pax_global_header 0000666 0000000 0000000 00000000064 12536525416 0014523 g ustar 00root root 0000000 0000000 52 comment=e3dc48e8e86242ef54102446aadf6ba466406350
ClonalOrigin-1.0/ 0000775 0000000 0000000 00000000000 12536525416 0013743 5 ustar 00root root 0000000 0000000 ClonalOrigin-1.0/README.md 0000664 0000000 0000000 00000005755 12536525416 0015236 0 ustar 00root root 0000000 0000000 # ClonalOrigin
# Introduction #
Bacteria, unlike us, can reproduce on their own. They do however have mechanisms that transfer DNA between organisms, a process more formally known as recombination. The mechanisms by which recombination takes place have been studied extensively in the laboratory but much remains to be understood concerning how, when and where recombination takes place within natural populations of bacteria and how it helps them to adapt to new environments. ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.
ClonalOrigin is described in the following paper:
Didelot X, Lawson D, Darling A, Falush D (2010) Inference of homologous recombination in bacteria using whole genome sequences. Genetics 186 (4), 1435-1449 doi:10.1534/genetics.110.120121 http://www.genetics.org/cgi/content/abstract/genetics.110.120121v1
# Usage #
Instructions for how to download and install ClonalOrigin are available at:
https://github.com/xavierdidelot/ClonalOrigin/wiki/Install
Instructions for how to use ClonalOrigin once installed are available at:
https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage
# Estimating strength of bias in the recombination process #
We define biased recombination in contrast to free recombination where all individuals in the population are equally likely to recombine. There are many factors contributing to recombination being biased rather than free. Laboratory experiments have shown that the recombination process is homology dependent whereby it tends to happen more often between individuals that are less diverged. Furthermore, the geographical and ecological structures observed in many bacterial populations implies a greater opportunity of recombination for pairs of cells that are closely related. Purifying selection may also effectively prevent recombination between distantly related bacteria. All these effects would clearly be hard to disentangle, and here we group them all under the single concept of biased recombination. The strength of this bias is an important factor to take into account in order to understand recombination in bacteria. In particular, this determines how often recombination happens within the diversity of the population under study rather than from other sources.
We have introduced a model for biased recombination which is based on the ClonalOrigin model. We use approximate Bayesian computation and whole genome data to infer the rate of bias in the recombination process in bacteria. The user guide and Matlab code can be downloaded from:
http://www.stats.ox.ac.uk/~ansari/BiasedRecV1.tgz
Full details of the biased recombination model have been published in the following paper:
Ansari MA, Didelot X. Inference of the Properties of the Recombination Process from Whole Bacterial Genomes. Genetics. 2014;196: 253–265. doi:10.1534/genetics.113.157172
http://www.genetics.org/content/early/2013/10/21/genetics.113.157172
ClonalOrigin-1.0/gui/ 0000775 0000000 0000000 00000000000 12536525416 0014527 5 ustar 00root root 0000000 0000000 ClonalOrigin-1.0/gui/coloured.ui 0000664 0000000 0000000 00000010331 12536525416 0016700 0 ustar 00root root 0000000 0000000
Dialog
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Setup coloured plot
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QDialogButtonBox::Cancel|QDialogButtonBox::NoButton|QDialogButtonBox::Ok
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Double-click nodes on the tree to add groups.
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Move up
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Move down
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Remove
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Colour...
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Show density of:
-
Qt::Vertical
-
Coloured according to:
-
Arrival
true
false
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Arrival
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Departure
false
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Departure
true
false
ClonalOrigin-1.0/gui/colouredimpl.cpp 0000664 0000000 0000000 00000004473 12536525416 0017741 0 ustar 00root root 0000000 0000000 #include "colouredimpl.h"
//
ColouredImpl::ColouredImpl( QWidget * parent, Qt::WFlags f)
: QDialog(parent, f)
{
setAttribute(Qt::WA_DeleteOnClose);
setupUi(this);
}
//
void ColouredImpl::on_buttonBox_accepted()
{
QStringList * nodes=new QStringList();
QStringList * colors=new QStringList();
for (int i=0;icount();i++) {
QListWidgetItem * item=listWidget->item(i);
nodes->append(item->text());
colors->append(item->textColor().name());
}
if (nodes->size()>0) ((MainWindowImpl*)parent())->doColourPlot(nodes,colors,denDep->isChecked(),colDep->isChecked());
close();
}
void ColouredImpl::on_buttonBox_rejected()
{
close();
}
void ColouredImpl::closeEvent(QCloseEvent * event)
{
event=0;
connect(((MainWindowImpl*)parent()),SIGNAL(wasDbClicked(int,QMouseEvent*)),((MainWindowImpl*)parent()),SLOT(computeAfterDbClick(int,QMouseEvent*)));
destroy();
}
void ColouredImpl::addGroup(int id)
{
QListWidgetItem * item=new QListWidgetItem(QString::number(id));
item->setTextColor(Qt::red);
listWidget->addItem(item);
}
void ColouredImpl::on_colour_clicked()
{
QListWidgetItem * item=listWidget->currentItem();
if (item==NULL) return;
QColor c0=item->textColor();
QColor c=QColorDialog::getColor(c0);
if (!c.isValid()) return;
item->setTextColor(c);
}
void ColouredImpl::on_moveUp_clicked()
{
QListWidgetItem * item=listWidget->currentItem();
if (item==NULL) return;
int c=listWidget->currentRow();
if (c==0) return;
item=listWidget->takeItem(listWidget->currentRow());
listWidget->insertItem(c-1,item);
listWidget->setCurrentRow(c-1);
}
void ColouredImpl::on_moveDown_clicked()
{
QListWidgetItem * item=listWidget->currentItem();
if (item==NULL) return;
int c=listWidget->currentRow();
if (c==listWidget->count()-1) return;
item=listWidget->takeItem(listWidget->currentRow());
listWidget->insertItem(c+1,item);
listWidget->setCurrentRow(c+1);
}
void ColouredImpl::on_remove_clicked()
{
QListWidgetItem * item=listWidget->currentItem();
if (item==NULL) return;
listWidget->takeItem(listWidget->currentRow());
}
void ColouredImpl::on_denArr_clicked()
{
denDep->setChecked(false);
}
void ColouredImpl::on_colArr_clicked()
{
colDep->setChecked(false);
}
void ColouredImpl::on_denDep_clicked()
{
denArr->setChecked(false);
}
void ColouredImpl::on_colDep_clicked()
{
colArr->setChecked(false);
}
ClonalOrigin-1.0/gui/colouredimpl.h 0000664 0000000 0000000 00000001201 12536525416 0017370 0 ustar 00root root 0000000 0000000 #ifndef COLOUREDIMPL_H
#define COLOUREDIMPL_H
//
#include
#include "ui_coloured.h"
#include "mainwindowimpl.h"
//
class ColouredImpl : public QDialog, public Ui::Dialog
{
Q_OBJECT
public:
ColouredImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
private:
void closeEvent(QCloseEvent * event);
private slots:
void on_denArr_clicked();
void on_colArr_clicked();
void on_denDep_clicked();
void on_colDep_clicked();
void on_moveUp_clicked();
void on_moveDown_clicked();
void on_remove_clicked();
void on_colour_clicked();
void addGroup(int id);
void on_buttonBox_accepted();
void on_buttonBox_rejected();
};
#endif
ClonalOrigin-1.0/gui/densityontree.cpp 0000664 0000000 0000000 00000007444 12536525416 0020140 0 ustar 00root root 0000000 0000000 #include "densityontree.h"
//
DensityOnTree::DensityOnTree(Tree * tree,double timeScale)
{
this->timeScale=timeScale;
precision=0.005*tree->getNode(tree->getN()*2-2)->getAge();
this->tree=tree;
int siz=0;
for (int i=0;igetN()*2-2;i++) siz+=floor(tree->getDist(i)/precision);
siz+=max(0.0,floor((timeScale-tree->getNode(tree->getN()*2-2)->getAge())/precision));
d=vector(siz,0.0);
above=0.0;
}
void DensityOnTree::add(int edge,double age,double relcon)
{
int which=0;
int n=tree->getN();
for (int e=0;egetDist(e)/precision);
int end=which;
which+=floor(age/precision);
if (edgegetDist(edge)/precision);if (which>=end) return;}
else
{end+=floor((timeScale-tree->getNode(n*2-2)->getAge())/precision);if (which>=end) {above++;return;};}
if(which>=d.size()) {d[d.size()-1]+=relcon;
}else d[which]+=relcon; //*** See below. There is a danger that something is wrong here because when mapping to a consensus tree sometimes end>d.size....
}
void DensityOnTree::smooth()
{
int n=tree->getN();
vector d2(d.size(),0);
vector count(d.size(),0);
for (int edge=0;edge<=n*2-1;edge++) {
int beg=0;
for (int e=0;egetDist(e)/precision);
int end=beg;
if (edgegetDist(edge)/precision);else end+=floor((timeScale-tree->getNode(n*2-2)->getAge())/precision);
for (int w=beg;w=end) {a-=w+b-end+1;}
for (int k=a;k<=b;k++) if (w+k>=beg && w+kd.size....
}
}
for (unsigned int i=0;i0) d.at(i)=d2.at(i)/count.at(i);//else cout<<"error in smoothing"<*x,vector*y,double scale,QBrush brush)
{
int n=tree->getN();
for (int i=0;igetDist(e)/precision);
for (unsigned int j=0;(i==n*2-2&&jgetNode(i)->getAge())/precision))||(igetDist(i)/precision));j++) {
double beg=x->at(i)-(j+1)*precision/timeScale;
painter->fillRect(QRectF(beg,y->at(i)+0.002*((scale<0)?-1:1),precision/timeScale*1.05,d[which]*scale/n),brush);
which++;
}
}
if (above>0) painter->fillRect(QRectF(0.0,y->at(n+n-2),-0.1,above*scale/n*precision/timeScale*10.0),brush);
}
void DensityOnTree::add2(RecTree *treefrom,int i,bool goingto,double relcon)
{
vector alle;
double distto=0;
if(goingto) alle =treefrom->getAllSampledSeqs(treefrom->getEdge(i)->getEdgeTo());
else alle =treefrom->getAllSampledSeqs(treefrom->getEdge(i)->getEdgeFrom());
vector allaffected=tree->getMinEdgeList(alle);
for(unsigned int j=0;jgetRoot()->getId()) distto=treefrom->getRecEdge(i)->getTimeTo();
else if(treefrom->getRecEdge(i)->getEdgeTo()==treefrom->getRoot()->getId()) {distto = tree->getNode(allaffected[j])->getDist()*0.99;}
else distto=treefrom->getRecEdge(i)->getTimeTo()/ treefrom->getNode(treefrom->getRecEdge(i)->getEdgeTo())->getDist() * tree->getNode(allaffected[j])->getDist();
}else {
if(allaffected[j]==tree->getRoot()->getId()) distto=treefrom->getRecEdge(i)->getTimeFrom();
else if(treefrom->getRecEdge(i)->getEdgeFrom()==treefrom->getRoot()->getId()) {distto = tree->getNode(allaffected[j])->getDist()*0.99;}
else distto=treefrom->getRecEdge(i)->getTimeFrom()/ treefrom->getNode(treefrom->getRecEdge(i)->getEdgeFrom())->getDist() * tree->getNode(allaffected[j])->getDist();
}
add(allaffected[j],distto,relcon/allaffected.size());
}
}
//
ClonalOrigin-1.0/gui/densityontree.h 0000664 0000000 0000000 00000001267 12536525416 0017602 0 ustar 00root root 0000000 0000000 #ifndef DENSITYONTREE_H
#define DENSITYONTREE_H
//
#include "gelmanrubinimpl.h"
//
class DensityOnTree
{
public:
DensityOnTree(Tree*tree,double timeScale);
void display(QPainter * painter,vector*x,vector*y,double scale,QBrush brush);
void add(int edge ,double age,double relcon=1.0);
void smooth();
//inline int maximum(){int max=0;for (unsigned int i=0;itree=tree;}
void add2(RecTree *treefrom,int i,bool goingto,double relcon=1.0);/// d;
double above;
double precision;
double timeScale;
};
#endif
ClonalOrigin-1.0/gui/gelmanrubin.ui 0000664 0000000 0000000 00000013141 12536525416 0017371 0 ustar 00root root 0000000 0000000
GelmanRubin
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0
604
566
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0
Gelman-Rubin test
9
9
9
9
6
6
-
0
0
0
0
6
6
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Export...
