilities comparable to many flat file DBMS systems. debian/examples0000644000000000000000000000000511534341443010724 0ustar eg/* debian/source/0000755000000000000000000000000011534350237010471 5ustar debian/source/format0000644000000000000000000000001411534345431011677 0ustar 3.0 (quilt)