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qtWGCNA.cpp
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qtWGCNA.cpp
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#include "qtWGCNA.h"
#include "ui_qtWGCNA.h"
#include <QDebug>
#include <QFileDialog>
#include <QMessageBox>
#include <QProcess>
#include <QDesktopWidget>
#include <QProgressDialog>
#include <QtConcurrent>
using namespace QtConcurrent;
qtWGCNA::qtWGCNA(QWidget *parent) : QWidget(parent),ui(new Ui::qtWGCNA)
{
ui->setupUi(this);
connect(ui->line_exp, SIGNAL(textChanged(QString)), this, SLOT(checkLineEdits_start()));
connect(ui->line_work_dir, SIGNAL(textChanged(QString)), this, SLOT(checkLineEdits_start()));
}
qtWGCNA::~qtWGCNA()
{
delete ui;
}
void qtWGCNA::checkLineEdits_start()
{
bool ok = !ui->line_exp->text().isEmpty()
&& !ui->line_work_dir->text().isEmpty();
if(ok){
ui->start->setEnabled(true);
}
}
void qtWGCNA::on_start_clicked()
{
// Basic:
QString exp=ui->line_exp->text();
QString work_dir=ui->line_work_dir->text();
QString blockwiseModules_para=ui->line_blockwiseModules_para->text();
if(blockwiseModules_para!=""){blockwiseModules_para = "-p "+blockwiseModules_para;}else {blockwiseModules_para = "";}
// Checkbox:
QString enableWGCNAThreads = ui->checkBox_enableWGCNAThreads->text();
if(ui->checkBox_enableWGCNAThreads->isChecked()){enableWGCNAThreads = "--enableWGCNAThreads";}else {enableWGCNAThreads = "";}
QString skipSaveBlocks = ui->checkBox_skipSaveBlocks->text();
if(ui->checkBox_skipSaveBlocks->isChecked()){skipSaveBlocks = "--skipSaveBlocks";}else {skipSaveBlocks = "";}
QString gzipTOMs = ui->checkBox_gzipTOMs->text();
if(ui->checkBox_gzipTOMs->isChecked()){gzipTOMs = "--gzipTOMs";}else {gzipTOMs = "";}
qDebug()<<"Input exp file <bed>:"<<exp;
qDebug()<<"ouput work directory <bed>:"<<work_dir;
QStringList qtWGCNA_command;
qtWGCNA_command<<"iterativeWGCNA"
<<"-i"
<<exp
<<"-o"
<<work_dir
<<enableWGCNAThreads
<<skipSaveBlocks
<<gzipTOMs
<<blockwiseModules_para;
QString qtWGCNA_command_join = qtWGCNA_command.join(" ");
qDebug()<<"qtWGCNA command:"<<qtWGCNA_command_join;
QString qPath("qtWGCNA_config.txt");
QFile qFile(qPath);
if (qFile.open(QIODevice::WriteOnly)) {
QTextStream out(&qFile); out << qtWGCNA_command_join;
qFile.close();
}
qtWGCNA_command_join = "\""+qtWGCNA_command_join+"\"";
qDebug()<<"run qtWGCNA.sh command: "<<qtWGCNA_command_join;
QEventLoop loop;
QProgressDialog dialog;
dialog.setWindowModality(Qt::WindowModal);
dialog.setWindowTitle("qtWGCNA: for seeking the reverse transcriptase stop sites");
dialog.setWindowIcon(QIcon(":/images/qtWGCNAlogo.png"));
dialog.setMinimumWidth(800);
dialog.setRange(0,0);
dialog.setLabelText(QString("qtWGCNA ROC mode is running (%1 threads)...").arg(QThread::idealThreadCount()));
dialog.show();
QProcess p;
p.start("bash "+QCoreApplication::applicationDirPath()+"/qtWGCNA.sh "+"-c"+qtWGCNA_command_join+" -d "+"\""+work_dir+"\"");
connect(&p,SIGNAL(finished(int,QProcess::ExitStatus)),&loop,SLOT(quit()));
loop.exec();
QString getStr=QString(p.readAllStandardOutput());
ui->textEdit->setText(getStr);
QMessageBox::information(this,"qtWGCNA log: \n","A qtWGCNA job is done!");
QString getStr_Error=QString(p.readAllStandardError());
if(getStr_Error!=""){
QMessageBox::information(this,"qtWGCNA Error: \n",getStr_Error);
}
}
void qtWGCNA::on_browse_exp_clicked()
{
QFileDialog dialog(this);
dialog.setAcceptMode(QFileDialog::AcceptSave);
QString exp = dialog.getOpenFileName(this,tr("Locate gene expression file"),"txt",tr("Find gene expression file (*.txt)"));
if (!exp.isEmpty()) {
ui->line_exp->setText(exp);
}
}
void qtWGCNA::on_browse_work_dir_clicked()
{
QFileDialog dialog(this);
QString out_dir = dialog.getExistingDirectory(this,
tr("Find directory"), QDir::currentPath());
if (!out_dir.isEmpty()) {
ui->line_work_dir->setText(out_dir);
}
}
void qtWGCNA::on_config_clicked()
{
QString fileName = QFileDialog::getOpenFileName(this,tr("Open qtWGCNA config text"),"txt",tr("config text(qtWGCNA_config.txt)"));
if (!fileName.isEmpty())
loadFile(fileName);
}
void qtWGCNA::loadFile(const QString &fileName)
{
QFile file(fileName);
if (!file.open(QFile::ReadOnly | QFile::Text)) {
QMessageBox::warning(this, tr("Application"),
tr("Cannot read file %1:\n%2.")
.arg(QDir::toNativeSeparators(fileName), file.errorString()));
return;
}
QTextStream in(&file);
QString config_text=in.readAll();
QStringList config_list = config_text.split(' ');
ui->line_exp->setText(config_list[2]);
ui->line_work_dir->setText(config_list[4]);
if(config_list[5]!=""){
ui->checkBox_enableWGCNAThreads->setChecked(true);
}
if(config_list[6]!=""){
ui->checkBox_skipSaveBlocks->setChecked(true);
}
if(config_list[7]!=""){
ui->checkBox_gzipTOMs->setChecked(true);
}
if(config_list[8]!=""){
ui->line_blockwiseModules_para->setText(config_list[9]);
}
}