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Qt::Horizontal
QDialogButtonBox::Cancel|QDialogButtonBox::NoButton|QDialogButtonBox::Ok
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0
0
5
4
|
|
|
|
|
-
Result of the Gelman-Rubin test:
-
true
0
100
0
100
Test options:
10
20
301
22
Parameters only (fastest)
10
40
301
22
Parameters + Edges (for constant trees)
true
10
60
361
22
Parameters + Pairwise Distances (for varying trees)
10
80
391
22
Parameters + Edges + Pairwise Distance (for fixed topology)
10
100
391
22
Branch lengths only
470
60
111
31
Perform Test
ClonalOrigin-1.0/gui/gelmanrubinimpl.cpp 0000664 0000000 0000000 00000031745 12536525416 0020432 0 ustar 00root root 0000000 0000000 #include "gelmanrubinimpl.h"
//
GelmanRubinImpl::GelmanRubinImpl( QWidget * parent, Qt::WFlags f)
: QDialog(parent, f) {
setupUi(this);
param=NULL;
outputFile=NULL;
out=NULL;
sep=",";
doGR=true;
groupBox->setEnabled(true);
// groupBox->setMinimumSize(QSize(0, 0));
groupBox->setHidden(true);
//connect(pushGo,SIGNAL(wasDbClicked(int,QMouseEvent*)),this,SLOT(computeAfterClick(int,QMouseEv
//QObject::connect(pushGo, SIGNAL(clicked()), auxSignals, SLOT(buttonClicked()));
}
//
void GelmanRubinImpl::compute(ParamQt*param,OutputFile*outputFile,QStringList*others,ostream* out,bool getparams,bool getnumedges,bool getpairwisedists) {
vector< vector< vector > > v;//Store:file x iteration x property
int m=1+others->size();//Number of files
v.push_back(vector< vector >());
outputFile->startOver();
while (outputFile->getIt(param)) {
v[0].push_back(extractInfo(param,false,getparams,getnumedges,getpairwisedists));
}
for (int i=0;isize();i++) {
OutputFile * out2=new OutputFile(QStringList(others->at(i)),false);
v.push_back(vector< vector >());
while (out2->getIt(param)) {
v[i+1].push_back(extractInfo(param,false,getparams,getnumedges,getpairwisedists));
}
}
//Table headers
table->setRowCount(1+v[0][0].size());
table->setColumnCount(m+2);
table->setColumnWidth(0,table->columnWidth(0)*2);
table->setItem(0,0,new QTableWidgetItem(QString("Parameter")));
for (int i=1;i<=m;i++) table->setItem(0,i,new QTableWidgetItem(QString("File ")+QString::number(i)));
table->setItem(0,1+m,new QTableWidgetItem(QString("Gelman-Rubin")));
nameTable(param,getparams,getnumedges,getpairwisedists);
//Table
for (unsigned int whichP=0;whichP > data;
for (int i=0;i());
for (unsigned int j=0;jsetItem(whichP+1,i,new QTableWidgetItem(QString::number(mean)));
}
table->setItem(whichP+1,1+m,new QTableWidgetItem(QString::number(R)));
}
if(out!=NULL){
for(int i=0;irowCount();i++){
for(int j=0;jcolumnCount()-1;j++){
*out<item(i,j)->text().toStdString()<item(i,table->columnCount()-1)->text().toStdString()<size();//Number of files
int iso=param->getTree()->getN();//Number of isolates
QHash > hash;
for (int i=0;isize();i++) {
OutputFile * out2=new OutputFile(QStringList(files->at(i)),false);
int its=0;
while (out2->getIt(param)) {
its++;
for (int ii=iso;iigetTree()->getNode(ii);
QString key(iso,'0');
ParamTreeCons::makeKey(node,&key);
if (!hash.contains(key)) hash[key]=vector(m,0.0);
hash[key][i]++;
}
};
QStringList keys=hash.uniqueKeys();
for (int ii=0;ii > > v;//Store:file x iteration x property
v.push_back(vector< vector >());
QStringList keys=hash.uniqueKeys();
//Average standard deviation of split frequencies
double asdsf=0.0;
int cmp=0;
for (int i=0;isetText(QString("Average standard deviation of split frequencies=")+QString::number(asdsf));
//Table headers
table->setRowCount(keys.size()+1);
table->setColumnCount(m+1);
table->setColumnWidth(0,table->columnWidth(0)*2);
if(out!=NULL) *out<setItem(0,i,new QTableWidgetItem(QString("File ")+QString::number(i)));
if(out!=NULL) *out<<"File "<setItem(i+1,0,new QTableWidgetItem(keys[i]));
//Table
for (int i=0;isetItem(i+1,j+1,new QTableWidgetItem(QString::number(hash[keys[i]][j])));
if(out!=NULL) *out<getTree()->getN();//Number of isolates
if(getparams){
table->setItem(rownumber++,0,new QTableWidgetItem(QString("theta")));
table->setItem(rownumber++,0,new QTableWidgetItem(QString("rho")));
table->setItem(rownumber++,0,new QTableWidgetItem(QString("delta")));
table->setItem(rownumber++,0,new QTableWidgetItem(QString("Num Edges")));
table->setItem(rownumber++,0,new QTableWidgetItem(QString("Likelihood")));
table->setItem(rownumber++,0,new QTableWidgetItem(QString("TMRCA")));
table->setItem(rownumber++,0,new QTableWidgetItem(QString("SumBraLen")));
}
if(getnumedges){
for (int i=0;isetItem(rownumber++,0,new QTableWidgetItem(QString("Edges on branch ")+QString::number(i)));
}
if(getpairwisedists){
for (int i=0;isetItem(rownumber++,0,new QTableWidgetItem(QString("PairwiseDistance")+QString::number(i)+QString("to")+QString::number(j)));
}
}
vector GelmanRubinImpl::extractInfo(ParamQt*p, bool csv,bool getparams,bool getnumedges,bool getpairwisedists) {
vector v;
int ccount=0;
if (csv) ccount=p->countConv();
int iso=p->getTree()->getN();
if(getparams) { for (int whichP=0;whichP<7+ccount;whichP++) {
if (whichP==0) {v.push_back(p->getTheta());continue;}
if (whichP==1) {v.push_back(p->getRho ());continue;}
if (whichP==2) {v.push_back(p->getDelta());continue;}
if (whichP==3) {v.push_back(p->getTree()->numRecEdge());continue;}
if (whichP==4) {v.push_back(p->getLL());continue;}
if (whichP==5) {v.push_back(p->getTree()->getNode(iso+iso-2)->getAge());continue;}
if (whichP==6) {v.push_back(p->getTree()->getTTotal());continue;}
if (whichP>6 && whichP<7+ccount) {v.push_back(p->getConvData(whichP-7));continue;}
} }
if(getnumedges) {for (int whichP=0;whichP<(iso+iso-2);whichP++) {
v.push_back(p->getTree()->numRecEdgeOnBranch(whichP));
}}
if(getpairwisedists) {
vector vt=p->pairwiseDistanceList();
for(unsigned int c1=0;c1 vt;
p->consistentAgeList(&vt);
for(unsigned int c1=0;c1 >*data) {
vector means;
double mean;
unsigned int m=data->size();
unsigned int n=data->at(0).size();
for (unsigned int i=0;iat(i).size()at(i).size();
for (unsigned int i=0;iat(i).at(j);
}
mean/=n;
means.push_back(mean);
}
mean=0.0;
for (unsigned int j=0;jat(j).at(t)-means[j]),2.0);
W=W/m/(n-1.0);
double V=(n-1.0)/n*W+B/n;
return V/W;
}
void GelmanRubinImpl::on_exportButton_clicked() {
QString qstr = QFileDialog::getSaveFileName(this, tr("Save output file"),".","CSV files (*.csv);;All files (*)");
if (qstr==NULL) return;
QFile file(qstr);
if ( !file.open(QIODevice::WriteOnly)) return;
QTextStream ts( &file );
for (int i=0;irowCount();i++)
for (int j=0;jcolumnCount();j++) {
if (table->item(i,j)!=NULL) ts<item(i,j)->text();
if (jcolumnCount()-1) ts<<","; else ts< > v;//Store:iteration x property
int iso=param->getTree()->getN();//Number of isolates
outputfile->startOver();
while (outputfile->getIt(param)) {
v.push_back(extractInfo(param,csv,getparams,getnumedges,getpairwisedists));
}
//Write header
int ccount=0;
if (csv) ccount=param->countConv();
QFile file(*qstr);
if ( !file.open(QIODevice::WriteOnly)) return;
QTextStream ts( &file );
QString sep;
if (csv) sep=",";else sep="\t";
if (csv && getparams) {
ts<<"\"iter\",\"theta\",\"rho\",\"delta\",\"numrecedge\",\"likelihood\",\"TMRCA\",\"SumBraLen\",";
for (int i=0;igetConvName(i).c_str()<< "\"";
if (igetTree()->getN();//Number of isolates
QHash > hash;
//Analyze partitions in the output file
OutputFile * out2=new OutputFile(QStringList(outputfile),false);
int its=0;
while (out2->getIt(param)) {
its++;
for (int ii=iso;iigetTree()->getNode(ii);
QString key(iso,'0');
ParamTreeCons::makeKey(node,&key);
if (!hash.contains(key)) hash[key]=vector(2,0.0);
hash[key][0]++;
}
};
QStringList keys=hash.uniqueKeys();
for (int ii=0;iigetNode(ii);
QString key(iso,'0');
ParamTreeCons::makeKey(node,&key);
if (!hash.contains(key)) hash[key]=vector(2,0.0);
hash[key][1]=1.0;
}
//Calculate stats
keys=hash.uniqueKeys();
double score=0.0;
double efficiency=0.0;double eff2=0.0;
double accuracy=0.0;double acc2=0.0;
for (int ii=0;ii=0.5) efficiency++;};
if (hash[keys[ii]][0]>=0.5) {acc2++;if (hash[keys[ii]][1]==1.0) accuracy ++;};
}
return QString("Score=%1; Efficiency=%2; Accuracy=%3").arg(score).arg(efficiency/eff2).arg(accuracy/acc2);
}
void GelmanRubinImpl::on_buttonBox_accepted() {
if(!doGR) {
bool usecsv=true;
if(sep.compare(",")!=0)usecsv=false;
if(param==NULL) throw("Export not initalised!");
if(radioType1->isChecked()) outputTracer(param,outputFile,&(others[0]),usecsv,true,false,false);
