Merge branch 'devel'

CHANGELOG

@@ -3,7 +3,13 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/) 
 and this project adheres to [Semantic Versioning](http://semver.org/)
-.
+
+## [0.2.3] - 2017-14-03
+### Changed
+- Fix delay time before running. Now analysis doesn't wait to run
+- Remove debugging message
+- Fix bug when exporting PNG data.
+
 ## [0.2.2] - 2017-03-03
 ### Changed
 - Fix Crash when reading .xz file 

FastQt.pro

@@ -6,7 +6,7 @@
 QT       += core gui concurrent charts svg
 #QMAKE_CXXFLAGS  += -Ofast
 QMAKE_CXXFLAGS += -std=c++11
-#CONFIG(release, debug|release):DEFINES += QT_NO_DEBUG_OUTPUT
+CONFIG(release, debug|release):DEFINES += QT_NO_DEBUG_OUTPUT
 
 
 # METHOD 1 : If KArchive is not installed as a Qt Module then copy to your Qt installation :

analysis/analysis.cpp

@@ -40,7 +40,7 @@ void Analysis::save(const QString &path)
     QString pngPath = dir.filePath(QString("%1.png").arg(name));
 
     capture(svgPath);
-    capture(pngPath);
+    capture(pngPath, ImageFormat::PngFormat);
 }
 
 

analysis/analysisrunner.cpp

@@ -61,30 +61,30 @@ void AnalysisRunner::run()
 
     QFileInfo fileInfo(mFilename);
 
-    QIODevice * file = Q_NULLPTR;
+    QIODevice * file    = Q_NULLPTR;
+    QIODevice * rawFile = new QFile(mFilename);
 
-    file = new QFile(mFilename);
-    if (is_gz(file))
+    if (is_gz(rawFile))
     {
-        file = new KCompressionDevice(mFilename, KCompressionDevice::GZip);
+        file = new KCompressionDevice(rawFile,true,KCompressionDevice::GZip);
         if (!is_fastq(file))
             file = Q_NULLPTR;
     }
-    else if (is_bz2(file))
+    else if (is_bz2(rawFile))
     {
-        file = new KCompressionDevice(mFilename, KCompressionDevice::BZip2);
+        file = new KCompressionDevice(rawFile, true, KCompressionDevice::BZip2);
         if (!is_fastq(file))
             file = Q_NULLPTR;
     }
-    else if (is_xz(file))
+    else if (is_xz(rawFile))
     {
-        file = new KCompressionDevice(mFilename, KCompressionDevice::Xz);
+        file = new KCompressionDevice(rawFile,true, KCompressionDevice::Xz);
         if (!is_fastq(file))
             file = Q_NULLPTR;
     }
-    else if (is_fastq(file))
+    else if (is_fastq(rawFile))
     {
-        file = new QFile(mFilename);
+        file = rawFile;
     }
 
     if (file == Q_NULLPTR)
@@ -108,11 +108,6 @@ void AnalysisRunner::run()
         FastqReader reader(file);
         mStartTime.start();
 
-        // pre compute total size for sequencial access .
-        //emitUpdate(tr("Analysis ..."));
-        reader.computeTotalSize();
-
-
 
         for (Analysis * a : mAnalysisHash)
             a->before();
@@ -137,7 +132,7 @@ void AnalysisRunner::run()
             // this is critcal and can decrease the speed. Send message only 1 sequence / 1000
             if (mSequenceCount % 1000 == 0)
             {
-                int percentNow = reader.percentComplete();
+                int percentNow = (float)(rawFile->pos()) / fileInfo.size() * 100;
                 // if percentNow is still null, return empty percent ...
                 if ( (percentNow >= mProgression + 5) || (percentNow == 0))
                 {

analysis/analysisrunner.h

@@ -24,6 +24,7 @@ Copyright Copyright 2016-17 Sacha Schutz
 #define ANALYSISRUNNER_H
 #include <QtCore>
 #include <KCompressionDevice>
+#include <KFilterBase>
 #include "analysis.h"
 #include "fastqreader.h"
 #include "imageformatdefinition.h"

main.cpp

@@ -40,7 +40,7 @@ int main(int argc, char *argv[])
     a.setApplicationName("FastQt");
     a.setOrganizationName("Labsquare");
     a.setOrganizationDomain("labsquare.org");
-    a.setApplicationVersion("0.2.2");
+    a.setApplicationVersion("0.2.3");
 
