Merge pull request labsquare#73 from bokic/master

Some improvements here and there ver2

Author: dridk

.coveralls.yml

@@ -0,0 +1 @@
+repo_token: Dj6d3Ke8T5Ikm96bvMvronbJV1AI1Cu9I

CHANGELOG

@@ -4,11 +4,19 @@ 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/)
 
+<<<<<<< HEAD
+## [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.
+=======
 ## [0.2.3] - 2017-29-03
 ### Changed
 - Exporting file displays a progress dialog
 - Add recent menu
 
+>>>>>>> devel
 
 ## [0.2.2] - 2017-03-03
 ### Changed
@@ -21,7 +29,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/)
 ### Changed
 - Remove filter of file by extension
 
-
 ## [0.2] - 2017-02-10
 ### Changed 
 - Main UI is now a list of analysis 

FastQt.pro

@@ -5,7 +5,7 @@
 #-------------------------------------------------
 QT       += core gui concurrent charts svg
 #QMAKE_CXXFLAGS  += -Ofast
-QMAKE_CXXFLAGS += -std=c++11
+CONFIG   += c++11
 
 CONFIG(release, debug|release):DEFINES += QT_NO_DEBUG_OUTPUT
 

QFontIcon/qfonticon.cpp

@@ -25,7 +25,7 @@ SOFTWARE.
 #include "qfonticon.h"
 #include <QDebug>
 #include <QFontDatabase>
-QFontIcon * QFontIcon::mInstance = Q_NULLPTR;
+QFontIcon * QFontIcon::mInstance = nullptr;
 
 bool QFontIcon::addFont(const QString &filename)
 {

QFontIcon/qfonticon.h

@@ -64,7 +64,7 @@ class QFontIcon : public QObject
     static bool addFont(const QString& filename);
     static QFontIcon * instance();
     // main methods. Return icons from code
-    static QIcon icon(const QChar& code, const QColor& baseColor = QColor(),const QString& family = QString());
+    static QIcon icon(const QChar& code, const QColor& baseColor = QColor(),const QString& family = QStringLiteral());
     // return added fonts
     const QStringList& families() const;
 

README.md

@@ -1,31 +1,36 @@
-#FastQt ![travis](https://api.travis-ci.org/labsquare/fastQt.svg?branch=master) ![Qt](https://img.shields.io/badge/Qt-qmake-green.svg) [![Gitter](https://badges.gitter.im/labsquare/fastQt.svg)](https://gitter.im/labsquare/fastQt?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+# FastQt 
+
+![travis](https://api.travis-ci.org/labsquare/fastQt.svg?branch=master) [![Gitter](https://badges.gitter.im/labsquare/fastQt.svg)](https://gitter.im/labsquare/fastQt?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [![Build status](https://ci.appveyor.com/api/projects/status/skmgugijflggfq4x?svg=true)](https://ci.appveyor.com/project/dridk/fastqt) [![Coverage Status](https://coveralls.io/repos/github/labsquare/fastQt/badge.svg?branch=master)](https://coveralls.io/github/labsquare/fastQt?branch=master)   
+
 FastQt is the clone of [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) application ported 
 from Java to [C++/Qt5](https://www.qt.io/) 
 
+
 ![Preview](https://raw.githubusercontent.com/labsquare/fastQt/master/screenshot.gif)
 
-##Installation 
-### Ubuntu
-deb package has not yet ready. But An [AppImage](http://appimage.org/) has been made for Linux x86_64 and has been tested on ubuntu 16.04.  
-You can download it from [here](https://github.com/labsquare/fastQt/releases/download/0.1/fastqt-0.1-linux-x86_64.AppImage) and run it as follow : 
+## Installation 
 
-    chmod +x fastqt-0.1-linux-x86_64.AppImage
-    ./fastqt-0.1-linux-x86_64.AppImage
+### Linux 
+An [AppImage](http://appimage.org/) has been created and should work on recent Linux distribution.     
+Download the last release from [here](https://github.com/labsquare/fastQt/releases/) and run it as follow : 
+
+    chmod +x fastqt-0.2.3-linux-x86_64.AppImage
+    ./fastqt-0.2.3-linux-x86_64.AppImage
 