else if(radioType2->isChecked()) outputTracer(param,outputFile,&(others[0]),usecsv,true,true,false);
else if(radioType3->isChecked()) outputTracer(param,outputFile,&(others[0]),usecsv,true,false,true);
else if(radioType4->isChecked()) outputTracer(param,outputFile,&(others[0]),usecsv,true,true,true);
else if(radioType5->isChecked()) outputTracer(param,outputFile,&(others[0]),usecsv,false,false,false);
}
close();
}
void GelmanRubinImpl::on_buttonBox_rejected() {
close();
}
void GelmanRubinImpl::on_pushGo_clicked()
{
if(param==NULL) throw("Gelman Rubin not initalised!");
if(radioType1->isChecked()) compute(param,outputFile,&others,NULL,true,false,false);
else if(radioType2->isChecked()) compute(param,outputFile,&others,NULL,true,true,false);
else if(radioType3->isChecked()) compute(param,outputFile,&others,NULL,true,false,true);
else compute(param,outputFile,&others,NULL,true,true,true);
groupBox->setEnabled(false);
}
ClonalOrigin-1.0/gui/gelmanrubinimpl.h 0000664 0000000 0000000 00000003762 12536525416 0020075 0 ustar 00root root 0000000 0000000 #ifndef GELMANRUBINIMPL_H
#define GELMANRUBINIMPL_H
//
#include "ui_gelmanrubin.h"
#include
#include
#include
#include
#include
#include
#include "paramqt.h"
#include "../warg/src/tree.h"
#include "../warg/src/rectree.h"
#include "../warg/src/param.h"
#include "../warg/src/data.h"
#include "outputfile.h"
#include "paramtreecons.h"
//
using namespace std;
class GelmanRubinImpl : public QDialog, public Ui::GelmanRubin
{
Q_OBJECT
public:
GelmanRubinImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
void compute(ParamQt*param,OutputFile*outputFile,QStringList*others, ostream* out=NULL,bool getparams=true,bool getnumedges=true,bool getpairwisedists=false);
void computeTree(ParamQt*,QStringList*,ostream* out=NULL);
void outputTracer(ParamQt*param,OutputFile*outputfile,QString*qstr,bool csv=false,bool getparams=true,bool getnumedges=true,bool getpairwisedists=false);
static QString compareTrueTree(ParamQt*,QString,QString);
inline void setFiles(ParamQt*param,OutputFile*outputFile,QStringList others){
this->param=param;
this->outputFile=outputFile;
this->others=others;
}
inline void showOptions(){
groupBox->setHidden(false);
}
inline void setExport(){
groupBox->setHidden(false);
table->setHidden(true);
exportButton->setHidden(true);
label->setHidden(true);
pushGo->setHidden(true);
doGR=false;
this->setFixedHeight(170);
this->setWindowTitle(QString("Export"));
}
inline void setSep(string s){sep=s;}
protected:
void nameTable(ParamQt*p,bool getparams,bool getnumedges,bool getpairwisedists);
vector extractInfo(ParamQt*p, bool csv=false,bool getparams=true,bool getnumedges=true,bool getpairwisedists=false);
double test(vector< vector >*data);
ParamQt*param;
OutputFile*outputFile;
QStringList others;
ostream* out;
string sep;
bool doGR;
private slots:
void on_exportButton_clicked();
void on_buttonBox_accepted();
void on_buttonBox_rejected();
void on_pushGo_clicked();
};
#endif
ClonalOrigin-1.0/gui/gui.cpp 0000664 0000000 0000000 00000016271 12536525416 0016026 0 ustar 00root root 0000000 0000000 #include
#include
#include "mainwindowimpl.h"
#include "../warg/src/rng.h"
#include "../warg/src/mpiutils.h"
#include "mainapplicationdbusadaptor.h"
#include
bool verbose=false;
namespace weakarg
{
//void opt() {};
ProgramOptions& opt() {static ProgramOptions po;return po;}
}
static const char * help=
"\n\
Usage: gui [OPTIONS] \n\
For graphical use, no options are necessary. \n\
To pre-run a limited set of functions, or use batch \n\
mode, the following options can be used.\n\
NOTE: They are processed IN ORDER, so be sure to open\n\
the file before using it, and set output names before\n\
producing the output!\n\
\n\
Options:\n\
-b Batch mode. Perform operations then quit \n\
without displaying the gui.\n\
-o Open the specified input XML file.\n\
-c <:num> \n\
Write a csv file of the main features. If\n\
:num is provided then it changes the variables\n\
in the output (default 2):\n\
:1 - Parameters only\n\
:2 - Parameters + Number of recedges\n\
:3 - Parameters + Clonal Pairwise Distances\n\
:4 - All of the above.\n\
-T Redirect the batch processed output \n\
from stdout to the file specified.\n\
Specify "" to display to the gui.\n\
-t Perform a convergence of trees test \n\
between the open file and the set of \n\
specified files (separated by commas).\n\
-g <:num> Perform a gelman-rubin test \n\
between the open file and the set of \n\
specified files (separated by commas). \n\
takes the same meaning as for -c.\n\
-S Redirect the Score against true tree output \n\
from stdout to the file specified.\n\
Specify "" to display to the gui.\n\
-s Perform a score against true tree test\n\
against the newick-format file specified.\n\
-C Performs a consensus-of-trees either with\n\
the specified cutoff (integer i=0-100) or \n\
an extended consensus if i<0.\n\
-H 0/1/2/3 Extract the heatmap. Pass 0 for no prior correction,\n\
1 for correction in number of std, 2 for correction\n\
measured in proportion or 3 for prior only.\n\
-d 0/1/2/3 Extract the pairwise clonal tree heatmap. Pass 0 for \n\
no prior correction,\n\
1 for correction in number of std, 2 for correction\n\
measured in proportion or 3 for prior only.\n\
-e ::\n\
Extract iterations and thin. is either\n\
either \"thin\" with value \"x\" to thin every\n\
x'th iteration, or \"extract\" with value \"x-y\" to extract\n\
iterations between x and y. The outputfile is after\n\
the final colon.\n\
-E :\n\
Combines the list of output files specified NOT \n\
including the current one, separated by commas, and\n\
outputs to the file after the colon.\n\
-n Start in the display mode without recombination (You must\n\
specify the outputfile with -o).\n\
-h This help message.\n\
\n\
Examples:\n\
\n\
-o test1.xml -t test2.xml -b:\n\
Performs a convergence of tree test between files\n\
test1.xml and test2.xml, printing the results to\n\
stdout and exiting the program.\n\
-o test1.xml -t test2.xml:\n\
As above, but leave the gui window open.\n\
-o test1.xml -T "" -t test2.xml:\n\
As above, but opens the results in the gui \n\
and with the gui window open.\n\
-o test1.xml -t test2.xml,test3.xml -b:\n\
Performs a convergence of tree test between files\n\
test1.xml, test2.xml and test3.xml.\n\
-t test1.xml -o test2.xml -b:\n\
Fails.\n\
";
int main(int argc, char *argv[])
{
srand(time(NULL));
QApplication app(argc, argv);
MainWindowImpl mainwindowimpl;
// register a DBus adaptor for communication with genome browser apps
MainApplicationAdaptor* maa = new MainApplicationAdaptor(&mainwindowimpl);
// connect to D-BUS and register as an object:
QDBusConnection qdbc = QDBusConnection::connectToBus(QDBusConnection::SessionBus, "org.gel.mauve.remote.WargInterface");
qdbc.registerService("org.gel.mauve.remote.WargInterface");
qdbc.registerObject("/weakarg", maa, QDBusConnection::ExportAllContents);
int grmode=2;
int expmode=2;
optind=0;
bool batch=false;
int priorcorrectHM=0;
int priorcorrectPD=0;
int recstart=0;
QString sof("COUT"),tof("COUT"),tmp;
int c;
QStringList ts,ts2;
while ((c = getopt (argc, argv, "c:o:s:d:C:S:T:t:g:be:E:H:hn")) != -1)
switch (c)
{
cout<1){expmode=ts[1].toInt();}mainwindowimpl.on_actionExport_in_CSV_format_activated(ts[0],expmode);break;
case('S'):sof=QString(optarg);break;
case('s'):mainwindowimpl.on_actionScore_against_true_tree_activated(QString(optarg),sof);break;
case('C'):if(atoi(optarg)<0) { mainwindowimpl.on_actionExtended_consensus_of_trees_activated(tof); }else { mainwindowimpl.on_actionMajority_rule_consensus_of_trees_activated(atoi(optarg),tof);}; break;
case('T'):tof=QString(optarg);break;
case('t'):tmp=QString(optarg);ts=tmp.split(",");
mainwindowimpl.on_actionTest_convergence_of_trees_activated(ts,tof);break;
case('g'):tmp=QString(optarg);ts=tmp.split(":");if(ts.size()>1){grmode=ts[1].toInt();}
ts=ts[0].split(",");
mainwindowimpl.on_actionGelman_Rubin_test_activated(ts,tof,grmode);break;
case('H'):priorcorrectHM=atoi(optarg);
mainwindowimpl.on_actionHeat_map_activated(priorcorrectHM,tof);break;
case('d'):priorcorrectPD=atoi(optarg);
mainwindowimpl.on_actionPheat_map_activated(priorcorrectPD,tof);break;
case('e'):tmp=QString(optarg);ts2=tmp.split(":");
if(ts2.size()!=3){cout<<"Wrong arguments: Need to specify :: for -e"< for -e"<=1) {
QStringList qstrs;
for (int i=1;i
Heat
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Heat Map
-
3
3
|
|
|
Save as...
