Fix #38. Percent is now computed compressFile->pos() / compressFile->…

…size()
labsquare · Mar 14, 2017 · 7605421 · 7605421
1 parent 8393fa8
commit 7605421
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Showing 5 changed files with 11 additions and 60 deletions.
diff --git a/analysis/analysisrunner.cpp b/analysis/analysisrunner.cpp
@@ -57,28 +57,29 @@ AnalysisRunner::~AnalysisRunner()
 
 void AnalysisRunner::run()
 {
-    setStatus(Prepare);
+    setStatus(Running);
 
     QFileInfo fileInfo(mFilename);
 
+    QFile * compressFile = new QFile(mFilename);
     QIODevice * file = Q_NULLPTR;
 
     file = new QFile(mFilename);
     if (is_gz(file))
     {
-        file = new KCompressionDevice(mFilename, KCompressionDevice::GZip);
+        file = new KCompressionDevice(compressFile,true,KCompressionDevice::GZip);
         if (!is_fastq(file))
             file = Q_NULLPTR;
     }
     else if (is_bz2(file))
     {
-        file = new KCompressionDevice(mFilename, KCompressionDevice::BZip2);
+        file = new KCompressionDevice(compressFile, true, KCompressionDevice::BZip2);
         if (!is_fastq(file))
             file = Q_NULLPTR;
     }
     else if (is_xz(file))
     {
-        file = new KCompressionDevice(mFilename, KCompressionDevice::Xz);
+        file = new KCompressionDevice(compressFile,true, KCompressionDevice::Xz);
         if (!is_fastq(file))
             file = Q_NULLPTR;
     }
@@ -108,12 +109,6 @@ void AnalysisRunner::run()
         FastqReader reader(file);
         mStartTime.start();
 
-        // pre compute total size for sequencial access .
-        //emitUpdate(tr("Analysis ..."));
-        reader.computeTotalSize();
-
-        setStatus(Running);
-
 
         for (Analysis * a : mAnalysisHash)
             a->before();
@@ -138,7 +133,7 @@ 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)(compressFile->pos()) / fileInfo.size() * 100;
                 // if percentNow is still null, return empty percent ...
                 if ( (percentNow >= mProgression + 5) || (percentNow == 0))
                 {

diff --git a/analysis/analysisrunner.h b/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"
@@ -43,8 +44,7 @@ class AnalysisRunner : public QRunnable
         Waiting,
         Running,
         Canceled,
-        Finished,
-        Prepare
+        Finished
     };
 
     AnalysisRunner();

diff --git a/model/mainanalysemodel.cpp b/model/mainanalysemodel.cpp
@@ -45,8 +45,6 @@ QVariant MainAnalyseModel::data(const QModelIndex &index, int role) const
             case AnalysisRunner::Canceled : return tr("Canceled"); break;
             case AnalysisRunner::Running : return tr("Running"); break;
             case AnalysisRunner::Finished : return tr("Finished"); break;
-            case AnalysisRunner::Prepare : return tr("Preparing ..."); break;
-
             }
 
         }
@@ -55,12 +53,9 @@ QVariant MainAnalyseModel::data(const QModelIndex &index, int role) const
             return mRunners.at(index.row())->humanFileSize();
 
 
-        if (index.column() == ProgressColumn){
-            if (mRunners.at(index.row())->status() == AnalysisRunner::Prepare )
-                return -1;
-            else
-                return mRunners.at(index.row())->progression();
-        }
+        if (index.column() == ProgressColumn)
+            return mRunners.at(index.row())->progression();
+
 
         if (index.column() == ReadsColumn)
             return mRunners.at(index.row())->sequenceCount();

diff --git a/sequence/abstractsequencereader.cpp b/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;

diff --git a/sequence/abstractsequencereader.h b/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