 ### Archlinux
 There is an AUR package for Archlinux. [Just get it from the AUR](https://aur.archlinux.org/packages/fastqt/).
-    
-    
-Other package will come soon for Windows and MacOS. You can try to compile it anyway.
-    
+ 
+### Windows 
+Windows installer and portable version are avaible [here]( https://github.com/labsquare/fastQt/releases/)
+        
 ## Compilation 
 ### Prerequisites - Install KArchive
-You need to install karchive before compiling FastQt.    
+On Linux, you need to install karchive before compiling FastQt.    
 **From ubuntu** >xenial you can install it from repositories : 
 
      sudo apt install libkf5archive-dev
 
-**From fedoar** >= 24 you can install it from repositories :
+**From fedora** >= 24 you can install it from repositories :
 
     sudo dnf install kf5-karchive-devel
 
@@ -43,14 +48,17 @@ You need to install karchive before compiling FastQt.
     cmake .. -DCMAKE_INSTALL_PREFIX=/usr/
     make 
     sudo make install
+    
+** From Windows **    
+Nothing to do. Compiled library are avaible in win32 directory.  
 
 ### Install Qt >5.7
 
 **From website** : Download Qt > 5.7 from https://www.qt.io/.   
 Don't forget to check QtChart module during installation. 
 
 **From ubuntu** : Qt 5.7 is not yet avaible with ubuntu. But you can add PPA to your software system. 
-For exemple for xenial 
+For exemple from xenial 
 
     sudo add-apt-repository ppa:beineri/opt-qt57-xenial
     sudo apt-get install qt57base qt57charts-no-lgpl
@@ -61,7 +69,7 @@ For exemple for xenial
     sudo dnf install qt5-qtbase-devel qt5-qtcharts-devel 
 
 ### Compile FastQt 
-Be sure you have the correct version of Qt (>5.7) by using qmake. You will find qmake in bin folder where you installed Qt. For exemple, if you installed Qt from ppa:beineri, you will find it under /opt/qt57/bin/qmake. Then launch the compilation from FastQC folder as follow.
+Be sure you have the correct version of Qt (>5.7) by using qmake --version. For exemple, if you have installed Qt from ppa:beineri, you will find it under /opt/qt57/bin/qmake. Then launch the compilation from FastQC folder as follow.
 
      /opt/qt57/bin/qmake --version
      /opt/qt57/bin/qmake 
@@ -70,7 +78,14 @@ Be sure you have the correct version of Qt (>5.7) by using qmake. You will find
 
 ## Usage
 
-You can use FastQt as GUI application or in Command Line Interface.
+FastQt can analyse uncompress and compress fastq files. The following extensions are supported :
+
+- *.fastq
+- *.fastq.gz
+- *.fastq.xz
+- *.fastq.bz2
+
+You can use FastQt as GUI application or as a Command Line Interface.
 
 Some usage example :
 