Quit
true
true
Table
true
Graph
true
Represent lengths
true
true
States
true
Events
true
true
None
true
In standard deviations
true
As a proportion
Prior only
ClonalOrigin-1.0/gui/heatimpl.cpp 0000664 0000000 0000000 00000015161 12536525416 0017042 0 ustar 00root root 0000000 0000000 #include "heatimpl.h"
//
HeatImpl::HeatImpl(int n, QWidget * parent, Qt::WFlags f)
: QMainWindow(parent, f) {
this->n=n;
states=vector >(n,vector(n,0.0));
setupUi(this);
its=0;
expected=0.0;
}
void HeatImpl::account(ParamQt * p)
{
param=p;
its++;
RecTree * rectree=p->getTree();
expected+=p->getRho()*0.5*rectree->getTTotal();
if(!p->displaySet()) {
for (int i=0;inumRecEdge();i++)
states[rectree->getRecEdge(i)->getEdgeFrom()][rectree->getRecEdge(i)->getEdgeTo()]++;
}else{
for (int i=0;inumRecEdge();i++)
{
vector allto,allfrom;
allto =rectree->getAllSampledSeqs(rectree->getEdge(i)->getEdgeTo());
allfrom =rectree->getAllSampledSeqs(rectree->getEdge(i)->getEdgeFrom());
vector allaffto=p->getDisplayTree()->getMinEdgeList(allto);
vector allafffrom=p->getDisplayTree()->getMinEdgeList(allfrom);
for(unsigned int j=0;jsetRowCount(n);
table->setColumnCount(n);
for (int i=0;isetItem(i,j,new QTableWidgetItem(QString::number(states[i][j]/its)));
}
void HeatImpl::compute_correct(int mode)
{
RecTree * t=param->getTree();
int num=0;for (int i=0;i >(n,vector(n,0.0));
double s=0;
for (int i=0;igetNode(i)->getAge();
double j0=t->getNode(j)->getAge();
double il=t->getNode(i)->getDist();
double jl=t->getNode(j)->getDist();
if (i==t->getN()*2-2) il=10.0;
for (int a=0;a<100;a++) for (int b=0;b<100;b++)
corr[i][j]+=t->priorEdge(i0+il*(a+1)/101.0,j0+jl*(b+1)/101.0);
corr[i][j]*=jl*il/10000.0;
s+=corr[i][j];
}
for (int i=0;isetRowCount(n);
table->setColumnCount(n);
for (int i=0;isetItem(i,j,new QTableWidgetItem(val));
}
}
void HeatImpl::on_actionSave_as_activated() {
if (actionGraph->isChecked()==false) {
QString qstr = QFileDialog::getSaveFileName(this, tr("Save output file"),".","CSV files (*.csv);;All files (*)");
if (qstr==NULL) return;
QFile file(qstr);
if ( !file.open(QIODevice::WriteOnly)) return;
QTextStream ts( &file );
for (int i=0;irowCount();i++)
for (int j=0;jcolumnCount();j++) {
if (table->item(i,j)!=NULL) ts<item(i,j)->text();
if (jcolumnCount()-1) ts<<","; else ts<setChecked(true);
actionGraph->setChecked(false);
table->show();
repaint();
}
void HeatImpl::on_actionGraph_activated() {
actionGraph->setChecked(true);
actionTable->setChecked(false);
table->hide();
repaint();
}
void HeatImpl::paintEvent(QPaintEvent*) {
if (actionGraph->isChecked()) drawGraph(this);
}
void HeatImpl::drawGraph(QPaintDevice * qpd) {
QPainter painter(qpd);
double sup=0.0;
for (int i=0;iitem(i,j)->text().toDouble()));
if (!action0->isChecked()) sup=5.0;
//Colorbar legend
double leg=1.0;
for (int i=0;i<11;i++) {
painter.drawText(width()*0.92,height()*(0.11+0.8*i/10),QString::number(leg*sup,'f',3));
leg-=0.2;
}
//YAxis labels
for (int i=0;iitem(i,j)->text().toDouble();
int gain=255*l*(l>0)/sup;
int loss=255*(-l)*(-l>0)/sup;
if (gain>255) gain=255;
if (loss>255) loss=255;
painter.fillRect(QRectF(1.0*j/n,1.0*i/n,1.0/n,1.0/n),QColor(255-loss,255-gain-loss,255-gain));
}
}
painter.drawRect(QRectF(0.0,0.0,1.0,1.0));
for (int i=0;i0);
int loss=-i*(i<0);
painter.fillRect(QRectF(1.1,1.0-1.0*(255+i)/511,0.05,1.0/511),QColor(255-loss,255-gain-loss,255-gain));
}
painter.drawRect(QRectF(1.1,0.0,0.05,1.0));
}
void HeatImpl::print(ostream* f_out)
{
for (int i=0;iitem(i,j)->text().toStdString()<<",";
*f_out<item(i,n-1)->text().toStdString()<setChecked(true );action1->setChecked(false);action2->setChecked(false);action3->setChecked(false);compute();}
if (a==action1) {action0->setChecked(false);action1->setChecked(true );action2->setChecked(false);action3->setChecked(false);compute_correct(1);}
if (a==action2) {action0->setChecked(false);action1->setChecked(false);action2->setChecked(true );action3->setChecked(false);compute_correct(2);}
if (a==action3) {action0->setChecked(false);action1->setChecked(false);action2->setChecked(false);action3->setChecked(true );compute_correct(3);}
repaint();
}
ClonalOrigin-1.0/gui/heatimpl.h 0000664 0000000 0000000 00000001566 12536525416 0016513 0 ustar 00root root 0000000 0000000 #ifndef HEATIMPL_H
#define HEATIMPL_H
//
#include
#include "ui_heat.h"
#include
#include "paramqt.h"
#include "../warg/src/param.h"
using namespace std;
//
class HeatImpl : public QMainWindow, public Ui::Heat
{
Q_OBJECT
public:
HeatImpl(int n, QWidget * parent = 0, Qt::WFlags f = 0 );
void account(ParamQt * p);
void compute();
void compute_correct(int mode);
void print(ostream* f_out);
private slots:
void on_menuPrior_correction_triggered(QAction * a);
void on_actionSave_as_activated();
void on_actionQuit_activated();
void on_actionTable_activated();
void on_actionGraph_activated();
protected:
ParamQt * param;
int n;
int its;
double expected;
void paintEvent(QPaintEvent*);
void drawGraph(QPaintDevice * qpd);
vector > states;
vector > corr;
};
#endif
ClonalOrigin-1.0/gui/mainapplicationdbusadaptor.h 0000664 0000000 0000000 00000001050 12536525416 0022275 0 ustar 00root root 0000000 0000000 #include "mainwindowimpl.h"
#include
class MainApplicationAdaptor: public QDBusAbstractAdaptor
{
Q_OBJECT
Q_CLASSINFO("weakarg", "org.gel.mauve.remote.WargInterface")
private:
MainWindowImpl *app;
public:
MainApplicationAdaptor(MainWindowImpl *window)
: QDBusAbstractAdaptor(window), app(window)
{
}
public slots:
int getViewingSite()
{
return 0;
}
void setViewingSite(const int block, qlonglong site)
{
app->jumpToSite(site);
return;
}
};
ClonalOrigin-1.0/gui/mainwindow.ui 0000664 0000000 0000000 00000063324 12536525416 0017252 0 ustar 00root root 0000000 0000000
MainWindow
0
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weakarg-gui
Load tree...
Load data...
true
Run MCMC...
About...
Load example data
true
Next iteration
Right
Qt::ApplicationShortcut
true
Previous iteration
<
Qt::ApplicationShortcut
Reopen output file
Open output file...
Save output file...
Exit
Show Comment
Save picture...
true
Strict Consensus
true
First iteration
Home
true
Last iteration
Simulate tree...
Simulate data...
Save current state...
Save tree...
Save data...
Help contents...
Edit list of moves...
Gelman-Rubin test...
Edit priors...
Load names...
Set initial values...
Power study...
Trajectory
Histogram
Trajectory
Histogram
Trajectory
Histogram
Trajectory
Histogram
Trajectory
Histogram
Reinitiate random generator...
Ancestral states...
Combine output files...
Extract Iterations...
Thin Iterations...
true
Show node ids
vdfd
Number only
true
false
Unformatted
true
true
Mauve Format (... + Name)
true
false
Mauve Format (... + Name + .extension)
true
false
true
true
All genes
true
Only one gene...
All iterations
Distribution along the genome
Distribution of ending points
Recombination
Weighted Recombination
Starting points
Ending points
Save movie...
Toggle recombination drawing style
Show proportions in ClonalFrame on tree
Departure/arrival density
Compute raw
Recombination Distance Weighted Density
Trajectory
Histogram
Trajectory
Histogram
Scale up
+
Scale down
-
Export in Tracer format...
Export in CSV format...
Save tree to Newick file...
Save all clonal trees to Nexus file...
Time scale up
PgUp
Time scale down
PgDown
Majority-rule Density
Trajectory
Histogram
Trajectory
Histogram
Majority-rule consensus of trees
Extended consensus of trees
Trajectory
Histogram
Trajectory
Histogram
Change scale...
Colour density plot
Heat map
Pairwise Distances Recombination map
Pairwise Recombination Rate map
Pairwise Recombination map (SLOW!)
Test convergence of trees...
Score against true tree...
Trajectory
Histogram
Trajectory
Histogram
Next site
+
Prev site
-
Set cutoff...
Jump to site...
Export movie...
Export to CSV...
Export to Artemis...
Compute prior corrected
ClonalOrigin-1.0/gui/mainwindowimpl.cpp 0000664 0000000 0000000 00000102422 12536525416 0020272 0 ustar 00root root 0000000 0000000 #include "mainwindowimpl.h"
#include
#include
//
MainWindowImpl::MainWindowImpl( QWidget * parent, Qt::WFlags f):QMainWindow(parent, f) {
param=new ParamQt();
outputFile=NULL;
data=NULL;
explorerCutoff=70;
connect(this,SIGNAL(wasDbClicked(int,QMouseEvent*)),this,SLOT(computeAfterDbClick(int,QMouseEvent*)));
setupUi(this);
}
MainWindowImpl::~MainWindowImpl() {
if(param) delete(param);
if(outputFile) delete(outputFile);
}
void MainWindowImpl::on_actionAbout_activated() {
QMessageBox::about(0, "About...","This is weakarg-gui version 0.1.");
}
void MainWindowImpl::paintEvent(QPaintEvent*) {
param->display(this);
}
void MainWindowImpl::on_actionReOpen_output_file_activated() {
outputFile->startOver();
outputFile->reset();
param->setNames(outputFile->getNames());
param->setBlocks(outputFile->getBlocks());
loadIteration();
repaint();
}
void MainWindowImpl::on_actionOpen_output_file_activated() {
QStringList qstrs = QFileDialog::getOpenFileNames(this, tr("Open output file(s)"),".","XML files (*.xml);;All files (*)");
if (qstrs.isEmpty()) return;
openXMLFile(qstrs);
}
void MainWindowImpl::openXMLFile(QStringList qstrs) {
outputfilenames=qstrs;
if(outputFile) delete(outputFile);
outputFile=new OutputFile(qstrs,false);//set this to true to recover the previous behaviour of initialising on loading.