     QString locale = QLocale::system().name().section('_', 0, 0);
 

model/mainanalysemodel.cpp

@@ -9,7 +9,7 @@ MainAnalyseModel::MainAnalyseModel(QObject * parent)
     //    connect(mSignalMapper,SIGNAL(mapped(int)),this,SLOT(updated(int)));
     connect(mTimer,SIGNAL(timeout()),this,SLOT(timeUpdated()));
 
-    mTimer->setInterval(1000);
+    mTimer->setInterval(300);
 
 }
 
@@ -56,6 +56,7 @@ QVariant MainAnalyseModel::data(const QModelIndex &index, int role) const
         if (index.column() == ProgressColumn)
             return mRunners.at(index.row())->progression();
 
+
         if (index.column() == ReadsColumn)
             return mRunners.at(index.row())->sequenceCount();
 

sequence/abstractsequencereader.cpp

@@ -29,42 +29,13 @@ AbstractSequenceReader::AbstractSequenceReader(QIODevice *device)
 {
 
 
-}
-
-int AbstractSequenceReader::percentComplete() const
-{
-    if (totalSize() == 0)
-        return 0;
-
-    quint64 percent = qFloor(qreal(mDevice->pos()) / totalSize() * 100);
-    return percent;
-
 }
 
 const Sequence &AbstractSequenceReader::sequence() const
 {
     return mSequence;
 }
 
-void AbstractSequenceReader::computeTotalSize()
-{
-    if (mDevice->size() == 0) // sequential
-    {
-        while (!mDevice->atEnd())
-            mDevice->readLine();
-        mTotalSize = mDevice->pos();
-        mDevice->seek(0);
-    }
-    else { // Random access
-        mTotalSize = mDevice->size();
-    }
-}
-
-long long AbstractSequenceReader::totalSize() const
-{
-    return mTotalSize;
-}
-
 QIODevice *AbstractSequenceReader::device() const
 {
     return mDevice;

sequence/abstractsequencereader.h

@@ -50,11 +50,6 @@ class AbstractSequenceReader
      * \return false if the file end has been reach.
      */
     virtual bool next() = 0;
-    /*!
-     * \brief percentComplete return percent of bytes processed
-     * \return a a value between 0 and 100
-     */
-    virtual int percentComplete() const;
 
     /*!
      * \brief Return the current sequence.
@@ -63,18 +58,13 @@ class AbstractSequenceReader
      */
     const Sequence& sequence() const;
 
-
-    void computeTotalSize() ;
-    long long totalSize() const;
-
 protected:
     void setSequence(const Sequence& seq);
     QIODevice * device() const;
 
 private:
     QIODevice * mDevice;
     Sequence mSequence;
-    long long mTotalSize = 0;
 };
 
 #endif // ABSTRACTSEQUENCEREADER_H

ui/mainanalyseview.cpp

@@ -21,10 +21,10 @@ void MainAnalyseDelegate::paint(QPainter *painter, const QStyleOptionViewItem &o
 
 
         progressBarOption.minimum = 0;
-        progressBarOption.maximum = 100;
+        progressBarOption.maximum = progress == -1 ? 0 : 100;
         progressBarOption.textAlignment = Qt::AlignCenter;
         progressBarOption.progress = progress;
-        progressBarOption.text = QString ( "%1%" ).arg ( progress );
+        progressBarOption.text = progress == -1 ? QString("∞") : QString ( "%1%" ).arg ( progress );
         progressBarOption.textVisible = true;
         QApplication::style()->drawControl ( QStyle::CE_ProgressBar, &progressBarOption, painter );
 

utils/format_detection.cpp

@@ -92,8 +92,10 @@ bool is_fastq(QIODevice* file)
 
         line = file->readLine();
         // Some not alphabetic caractere are in range but you know isn't a problem
-        if (line[0] < 'A' || line[0] > 'z')
+        if (line[0] < 'A' || line[0] > 'z'){
+            file->close();
             return false;
+        }
 
         line = file->readLine();
         if (line[0] != '+')
@@ -103,11 +105,14 @@ bool is_fastq(QIODevice* file)
         }
 
         line = file->readLine();
-        if (line[0] < '!' || line[0] > '~')
+        if (line[0] < '!' || line[0] > '~'){
+            file->close();
             return false;
-
+        }
+        file->close();
         return true;
     }
+
     else
     {
         return false;