@@ -80,3 +95,6 @@ fastqt file1.fastq file2.fastq.gz file3.fastq.bzip # File save in file1 file 2 f
 fastqt file1.fastq -o specific_path # Create specific directory for each file in specific_path
 fastqt file1.fastq -t 2 # Fastqt run maximal two process this option is valid for GUI too
 ```
+
+## How to cite FastQt 
+Labsquare Team, et al (2017). FastQt: a quality control tool for high throughput sequence data. Available online at: https://github.com/labsquare/fastQt

analysis/analysis.cpp

@@ -24,7 +24,7 @@ Copyright Copyright 2016-17 Sacha Schutz
 Analysis::Analysis(QObject * parent)
     :QObject(parent)
 {
-    mParentRunner = Q_NULLPTR;
+    mParentRunner = nullptr;
 }
 
 Analysis::~Analysis()
@@ -36,8 +36,8 @@ void Analysis::save(const QString &path)
 {
     QString name = metaObject()->className();
     QDir dir(path);
-    QString svgPath = dir.filePath(QString("%1.svg").arg(name));
-    QString pngPath = dir.filePath(QString("%1.png").arg(name));
+    QString svgPath = dir.filePath(QStringLiteral("%1.svg").arg(name));
+    QString pngPath = dir.filePath(QStringLiteral("%1.png").arg(name));
 
     capture(svgPath);
     capture(pngPath, ImageFormat::PngFormat);

analysis/analysis.h

@@ -48,7 +48,7 @@ class Analysis : public QObject
         Success , Warning, Error, Unknown
     };
 
-    Analysis(QObject * parent = Q_NULLPTR);
+    Analysis(QObject * parent = nullptr);
 
     virtual ~Analysis();
     /*!

analysis/analysisrunner.cpp

@@ -61,42 +61,54 @@ void AnalysisRunner::run()
 
     QFileInfo fileInfo(mFilename);
 
-    QIODevice * file    = Q_NULLPTR;
-    QIODevice * rawFile = new QFile(mFilename);
+    QIODevice * file    = nullptr;
+    QFile rawFile(mFilename);
 
-    if (is_gz(rawFile))
+    if (is_gz(&rawFile))
     {
-        file = new KCompressionDevice(rawFile,true,KCompressionDevice::GZip);
+        file = new KCompressionDevice(&rawFile,true,KCompressionDevice::GZip);
         if (!is_fastq(file))
-            file = Q_NULLPTR;
+        {
+            delete file;
+            file = nullptr;
+        }
     }
-    else if (is_bz2(rawFile))
+    else if (is_bz2(&rawFile))
     {
-        file = new KCompressionDevice(rawFile, true, KCompressionDevice::BZip2);
+        file = new KCompressionDevice(&rawFile, true, KCompressionDevice::BZip2);
         if (!is_fastq(file))
-            file = Q_NULLPTR;
+        {
+            delete file;
+            file = nullptr;
+        }
     }
-    else if (is_xz(rawFile))
+    else if (is_xz(&rawFile))
     {
-        file = new KCompressionDevice(rawFile,true, KCompressionDevice::Xz);
+        file = new KCompressionDevice(&rawFile,true, KCompressionDevice::Xz);
         if (!is_fastq(file))
-            file = Q_NULLPTR;
+        {
+            delete file;
+            file = nullptr;
+        }
     }
-    else if (is_fastq(rawFile))
+    else if (is_fastq(&rawFile))
     {
-        file = rawFile;
+        rawFile.close();
+        file = new QFile(mFilename);
     }
 
-    if (file == Q_NULLPTR)
+    if (file == nullptr)
     {
         qDebug()<<Q_FUNC_INFO<<fileInfo.suffix()<< " file is not supported";
         setStatus(Canceled);
+        delete file;
         return;
     }
 
     if (fileInfo.size() == 0)
     {
         setStatus(Canceled);
+        delete file;
         return;
     }
 
@@ -123,6 +135,7 @@ void AnalysisRunner::run()
                 {
                     qCritical()<<Q_FUNC_INFO<<"Cannot read sequence. Are you sure it's a Fastq file ?";
                     setStatus(Canceled);
+                    delete file;
                     return ;
                 }
             }
@@ -132,12 +145,12 @@ void AnalysisRunner::run()
             // this is critcal and can decrease the speed. Send message only 1 sequence / 1000
             if (mSequenceCount % 1000 == 0)
             {
-                int percentNow = (float)(rawFile->pos()) / fileInfo.size() * 100;
+                int percentNow = qRound(static_cast<qreal>(file->pos()) / fileInfo.size() * 100);
                 // if percentNow is still null, return empty percent ...
                 if ( (percentNow >= mProgression + 5) || (percentNow == 0))
                 {
                     mProgression = percentNow;
-                    //emitUpdate(QString(tr("%1 Sequences procceed ( %2 \% )")).arg(mSequenceCount).arg(mProgression));
+                    //emitUpdate(tr("%1 Sequences procceed ( %2 \% )").arg(mSequenceCount).arg(mProgression));
                 }
             }
 
@@ -218,7 +231,7 @@ void AnalysisRunner::cancel()
     mStatus = Canceled;
 }
 
-quint64 AnalysisRunner::fileSize() const