param->setBlocks(outputFile->getBlocks());
param->setNames(outputFile->getNames());
param->setLabels(QStringList());
param->clearTreeData();
data=NULL;
//if(data!=NULL) delete(data);
loadIteration();
repaint();
}
void MainWindowImpl::loadIteration(bool startOver) {
if (outputFile==NULL) return;
if (param->isCons) {ParamQt * param2=new ParamQt();
param2->setTree(param->getTree());
param2->setBlocks(outputFile->getBlocks());
param2->setNames(outputFile->getNames());
if(param) delete(param);
param=param2;}
if (startOver) {outputFile->startOver(); param->setNames(outputFile->getNames());}
outputFile->getIt(param);
displayStatus();
}
void MainWindowImpl::on_actionExit_activated() {
close();
}
void MainWindowImpl::on_actionShowComment_activated() {
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
QMessageBox::about(0,"Outputfile comment",outputFile->getComment());
}
void MainWindowImpl::on_actionSave_picture_activated() {
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
QString qstr = QFileDialog::getSaveFileName(this, tr("Save picture file"),".",tr("Joint Photographic Experts Group (*.jpg *.jpeg);;Windows Bitmap (*.bmp);;Portable Network Graphics (*.png);;Portable Pixmap (*.ppm);;X11 Bitmap (*.xbm *.xpm);;SVG Format (*.svg);;PostScript Format (*.ps);;Abode PDF Format (*.pdf)"));
if (qstr==NULL) return;
if (qstr.endsWith("svg")) {
QSvgGenerator qsvg;
qsvg.setFileName(qstr);
qsvg.setSize(QSize(width(),height()));
param->display(&qsvg);
return;
}
if (qstr.endsWith("ps") || qstr.endsWith("pdf")) {
QPrinter qprint;
qprint.setOutputFileName(qstr);
// qprint.setOrientation( QPrinter::Landscape);
param->display(&qprint);
return;
}
QImage image(width(),height(),QImage::Format_ARGB32);
image.invertPixels();//Fill image in white
param->display(&image);
image.save(qstr);
}
void MainWindowImpl::on_actionSave_trees_to_Nexus_file_activated() {
if (outputFile==NULL) {QMessageBox::about(0, "Information","Need some data first.");return;}
QString qstr = QFileDialog::getSaveFileName(this, tr("Save trees file"),".","Nexus file (*.nex);;All files (*)");
if (qstr==NULL) return;
QFile file(qstr);
if ( !file.open(QIODevice::WriteOnly)) return;
QTextStream ts( &file );
ts<<"#nexus"<getTree()->getN()-1;i++) ts<<" "<getTree()->getN()-1<<" "<getTree()->getN()-1<startOver();
int treeon=0;
while (outputFile->getIt(param))
{
displayStatus();
ts << " tree "<getTree()->newickNoInternalLabels())<getTree()->newick());
file.close();
}
void MainWindowImpl::on_actionGelman_Rubin_test_activated(QStringList files,QString dest,int grmode) {
if (outputFile==NULL) {QMessageBox::about(0, "Information","Need some data first.");return;}
if(files.size()==0) files = QFileDialog::getOpenFileNames(this, tr("Select File(s)"),".","XML files (*.xml);;All files (*)");
if (files.size()==0) return;
GelmanRubinImpl * gr=new GelmanRubinImpl(this);
if(dest.length()==0) {
gr->showOptions();
gr->setFiles(param,outputFile,files);
// gr->compute(param,outputFile,&files,NULL,true,true,true);
gr->show();
}else {//gr->compute(param,outputFile,&files,&cout,true,true,true);
//}else{
ostream* f_out;
if(dest.compare("COUT")==0) f_out=&cout;
else f_out = new ofstream(qPrintable(dest));
if(grmode==1) gr->compute(param,outputFile,&files,f_out,true,false,false);
else if(grmode==2) gr->compute(param,outputFile,&files,f_out,true,true,false);
else if(grmode==3) gr->compute(param,outputFile,&files,f_out,true,false,true);
else gr->compute(param,outputFile,&files,f_out,true,true,true);
if(dest.compare("COUT")!=0) delete f_out;
}
loadIteration();
}
void MainWindowImpl::on_actionGelman_Rubin_test_activated(){
on_actionGelman_Rubin_test_activated(QStringList(),QString(""));
}
void MainWindowImpl::on_actionExport_as_Tracer_file_activated()
{
if (outputFile==NULL) {QMessageBox::about(0, "Information","Need some data first.");return;}
QString qstr = QFileDialog::getSaveFileName(this, tr("Save output file"),".","Tracer files (*.log);;All files (*)");
if (qstr==NULL) return;
GelmanRubinImpl * gr=new GelmanRubinImpl(this);
QStringList strlist=QStringList(qstr);
gr->setFiles(param,outputFile,strlist);
gr->setExport();
gr->setSep(string("\t"));
gr->show();
// gr->outputTracer(param,outputFile,&qstr);
outputFile->startOver();
loadIteration();
//delete(gr);
}
void MainWindowImpl::on_actionExport_in_CSV_format_activated(QString qstr,int grmode)
{
bool vis=false;
if (outputFile==NULL) {QMessageBox::about(0, "Information","Need some data first.");return;}
if(qstr.length()==0) {vis=true;qstr = QFileDialog::getSaveFileName(this, tr("Save output file"),".","CSV index files (*.csv);;All files (*)");}
if (qstr==NULL) return;
GelmanRubinImpl * gr=new GelmanRubinImpl(this);
if(vis){
QStringList strlist=QStringList(qstr);
gr->setFiles(param,outputFile,strlist);
gr->setExport();
gr->show();
}else {
if(grmode==1) gr->outputTracer(param,outputFile,&qstr,true,true,false,false);
else if(grmode==2) gr->outputTracer(param,outputFile,&qstr,true,true,true,false);
else if(grmode==3) gr->outputTracer(param,outputFile,&qstr,true,true,false,true);
else gr->outputTracer(param,outputFile,&qstr,true,true,true,true);
delete(gr);
}
outputFile->startOver();
loadIteration();
}
void MainWindowImpl::on_menuPlot_triggered(QAction* a) {
if (outputFile==NULL) {QMessageBox::about(0, "Information","Need some data first.");return;}
// Should give the user a warning this is slow!
if(!outputFile->isinitialised()) outputFile->countVectors();
PlotImpl * pi=new PlotImpl(this);
if (a==action11 || a==action12) pi->setValues(outputFile->getThetas());
if (a==action21 || a==action22) pi->setValues(outputFile->getRhos());
if (a==action31 || a==action32) pi->setValues(outputFile->getDeltas());
if (a==action41 || a==action42) pi->setValues(outputFile->getNumRecEdges());
if (a==action51 || a==action52) pi->setValues(outputFile->getLikelihoods());
if (a==action61 || a==action62) pi->setValues(outputFile->getRhoOverTheta());
if (a==action71 || a==action72) {
checkDataLoaded();
pi->setValues(outputFile->getRoverM(param));
repaint();
}
if (a==action81 || a==action82) pi->setValues(outputFile->getTMRCA());
if (a==action91 || a==action92) pi->setValues(outputFile->getTTotal());
if (a==actionA1 || a==actionA2) pi->setValues(outputFile->getPriors());
if (a==actionB1 || a==actionB2) pi->setValues(outputFile->getPosteriors());
if (a==actionC1 || a==actionC2) pi->setValues(outputFile->getThetaPerSite());
if (a==actionD1 || a==actionD2) pi->setValues(outputFile->getRhoPerSite());
if (a==actionRecombination) pi->setValues(outputFile->getGenoRec());
if (a==actionRelRecombination) pi->setValues(outputFile->getRelGenoRec(param));
if (a==actionStarting_points) pi->setValues(outputFile->getGenoBeg());
if (a==actionEnding_points) pi->setValues(outputFile->getGenoEnd());
if (a==action11 || a==action21 || a==action31 || a==action41 || a==action51 || a==action61 || a==action71 || a==action81 || a==action91 || a==actionA1 || a==actionB1 || a==actionC1 || a==actionD1) pi->setMode(0);else
if (a==action12 || a==action22 || a==action32 || a==action42 || a==action52 || a==action62 || a==action72 || a==action82 || a==action92 || a==actionA2 || a==actionB2 || a==actionC2 || a==actionD2) pi->setMode(1);else
{pi->setBlocks(param->getData()->getBlocks());pi->setMode(2);}
pi->show();
}
void MainWindowImpl::on_menuVisualisation_triggered(QAction* a) {
if (a==actionNext_iteration) loadIteration();
if (a==actionFirst_iteration) loadIteration(true);
if (a==actionChange_scale) {
bool ok;
double r=QInputDialog::getDouble(this,"Enter rate scale","Enter value for the scale of the rates:",param->getRateScale(),0,2147483647,10,&ok);
if (!ok) return;
param->setRateScale(r);
displayStatus(tr("Scale=")+QString::number(param->getRateScale()));
};
if (a==actionTime_scale_up) param->incrTimeScale();
if (a==actionTime_scale_down) param->decrTimeScale();
//if (a==actionTime_scale_up || a==actionTime_scale_down)
displayStatus();
repaint();
}
void MainWindowImpl::on_actionCombine_output_files_activated(QStringList files,QString dest)
{
QFile file(dest);
if ( !file.open(QIODevice::WriteOnly)) return;
QTextStream out(&file);
out << "" << endl;
out << "" << endl;
for (int i=0;i"<getFileName());
if ( !filefrom.open(QIODevice::ReadOnly)) return;
int iton=-1;
while (!filefrom.atEnd()) {
QByteArray line = filefrom.readLine();
if(line.contains("")) iton++;
if (iton<0 || line.contains("outputFile") || (iton>=istart && iton<=iend)) out<getFileName());
if ( !filefrom.open(QIODevice::ReadOnly)) return;
int iton=-1;
while (!filefrom.atEnd()) {
QByteArray line = filefrom.readLine();
if(line.contains("")) iton++;
if (iton<0 || line.contains("outputFile") || (iton%thin==0)) out<setChecked(true);
actionOnly_one_gene->setChecked(false);
param->setGene(-1);
repaint();
}
void MainWindowImpl::on_actionOnly_one_gene_activated()
{
actionAll_genes->setChecked(false);
actionOnly_one_gene->setChecked(true);
bool ok;
int i = QInputDialog::getInteger(this, tr("Pick a gene"),tr("Show events for gene number:"), 1, 1, param->getData()->getB(), 1, &ok);
if (ok) param->setGene(i);
repaint();
}
void MainWindowImpl::on_actionToggleView_activated(){
param->toggleRecView();
if(param->getRecView()==0)statusBar()->showMessage("Showing all recombination equally.");
else if(param->getRecView()==1)statusBar()->showMessage("Showing recombination weighted by tract length.");
else if(param->getRecView()==1)statusBar()->showMessage("Not showing recombination.");
repaint();
}
void MainWindowImpl::on_actionShowCF_activated(){
checkDataLoaded();
outputFile->makeCF(param);
param->setRecView(2);
repaint();
}
void MainWindowImpl::on_actionSave_movie_activated()
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
QString qstr = QFileDialog::getSaveFileName(this, tr("Save movie file"),".",tr("WMV files (*.wmv);;AVI files (*.avi)"));
if (qstr==NULL) return;
QImage image(width(),height(),QImage::Format_ARGB32);
outputFile->startOver();
QString time=QTime::currentTime().toString();
while (outputFile->getIt(param))
{
image.fill(0);
image.invertPixels();//Fill image in white
param->display(&image);
image.save(QString("/tmp/%1it%2.jpg").arg(time).arg(QString::number(outputFile->getCurIt()),7,'0'));
}
QProcess ffmpeg;
if (qstr.endsWith("wmv"))
ffmpeg.start("ffmpeg", QString("-y -r 10 -i /tmp/%1it%07d.jpg -vcodec wmv1 %2").arg(time).arg(qstr).split(" "));
else
ffmpeg.start("ffmpeg", QString("-y -r 10 -i /tmp/%1it%07d.jpg %2").arg(time).arg(qstr).split(" "));
ffmpeg.waitForFinished();
}
void MainWindowImpl::on_actionDeparture_arrival_density_activated()
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
ParamCons * paramcons=new ParamCons();
paramcons->setBlocks(outputFile->getBlocks());
paramcons->setNames(outputFile->getNames());
paramcons->setTimeScale(param->getTimeScale());
paramcons->setGene(param->getGene());
if(param->displaySet()) paramcons->newDisplayTree(param->getDisplayTree(),false);
if(param) delete(param);
param=paramcons;
if(doDeparture_arrival_density(paramcons)==-1) doDeparture_arrival_density(paramcons);
paramcons->set();
repaint();
}
int MainWindowImpl::doDeparture_arrival_density(ParamCons * paramcons,bool relative)
{
outputFile->startOver();
bool firstit=true;
while (outputFile->getIt(paramcons))
{
if(firstit && !paramcons->displaySet()) {
paramcons->newDisplayTree(paramcons->getTree());
firstit=false;
}
if(!paramcons->displaySet()) {
string s1(paramcons->getDisplayTree()->newick());
string s2(paramcons->getTree()->newick());
if(s1.compare(s2)!=0) {
ParamTreeCons * paramtreecons=newExtConsTree();
paramcons->unsetDisplayTree();
paramcons->newDisplayTree(paramtreecons->getTree());
delete(paramtreecons);
repaint();
return -1;
}
}
displayStatus();
if(relative)paramcons->accountrelative();
else paramcons->account();
}
return(0);
}
void MainWindowImpl::on_actionRelative_Departure_Arrival_density_activated()
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
ParamCons * paramcons=new ParamCons();
paramcons->setBlocks(outputFile->getBlocks());
paramcons->setNames(outputFile->getNames());
paramcons->setTimeScale(param->getTimeScale());
paramcons->setGene(param->getGene());
if(param) delete(param);
param=paramcons;
if(doDeparture_arrival_density(paramcons)==-1) doDeparture_arrival_density(paramcons,true);
paramcons->set();
repaint();
}
void MainWindowImpl::on_actionMajority_rule_Consensus_activated()
{
computeExplorer(false);
}
void MainWindowImpl::computeExplorer(bool correct)
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
// tell Mauve to order its sequences and focus on site 0
// FIXME: need to figure out how to get the genome indices and send them as an array.
QDBusMessage m = QDBusMessage::createMethodCall("org.gel.mauve.remote.MauveInterface","/MauveInterface","","hackOrder");
QDBusMessage response = QDBusConnection::sessionBus().call(m);
m = QDBusMessage::createMethodCall("org.gel.mauve.remote.MauveInterface","/MauveInterface","","setDisplayBlockAndColumn");
m << (int)0;
m << (qlonglong)0;
m << (qlonglong)500;
response = QDBusConnection::sessionBus().call(m);
explorerSite=0;
ParamMR * paramMR=new ParamMR();
paramMR->setBlocks(outputFile->getBlocks());
paramMR->setNames(outputFile->getNames());
paramMR->setTimeScale(param->getTimeScale());
if(param) delete(param);
param=paramMR;
outputFile->startOver();
bool firstit=true;
while (outputFile->getIt(paramMR))
{
if(firstit) {
paramMR->newDisplayTree(paramMR->getTree());
firstit=false;
}
//string s1(paramMR->getDisplayTree()->newick());
//string s2(paramMR->getTree()->newick());
//if(s1.compare(s2)!=0) {QMessageBox::about(0,"Information","Cannot do majority rule for non-constant trees.");return;}
displayStatus();
paramMR->account();
}
if (correct) paramMR->correctForPrior();
paramMR->consensus(explorerCutoff);
repaint();
}
void MainWindowImpl::on_actionMajority_rule_Density_activated()
{
on_actionMajority_rule_Consensus_activated();
ParamCons * paramcons=new ParamCons();
paramcons->setBlocks(outputFile->getBlocks());
paramcons->setNames(outputFile->getNames());
paramcons->setTimeScale(param->getTimeScale());
outputFile->startOver();
outputFile->getIt(paramcons);
((ParamMR*)param)->makeDensity(paramcons);
if(param) delete(param);
param=paramcons;
repaint();
}
void MainWindowImpl::on_actionMajority_rule_consensus_of_trees_activated(int cutoff, QString dest)
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
bool ok=true;
if(cutoff<0) cutoff=QInputDialog::getInteger(this,"Enter cutoff","Enter value of cutoff for majority-rule consensus:",95,0,100,1,&ok);
if (!ok || cutoff>100) return;
ParamTreeCons * paramtreecons=new ParamTreeCons();
paramtreecons->setBlocks(outputFile->getBlocks());
paramtreecons->setNames(outputFile->getNames());
paramtreecons->setTimeScale(param->getTimeScale());
if(param) delete(param);
param=paramtreecons;
outputFile->startOver();
while (outputFile->getIt(paramtreecons))
{
displayStatus();
paramtreecons->account();
}
paramtreecons->consensus(cutoff);
param->newDisplayTree(param->getTree(),false);
if(dest.length()==0) {
cout<getDisplayTree()->newick()<getDisplayTree()->newick()<getDisplayTree()->newick()<getDisplayTree()->newick()<getDisplayTree()->newick()<getDisplayTree()->newick()<newDisplayTree(param->getTree(),false);
}
void MainWindowImpl::mouseDoubleClickEvent ( QMouseEvent * event )
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
statusBar()->showMessage("Capturing node...");
int id=param->getIdAt(event->x(),event->y(),this);
displayStatus();
emit wasDbClicked(id,event);
}
void MainWindowImpl::computeAfterDbClick(int id,QMouseEvent * event)
{
bool getto=true;
statusBar()->showMessage("Computing...");
if(!outputFile->isinitialised()) outputFile->countVectors();
if (event->modifiers()==Qt::CTRL) getto=false;
PlotImpl * pi=new PlotImpl(this);
if (event->button() && event->modifiers()==Qt::SHIFT) pi->setValues(outputFile->getRelGenoRec(param,id));
else pi->setValues(outputFile->getGenoRec(id,getto));
pi->setBlocks(param->getData()->getBlocks());
pi->setMode(2);
if (param->isCons) {
param->unsetDisplayTree();
param->newDisplayTree(param->getTree());
outputFile->startOver();
((ParamCons*)param)->reset();
while (outputFile->getIt(param))
{
displayStatus();
((ParamCons*)param)->account(id,getto);
}
((ParamCons*)param)->set();
repaint();
}
pi->show();
displayStatus();
}
void MainWindowImpl::on_actionColour_density_plot_activated()
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
disconnect(this,SIGNAL(wasDbClicked(int,QMouseEvent*)),0,0);
ColouredImpl * ci=new ColouredImpl(this);
connect(this,SIGNAL(wasDbClicked(int,QMouseEvent*)),ci,SLOT(addGroup(int)));
ci->show();
}
ParamTreeCons * MainWindowImpl::newExtConsTree()
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return(NULL);}
ParamTreeCons * paramtreecons=new ParamTreeCons();
paramtreecons->setBlocks(outputFile->getBlocks());
paramtreecons->setNames(outputFile->getNames());
paramtreecons->setTimeScale(param->getTimeScale());
ParamQt * oldparam=param;
param=paramtreecons;
outputFile->startOver();
while (outputFile->getIt(paramtreecons))
{
displayStatus(tr("Computing consensus tree..."));
paramtreecons->account();
}
paramtreecons->consensusExt();
paramtreecons->setDisplayTree(paramtreecons->getTree());
param=oldparam;
return(paramtreecons);
}
void MainWindowImpl::doColourPlot(QStringList*nodes,QStringList*colors,bool denDep,bool colDep)
{
ParamConsMult * paramcons=new ParamConsMult(nodes,colors,denDep,colDep);
paramcons->setBlocks(outputFile->getBlocks());
paramcons->setNames(outputFile->getNames());
paramcons->setTimeScale(param->getTimeScale());
paramcons->setGene(param->getGene());
if(param->displaySet()) paramcons->newDisplayTree(param->getDisplayTree(),false);
else paramcons->newDisplayTree(param->getTree());
if(param) delete(param);
param=paramcons;
outputFile->startOver();
while (outputFile->getIt(param))
{
displayStatus();
paramcons->account();
}
paramcons->set();
repaint();
}
void MainWindowImpl::on_actionHeat_map_activated(int correctforprior,QString dest)
{
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
if(!param->displaySet()) param->newDisplayTree(param->getTree());
outputFile->startOver();
HeatImpl * hi=new HeatImpl(param->getTree()->getN()*2-1);
while (outputFile->getIt(param))
{
displayStatus();
hi->account(param);
}
if(correctforprior>0) hi->compute_correct(correctforprior);
else hi->compute();
if(dest.length()==0) {
hi->show();
}else {
ostream* f_out;
if(dest.compare("COUT")==0) f_out=&cout;
else f_out = new ofstream(qPrintable(dest));
hi->print(f_out);
if(dest.compare("COUT")!=0) delete f_out;
}
}
void MainWindowImpl::on_actionHeat_map_activated(){
on_actionHeat_map_activated(false,QString(""));
}
void MainWindowImpl::on_actionPd_map_activated(){
on_actionPd_map_activated(0,QString(""));
}
void MainWindowImpl::on_actionPheat_map_rel_activated(){
on_actionPheat_map_activated(0,QString(""),true);
}
void MainWindowImpl::on_actionPheat_map_activated(){
on_actionPheat_map_activated(0,QString(""),false);
}
void MainWindowImpl::on_actionPd_map_activated(int correctforprior,QString dest){
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
bool ok;
int sitejump=QInputDialog::getInteger(this,"Site Sample Rate","Enter gap between evaluated sites:",1,1,10000,1,&ok);
if(!ok) return;
if(!param->displaySet()) param->newDisplayTree(param->getTree());
outputFile->startOver();
PdImpl * pd=new PdImpl(param->getTree()->getN(),sitejump);
// outputFile->getIt(param);
while (outputFile->getIt(param))
{
displayStatus();
pd->account(param);
}
pd->compute(correctforprior);
if(dest.length()==0) {
pd->show();
}else {
ostream* f_out;
if(dest.compare("COUT")==0) f_out=&cout;
else f_out = new ofstream(qPrintable(dest));
pd->print(f_out);
if(dest.compare("COUT")!=0)delete f_out;
}
}
void MainWindowImpl::on_actionPheat_map_activated(int correctforprior,QString dest,bool reldists){
if (outputFile==NULL) {QMessageBox::about(0,"Information","Need some data first.");return;}
if(!param->displaySet()) param->newDisplayTree(param->getTree());
outputFile->startOver();
PHeatImpl * pd=new PHeatImpl(param->getTree()->getN(),reldists);
// outputFile->getIt(param);
while (outputFile->getIt(param))
{
displayStatus();
pd->account(param);
}
pd->compute(correctforprior);
if(dest.length()==0) {
pd->show();
}else {
ostream* f_out;
if(dest.compare("COUT")==0) f_out=&cout;
else f_out = new ofstream(qPrintable(dest));
pd->print(f_out);
if(dest.compare("COUT")!=0)delete f_out;
}
}
void MainWindowImpl::on_actionTest_convergence_of_trees_activated(QStringList files,QString dest)
{
if (outputFile==NULL) {QMessageBox::about(0, "Information","Need some data first.");return;}
if(files.size()==0) files = QFileDialog::getOpenFileNames(this, tr("Select File(s)"),".","XML files (*.xml);;All files (*)");
if (files.size()==0) return;
GelmanRubinImpl * gr=new GelmanRubinImpl(this);
files.push_front(outputFile->getFileName());
if(dest.length()==0) {
gr->computeTree(param,&files);
gr->show();
}else if(dest.compare("COUT")==0) gr->computeTree(param,&files,&cout);
else {
ostream* f_out;
f_out = new ofstream(qPrintable(dest));
gr->computeTree(param,&files,f_out);
// *f_out<getFileName(),qstr);
if(dest.length()==0) QMessageBox::about(0,"Result of comparison with true tree",qs);
else if(dest.compare("COUT")==0) cout<showMessage(tr("Sample ")+QString::number(outputFile->getCurIt()+1)
+tr(", Iteration ")+QString::number(param->getNumber())+(", Timescale=")+QString::number(param->getTimeScale())+tr(" ") + str);
}
void MainWindowImpl::on_actionNext_site_activated()
{
explorerSite++;if (explorerSite>=param->getData()->getL()) explorerSite=param->getData()->getL()-1;
((ParamMR*)param)->consensus(explorerCutoff,explorerSite);
statusBar()->showMessage(tr("Explorer mode, site=")+QString::number(explorerSite));
repaint();
}
void MainWindowImpl::on_actionPrev_site_activated()
{
explorerSite--;if (explorerSite<0) explorerSite=0;
((ParamMR*)param)->consensus(explorerCutoff,explorerSite);
statusBar()->showMessage(tr("Explorer mode, site=")+QString::number(explorerSite));
repaint();
}
void MainWindowImpl::on_actionSet_cutoff_activated()
{
bool ok;
int cutoff=QInputDialog::getInteger(this,"Enter cutoff","Enter value of cutoff:",explorerCutoff,0,100,1,&ok);
if (!ok) return;
explorerCutoff=cutoff;
((ParamMR*)param)->consensus(explorerCutoff,explorerSite);
repaint();
}
void MainWindowImpl::on_actionJump_to_site_activated()
{
bool ok;