+qint64 AnalysisRunner::fileSize() const
 {
     return mFileSize;
 }
@@ -227,11 +240,11 @@ QString AnalysisRunner::humanFileSize() const
 {
     int unit;
     const char *units [] = {" Bytes", " kB", " MB", " GB"};
-    quint64 size = fileSize(); // or whatever
+    qint64 size = fileSize(); // or whatever
 
     for (unit=-1; (++unit<3) && (size>1023); size/=1024);
 
-    return QString::number(size, 'f', 1) + QString(units[unit]);
+    return QString::number(size, 'f', 1) + QString::fromLatin1(units[unit]);
 
 }
 
@@ -262,7 +275,7 @@ Analysis *AnalysisRunner::analysis(const QString &className)
 {
     if (mAnalysisHash.contains(className))
         return mAnalysisHash[className];
-    return Q_NULLPTR;
+    return nullptr;
 }
 
 

analysis/analysisrunner.h

@@ -90,7 +90,7 @@ class AnalysisRunner : public QRunnable
 
     void cancel();
 
-    quint64 fileSize() const;
+    qint64 fileSize() const;
 
     QString humanFileSize() const;
 
@@ -123,7 +123,7 @@ class AnalysisRunner : public QRunnable
     QString mMessage;
     int mProgression = 0;
     int mSequenceCount = 0;
-    int mFileSize  = 0;
+    qint64 mFileSize  = 0;
     int mDuration  = 0;
     Status mStatus = Waiting;
     bool mCancel = false;

analysis/basicstatsanalysis.cpp

@@ -77,7 +77,7 @@ QWidget *BasicStatsAnalysis::createResultWidget()
     KeyValueModel * model = new KeyValueModel(view);
     view->setModel(model);
 
-    QString length = mMinLength == mMaxLength ? QString("%1").arg(mMaxLength) :  QString("%1-%2").arg(mMinLength).arg(mMaxLength);
+    QString length = mMinLength == mMaxLength ? QString::number(mMaxLength) :  QStringLiteral("%1-%2").arg(mMinLength).arg(mMaxLength);
 
 
     model->addValue(tr("Total Sequences"), QLocale::system().toString(mReadCount));
@@ -113,7 +113,7 @@ void BasicStatsAnalysis::save(const QString &path)
     QJsonObject json;
 
     QDir dir(path);
-    QString filename = dir.filePath(QString("%1.json").arg(metaObject()->className()));
+    QString filename = dir.filePath(QStringLiteral("%1.json").arg(metaObject()->className()));
 
     QFile file(filename);
     if (file.open(QIODevice::WriteOnly))

analysis/basicstatsanalysis.h

@@ -42,7 +42,7 @@ class BasicStatsAnalysis : public Analysis
     Q_PROPERTY(int readCount READ readCount)
 
 public:
-    BasicStatsAnalysis(QObject * parent = Q_NULLPTR);
+    BasicStatsAnalysis(QObject * parent = nullptr);
     void processSequence(const Sequence& sequence) Q_DECL_OVERRIDE;
     void reset() Q_DECL_OVERRIDE;
     QWidget * createResultWidget() Q_DECL_OVERRIDE;

analysis/lengthdistributionanalysis.cpp

@@ -29,11 +29,11 @@ QWidget *LengthDistributionAnalysis::createResultWidget()
     QChartView * view = new QChartView;
     view->setRenderHint(QPainter::Antialiasing);
 
-    QLineSeries * serie = new QLineSeries;
-
     if (mGraphCounts.isEmpty())
         return view;
 
+    QLineSeries * serie = new QLineSeries;
+
     int yMax = 0;
     auto graph_count_it = mGraphCounts.begin();
     for (int i=mMin; i < mMax+mIntervale; i += mIntervale)

analysis/lengthdistributionanalysis.h

@@ -15,7 +15,7 @@ class LengthDistributionAnalysis : public Analysis
 {
     Q_OBJECT
 public:
-    LengthDistributionAnalysis(QObject * parent = Q_NULLPTR);
+    LengthDistributionAnalysis(QObject * parent = nullptr);
     void processSequence(const Sequence& sequence) Q_DECL_OVERRIDE;
     void reset() Q_DECL_OVERRIDE;
     QWidget * createResultWidget() Q_DECL_OVERRIDE;

analysis/overrepresentedseqsanalysis.cpp

@@ -89,8 +89,8 @@ QWidget *OverRepresentedSeqsAnalysis::createResultWidget()
 void OverRepresentedSeqsAnalysis::save(const QString &path)
 {
     QDir dir(path);
-    QString tsvPath     = dir.filePath(QString("%1.tsv").arg(metaObject()->className()));
-    QString fastaPath   = dir.filePath(QString("%1.fasta").arg(metaObject()->className()));
+    QString tsvPath     = dir.filePath(QStringLiteral("%1.tsv").arg(metaObject()->className()));
+    QString fastaPath   = dir.filePath(QStringLiteral("%1.fasta").arg(metaObject()->className()));
 
     QFile tsvFile(tsvPath);
     QFile fastaFile(fastaPath);
@@ -106,7 +106,7 @@ void OverRepresentedSeqsAnalysis::save(const QString &path)
         {
             double percentage = ((double)mSequences[s] / mCount) * 100;
             tsvStream<<s<<"\t"<<mSequences[s]<<"\t"<<percentage<<"\n";
-            fastaStream<<QString(">Seq_%1;count=%2;percentage=%3").arg(index).arg(mSequences[s]).arg(percentage)<<"\n";
+            fastaStream<<QStringLiteral(">Seq_%1;count=%2;percentage=%3").arg(index).arg(mSequences[s]).arg(percentage)<<"\n";
             fastaStream<<s<<endl;
 
             ++index;