int site=QInputDialog::getInteger(this,"Enter site","Enter number of site:",explorerSite,0,param->getData()->getL()-1,1,&ok);
if (!ok) return;
jumpToSite(site);
}
void MainWindowImpl::jumpToSite(int site)
{
explorerSite=site;
((ParamMR*)param)->consensus(explorerCutoff,explorerSite);
statusBar()->showMessage(tr("Explorer mode, site=")+QString::number(explorerSite));
repaint();
}
void MainWindowImpl::on_actionExport_movie_activated()
{
QString qstr = QFileDialog::getSaveFileName(this, tr("Save movie file"),".",tr("WMV files (*.wmv);;AVI files (*.avi)"));
if (qstr==NULL) return;
bool ok;int step=QInputDialog::getInteger(this,"Enter step","Enter value of step:",1,1,100000,1,&ok);if (!ok) return;
QImage image(width(),height(),QImage::Format_ARGB32);
explorerSite=0;
QString time=QTime::currentTime().toString();
while (explorerSite<=param->getData()->getL())
{
image.fill(0);
image.invertPixels();//Fill image in white
statusBar()->showMessage(tr("Explorer mode, site=")+QString::number(explorerSite));
((ParamMR*)param)->consensus(explorerCutoff,explorerSite);
param->display(&image);
QPainter painter(&image);
painter.drawText(image.width()*0.05,image.height()*0.05,image.width()*0.1,image.height()*0.1,Qt::AlignCenter,QString::number(explorerSite));
image.save(QString("/tmp/%1it%2.jpg").arg(time).arg(QString::number(explorerSite/step),7,'0'));
explorerSite+=step;
}
explorerSite=0;
QProcess ffmpeg;
if (qstr.endsWith("wmv"))
ffmpeg.start("ffmpeg", QString("-y -r 10 -i /tmp/%1it%07d.jpg -vcodec wmv1 %2").arg(time).arg(qstr).split(" "));
else
ffmpeg.start("ffmpeg", QString("-y -r 10 -i /tmp/%1it%07d.jpg %2").arg(time).arg(qstr).split(" "));
ffmpeg.waitForFinished();
}
void MainWindowImpl::on_actionExport_CSV_activated()
{
QString qstr = QFileDialog::getSaveFileName(this, tr("Export to CSV"),".","CSV index files (*.csv);;All files (*)");
if (qstr==NULL) return;
bool ok;int step=QInputDialog::getInteger(this,"Enter step","Enter value of step:",1,1,100000,1,&ok);if (!ok) return;
QFile file(qstr);
if ( !file.open(QIODevice::WriteOnly)) return;
QTextStream out(&file);
((ParamMR*)param)->toCSV(&out,explorerCutoff,step);
file.close();
}
void MainWindowImpl::on_actionExport_to_Artemis_activated()
{
QString qstr = QFileDialog::getSaveFileName(this, tr("Export to Artemis"),".","GBK files (*.gbk);;All files (*)");
if (qstr==NULL) return;
QFile file(qstr);
if ( !file.open(QIODevice::WriteOnly)) return;
QTextStream out(&file);
((ParamMR*)param)->toArtemis(&out,explorerCutoff);
file.close();
}
void MainWindowImpl::on_actionCompute_prior_corrected_activated()
{
computeExplorer(true);
}
void MainWindowImpl::on_actionNameFormatm1_activated()
{
actionNameFormatm1->setChecked(true);
actionNameFormat0->setChecked(false);
actionNameFormat1->setChecked(false);
actionNameFormat2->setChecked(false);
param->setNameType(-1);
repaint();
}
void MainWindowImpl::on_actionNameFormat0_activated()
{
actionNameFormatm1->setChecked(false);
actionNameFormat0->setChecked(true);
actionNameFormat1->setChecked(false);
actionNameFormat2->setChecked(false);
param->setNameType(0);
repaint();
}
void MainWindowImpl::on_actionNameFormat1_activated()
{
actionNameFormatm1->setChecked(false);
actionNameFormat0->setChecked(false);
actionNameFormat1->setChecked(true);
actionNameFormat2->setChecked(false);
param->setNameType(1);
repaint();
}
void MainWindowImpl::on_actionNameFormat2_activated()
{
actionNameFormatm1->setChecked(false);
actionNameFormat0->setChecked(false);
actionNameFormat1->setChecked(false);
actionNameFormat2->setChecked(true);
param->setNameType(2);
repaint();
}
ClonalOrigin-1.0/gui/mainwindowimpl.h 0000664 0000000 0000000 00000012515 12536525416 0017742 0 ustar 00root root 0000000 0000000 #ifndef MAINWINDOWIMPL_H
#define MAINWINDOWIMPL_H
//
#include "ui_mainwindow.h"
#include "plotimpl.h"
#include "gelmanrubinimpl.h"
#include "paramcons.h"
#include "paramconsmult.h"
#include
#include "outputfile.h"
#include "parammr.h"
#include "paramtreecons.h"
#include "colouredimpl.h"
#include "heatimpl.h"
#include "pdimpl.h"
#include "pheatimpl.h"
//
class MainWindowImpl : public QMainWindow, public Ui::MainWindow {
Q_OBJECT
public:
MainWindowImpl( QWidget * parent = 0, Qt::WFlags f = 0 );
virtual ~MainWindowImpl();
void openXMLFile(QStringList qstrs);
void doColourPlot(QStringList*nodes,QStringList*colors,bool denDep,bool colDep);
void on_actionExport_in_CSV_format_activated(QString qstr,int grmode=2);
void on_actionScore_against_true_tree_activated(QString qstr,QString dest);
void on_actionTest_convergence_of_trees_activated(QStringList files,QString dest);
void on_actionHeat_map_activated(int correctforprior,QString dest);
void on_actionPd_map_activated(int correctforprior,QString dest);
void on_actionPheat_map_activated(int correctforprior,QString dest,bool reldists=true);
void on_actionGelman_Rubin_test_activated(QStringList files,QString dest,int grmode=2);
void on_actionMajority_rule_consensus_of_trees_activated(int p,QString dest);
void on_actionExtended_consensus_of_trees_activated(QString dest);
void on_actionCombine_output_files_activated(QStringList files,QString dest);
void on_actionThinIterations_activated(QString outputfile,int thin);
void on_actionExtractIterations_activated(QString outputfile,int istart,int iend);
void jumpToSite(int site);
inline void setRecView(int i){param->setRecView(i);}
signals:
void wasDbClicked(int node,QMouseEvent * event);
private slots:
void computeAfterDbClick(int id,QMouseEvent * event);
void on_actionGelman_Rubin_test_activated();
void on_actionShowComment_activated();
void on_actionExit_activated();
void on_actionSave_picture_activated();
void on_actionReOpen_output_file_activated();
void on_actionOpen_output_file_activated();
void on_actionAbout_activated();
void on_menuPlot_triggered(QAction* action);
void on_menuVisualisation_triggered(QAction* action);
void on_actionCombine_output_files_activated();
void on_actionExtractIterations_activated();
void on_actionThinIterations_activated();
void on_actionCompute_prior_corrected_activated();
void on_actionExport_to_Artemis_activated();
void on_actionExport_CSV_activated();
void on_actionExport_movie_activated();
void on_actionJump_to_site_activated();
void on_actionSet_cutoff_activated();
void on_actionPrev_site_activated();
void on_actionNext_site_activated();
void on_actionAll_genes_activated();
void on_actionOnly_one_gene_activated();
void on_actionSave_movie_activated();
void on_actionToggleView_activated();
void on_actionShowCF_activated();
void on_actionDeparture_arrival_density_activated();
void on_actionMajority_rule_Consensus_activated();
void on_actionExport_as_Tracer_file_activated();
void on_actionSave_tree_to_Newick_file_activated();
void on_actionSave_trees_to_Nexus_file_activated();
void on_actionMajority_rule_Density_activated();
void on_actionRelative_Departure_Arrival_density_activated();
void on_actionColour_density_plot_activated();
void on_actionHeat_map_activated();
void on_actionPd_map_activated();
void on_actionPheat_map_activated();
void on_actionPheat_map_rel_activated();
void on_actionNameFormatm1_activated();
void on_actionNameFormat0_activated();
void on_actionNameFormat1_activated();
void on_actionNameFormat2_activated();
inline void on_actionMajority_rule_consensus_of_trees_activated(){
on_actionMajority_rule_consensus_of_trees_activated(-1,QString());
}
inline void on_actionExtended_consensus_of_trees_activated(){
on_actionExtended_consensus_of_trees_activated(QString());
}
inline void on_actionExport_in_CSV_format_activated(){
on_actionExport_in_CSV_format_activated(QString());
}
inline void on_actionScore_against_true_tree_activated(){
on_actionScore_against_true_tree_activated(QString(),QString());
}
inline void on_actionTest_convergence_of_trees_activated(){
on_actionTest_convergence_of_trees_activated(QStringList(),QString());
};
int doDeparture_arrival_density(ParamCons * paramcons,bool relative=false);
ParamTreeCons * newExtConsTree();///subset(outputFile->getRegions(),-1);
param->setData(data);
}
}
protected:
QStringList outputfilenames;
ParamQt * param;
ParamQt * ioparam;
int explorerSite;
int explorerCutoff;
//QDomDocument * domDoc;
//QDomNodeList its;
OutputFile * outputFile;
Data * data;
//int currentIteration;
//int maxIteration;
void paintEvent(QPaintEvent*);
void loadIteration(bool startOver=false);
void mouseDoubleClickEvent ( QMouseEvent * event );
void displayStatus(QString str=tr(""));
};
#endif
ClonalOrigin-1.0/gui/outputfile.cpp 0000664 0000000 0000000 00000032606 12536525416 0017442 0 ustar 00root root 0000000 0000000 #include "outputfile.h"
//
OutputFile::OutputFile(QStringList qstrs,bool makeVectors)
{
xml.clear();
for (int i=0;i0) {
cerr<<"Error: You are trying to open more files than your shell allows. Try running: \"ulimit -n "<close();
if (!file[i]->open(QIODevice::ReadOnly)) {cerr<<"Unable to open file "<fileName().toStdString()<readNext();
while (str.compare("Blocks")!=0) {xml[i]->readNext();if (xml[i]->error()!=0) {cerr<<"Invalid file "<fileName().toStdString()<name().toString();}
xml[i]->readNext();
QString tmpBlocks=xml[i]->text().toString();
while( str.compare("Iteration")!=0){
while (str.compare("comment")!=0 && str.compare("Iteration")!=0 && str.compare("nameMap")!=0 && str.compare("regions")!=0) {xml[i]->readNext();if (xml[i]->error()!=0) {cerr<<"Invalid file "<fileName().toStdString()<name().toString();}
if(str.compare("comment")==0) {comment=xml[i]->readElementText();str=QString("");}
if(str.compare("nameMap")==0) {readNames(xml[i]->readElementText());str=QString("");}
if(str.compare("regions")==0) {addRegions(xml[i]->readElementText());str=QString("");}
}
addBlocks(tmpBlocks,i);
}
// rewind the document
xml.clear();
for (unsigned int i=0;iclose();
if (!file[i]->open(QIODevice::ReadOnly)) {cerr<<"Unable to open file "<fileName().toStdString()<setRho(0);p->setTheta(0);p->setLL(0);
for (unsigned int i=0;i0) deb=blocks.split("\n").at(i).split(",").last().toInt();
xml[i]->readNext();
while (xml[i]->isStartElement()==false || xml[i]->name().toString().compare("Iteration")!=0) {if (xml[i]->atEnd()) return false;xml[i]->readNext();}
xml[i]->readNext();
int start=0,end=0,efrom=0,eto=0;double ato=0,afrom=0;
while (xml[i]->name().toString().compare("Iteration")!=0) {
if(xml[i]->error()!=QXmlStreamReader::NoError) {
cerr<<"XML error of type "<error()<<":"<errorString().toStdString()<isStartElement() && xml[i]->name().toString().compare("Tree")==0) {
xml[i]->readNext();
string s=xml[i]->text().toString().toStdString();
while (s.at(0)==10 || s.at(0)==13) s=s.substr(1,s.length()-1);
while (s.at(s.size()-1)==10 || s.at(s.size()-1)==13) s=s.substr(0,s.length()-1);
if (i==0) p->setTreeData(new RecTree(getL(),s,false,false),blocks);
}
if (xml[i]->isEndElement() && xml[i]->name().toString().compare("recedge")==0) {
try{p->getTree()->addRecEdge(afrom,ato,start,end,efrom,eto);
}catch( char * str ){
cerr<<"Exception from getIt: "<setNumber(xml[i]->readElementText().toLong());
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("theta")==0) p->setTheta(p->getTheta()+xml[i]->readElementText().toDouble());
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("delta")==0) p->setDelta(xml[i]->readElementText().toDouble());
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("rho" )==0) p->setRho (p->getRho()+xml[i]->readElementText().toDouble());
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("ll" )==0) p->setLL(p->getLL()+xml[i]->readElementText().toDouble());
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("start")==0) start=deb+xml[i]->readElementText().toInt();
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("end" )==0) end =deb+xml[i]->readElementText().toInt();
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("efrom")==0) efrom=xml[i]->readElementText().toInt();
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("eto" )==0) eto =xml[i]->readElementText().toInt();
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("afrom")==0) afrom=xml[i]->readElementText().toDouble();
else if (xml[i]->isStartElement() && xml[i]->name().toString().compare("ato" )==0) ato =xml[i]->readElementText().toDouble();
else if (xml[i]->isStartElement() && xml[i]->name().toString().startsWith("est")) {
p->addConv(xml[i]->name().toString().toStdString(),xml[i]->readElementText().toDouble());
}
else if (xml[i]->isStartElement() && xml[i]->name().toString().startsWith("acc")) {
p->addConv(xml[i]->name().toString().toStdString(),xml[i]->readElementText().toDouble());
}
else if (xml[i]->isStartElement() && xml[i]->name().toString().startsWith("prop")) {
p->addConv(xml[i]->name().toString().toStdString(),xml[i]->readElementText().toDouble());
}
xml[i]->readNext();
}// end while loop
}
currentIteration++;
return true;
}
void OutputFile::countVectors()
{
double curNumRec=0.0;
int start=0;
int end=0;
int itercounts=0;
outputinitialised=true;
//
currentIteration=-1;
xml.clear();
//Open file
file[0]->close();
file[0]->open(QIODevice::ReadOnly);
xml.push_back(new QXmlStreamReader(file[0]));
QString str="";
xml[0]->readNext();
while (!xml[0]->atEnd()) {
xml[0]->readNext();
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("Blocks" )==0) {int L=xml[0]->readElementText().split(",").last().toInt();genorec=vector(L,0);genobeg=vector(L,0);genoend=vector(L,0);continue;}
if (xml[0]->isEndElement()&&xml[0]->name().toString().compare("Iteration")==0) {numrecedges.push_back(curNumRec);curNumRec=0.0;continue;}
if (xml[0]->isEndElement()&&xml[0]->name().toString().compare("recedge" )==0) {curNumRec++;genobeg[start]++;genoend[end-1]++;for (int i=start;iisStartElement()&&xml[0]->name().toString().compare("start")==0) {start=xml[0]->readElementText().toInt();continue;}
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("end" )==0) {end =xml[0]->readElementText().toInt();continue;}
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("theta")==0) {thetas.push_back(xml[0]->readElementText().toDouble());continue;}
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("delta")==0) {deltas.push_back(xml[0]->readElementText().toDouble());continue;}
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("rho" )==0) {rhos .push_back(xml[0]->readElementText().toDouble());continue;}
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("ll" )==0) {likelihoods.push_back(xml[0]->readElementText().toDouble());continue;}
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("prior")==0) {priors.push_back(xml[0]->readElementText().toDouble());continue;}
if (xml[0]->isStartElement()&&xml[0]->name().toString().compare("Tree" )==0) {itercounts++; string s=xml[0]->readElementText().toStdString();while (s.at(0)==10 || s.at(0)==13) s=s.substr(1,s.length()-1);while (s.at(s.size()-1)==10 || s.at(s.size()-1)==13) s=s.substr(0,s.length()-1);Tree * t=new Tree(s,false);tmrcas.push_back(t->getNode(t->getN()*2-2)->getAge());ttotals.push_back(t->getTTotal());delete(t);continue;}
}
for(unsigned int i=0;i* OutputFile::getRhoOverTheta()
{
vector*v=new vector();
for (unsigned int i=0;ipush_back(rhos[i]/thetas[i]);
return v;
}
vector* OutputFile::getRhoPerSite()
{
int L=getL();
int b=getB();
vector*v=new vector();
for (unsigned int i=0;ipush_back(rhos[i]/(deltas[i]*b+L-b));
return v;
}
vector* OutputFile::getThetaPerSite()
{
int L=getL();
vector*v=new vector();
for (unsigned int i=0;ipush_back(thetas[i]/L);
return v;
}
vector* OutputFile::getPosteriors()
{
vector*v=new vector();
for (unsigned int i=0;ipush_back(likelihoods[i]+priors[i]);
return v;
}
vector* OutputFile::getRoverM(ParamQt*param)
{
vector*v=new vector();
startOver();
while (getIt(param)) {
v->push_back(param->getRM());
}
startOver();
return v;
/*int L=getL();
int b=getB();
vector*v=new vector();
//for (unsigned int i=0;ipush_back(rhos[i]/thetas[i]*L*deltas[i]/(deltas[i]*b+L-b)*0.75*(1.0-exp(-4.0*thetas[i]/L)));
for (unsigned int i=0;ipush_back(rhos[i]/thetas[i]*L*deltas[i]/(deltas[i]*b+L-b)*3.0*thetas[i]/(3.0*L+4.0*thetas[i]));
return v;*/
}
void OutputFile::makeCF(ParamQt*param)
{
vector > *v=new vector >(0,vector(0.0));
startOver();
int count=0;
while (getIt(param)) {
param->makeCF(v);
count++;
}
param->setCF(v,count);
startOver();
}
vector* OutputFile::getGenoRec(int id,bool getto) {
vector * res=new vector(genorec.size(),0);
QFile f(file[0]->fileName());
f.open(QIODevice::ReadOnly);
QXmlStreamReader x(&f);
int start=0;
int end=0;
int edge=0;int efrom=0;
while (!x.atEnd()) {
x.readNext();
if (x.isEndElement()&&x.name().toString().compare("recedge" )==0) {
if (edge==id && getto) for (int i=start;iat(i))++;
else if(efrom==id && !getto) for (int i=start;iat(i))++;
continue;
}
if (x.isStartElement()&&x.name().toString().compare("start")==0) {start=x.readElementText().toInt();continue;}
if (x.isStartElement()&&x.name().toString().compare("end" )==0) {end=x.readElementText().toInt();continue;}
if (x.isStartElement()&&x.name().toString().compare("efrom")==0) {efrom=x.readElementText().toInt();continue;}
if (x.isStartElement()&&x.name().toString().compare("eto")==0) {edge=x.readElementText().toInt();continue;}
}
f.close();
for (unsigned int i=0;isize();i++) {res->at(i)/=thetas.size();}
return res;
}
vector* OutputFile::getRelGenoRec(ParamQt*param,int id) {
vector * res=new vector(genorec.size(),0);
QFile f(file[0]->fileName());
f.open(QIODevice::ReadOnly);
QXmlStreamReader x(&f);
double treedist;
startOver();
int counts=0;
while (getIt(param)) {
for(int i=0;i<(int)param->getRecTree()->numRecEdge();i++){
if(param->getRecTree()->getEdge(i)->getEdgeTo()==id){
treedist=param->getRecTree()->getEdgeTreeTime(i);
for (unsigned int j=param->getRecTree()->getEdge(i)->getStart();jgetRecTree()->getEdge(i)->getEnd();j++) (res->at(j))+=treedist/param->getRecTree()->getTTotal();
counts++;
}
}
}
f.close();
for (unsigned int i=0;isize();i++) res->at(i)/=counts;
return res;
}
vector* OutputFile::getRelGenoRec(ParamQt*param) {
vector * res=new vector(genorec.size(),0);
QFile f(file[0]->fileName());
f.open(QIODevice::ReadOnly);
QXmlStreamReader x(&f);
double treedist;
startOver();
int counts=0;
while (getIt(param)) {
for(int i=0;i<(int)param->getRecTree()->numRecEdge();i++){
treedist=param->getRecTree()->getEdgeTreeTime(i);
for (unsigned int j=param->getRecTree()->getEdge(i)->getStart();jgetRecTree()->getEdge(i)->getEnd();j++) (res->at(j))+=treedist/param->getRecTree()->getTTotal();
counts++;
}
}
f.close();
for (unsigned int i=0;isize();i++) res->at(i)*=param->getDelta()/counts;
return res;
}
void OutputFile::readNames(QString str){
names.clear();
QStringList list1 = str.split(";");
for(unsigned int i=0;i1){
int index=list2[0].toInt();
names<
#include
#include "paramqt.h"
//
using namespace std;
//
class OutputFile
{
public:
OutputFile(QStringList qstrs,bool makeVectors=true);
inline int getL() {return blocks.split(",").last().toInt();}
inline int getB() {return blocks.split(",").size()-1;}
inline QString getBlocks() {return blocks;}
bool getIt(ParamQt * p);
void startOver();
void reset();
inline int getCurIt() {return currentIteration;}
void addOtherData(string name,double val);
inline vector*getThetas(){vector *v=new vector(thetas);return v;}
inline vector*getRhos(){vector *v=new vector(rhos);return v;}
inline vector*getDeltas(){vector *v=new vector(deltas);return v;}
inline vector*getLikelihoods(){vector *v=new vector(likelihoods);return v;}
inline vector*getPriors(){vector *v=new vector(priors);return v;}
inline vector*getNumRecEdges(){vector *v=new vector(numrecedges);return v;}
inline vector*getGenoRec(){vector *v=new vector(genorec);return v;}
vector*getRelGenoRec(ParamQt*param);
vector*getGenoRec(int id,bool getto);
vector*getRelGenoRec(ParamQt*param,int id);
inline vector*getGenoBeg(){vector