Updated direct infusion receivers to include cluster number.

eugenemel · Oct 1, 2019 · b5f262b · b5f262b
1 parent 15efc21
commit b5f262b
Show file tree

Hide file tree

Showing 6 changed files with 48 additions and 15 deletions.
diff --git a/src/maven/background_directinfusion_update.cpp b/src/maven/background_directinfusion_update.cpp
@@ -11,11 +11,14 @@ BackgroundDirectInfusionUpdate::~BackgroundDirectInfusionUpdate() {
 
 void BackgroundDirectInfusionUpdate::run(void) {
 
+    int numSteps = samples.size() + 2; //prepare search database + each sample + agglomerate across samples
+    int stepNum = 0;
+
     QTime timer;
     timer.start();
 
     qDebug() << "Direct infusion analysis started.";
-    emit(updateProgressBar("Preparing search database...", 0, samples.size()));
+    emit(updateProgressBar("Preparing search database...", stepNum, numSteps));
 
     /**
      * ACTUAL WORK
@@ -28,8 +31,14 @@ void BackgroundDirectInfusionUpdate::run(void) {
                                                   false //debug
                                                   );
 
+    multimap<int, DirectInfusionAnnotation*> allDirectInfusionsAcrossSamples = {};
+
+    typedef map<int, DirectInfusionAnnotation*>::iterator diSampleIterator;
+
     for (unsigned int i = 0; i < samples.size(); i++){
 
+        stepNum++;
+
         mzSample* sample = samples.at(i);
 
          string msgStart = string("Processing sample ")
@@ -40,26 +49,53 @@ void BackgroundDirectInfusionUpdate::run(void) {
                  .append(sample->sampleName)
                  .append("\"");
 
-         emit(updateProgressBar(msgStart.c_str(), (i+1), (samples.size()+1)));
+         emit(updateProgressBar(msgStart.c_str(), stepNum, numSteps));
 
 
          /**
           * ACTUAL WORK
           */
-         vector<DirectInfusionAnnotation*> directInfusionAnnotations =
+         map<int, DirectInfusionAnnotation*> directInfusionAnnotations =
                  DirectInfusionProcessor::processSingleSample(
                      sample,
                      searchDb,
                      params,
                      false //debug
                      );
 
-         //DirectInfusionAnnotation* are deleted by the receiver (TableDockWidget)
-         for (DirectInfusionAnnotation* directInfusionAnnotation : directInfusionAnnotations) {
-             emit(newDirectInfusionAnnotation(directInfusionAnnotation));
+         for (diSampleIterator it = directInfusionAnnotations.begin(); it != directInfusionAnnotations.end(); ++it){
+             allDirectInfusionsAcrossSamples.insert(make_pair(it->first, it->second));
          }
+
+    }
+
+    //TODO: refactor as modular algorithm
+    //Organizing across samples
+    stepNum++;
+    updateProgressBar("Combining results across samples...", stepNum, numSteps);
+
+    for (auto directInfusionAnnotation : allDirectInfusionsAcrossSamples) {
+        emit(newDirectInfusionAnnotation(directInfusionAnnotation.second, directInfusionAnnotation.first));
     }
 
+//    typedef multimap<int, DirectInfusionAnnotation*>::iterator diMultimapIterator;
+
+//    for (int mapKey : searchDb->mapKeys){
+
+//        pair<diMultimapIterator, diMultimapIterator> directInfusionAnnotations = allDirectInfusionsAcrossSamples.equal_range(mapKey);
+
+//        for (diMultimapIterator it = directInfusionAnnotations.first; it != directInfusionAnnotations.second; ++it){
+//            emit(newDirectInfusionAnnotation(it->second, it->first));
+//        }
+
+//        //for (diMultimapIterator = allDirectInfusionsAcrossSamples.equal_range(mapKey);)
+//    }
+
+    //DirectInfusionAnnotation* are deleted by the receiver (TableDockWidget)
+//    for (DirectInfusionAnnotation* directInfusionAnnotation : directInfusionAnnotations) {
+//        emit(newDirectInfusionAnnotation(directInfusionAnnotation));
+//    }
+
     qDebug() << "Direct infusion analysis completed in" << timer.elapsed() << "msec.";
     updateProgressBar("Direct infusion analysis not yet started", 0, 1);
     emit(closeDialog());

diff --git a/src/maven/background_directinfusion_update.h b/src/maven/background_directinfusion_update.h
@@ -41,7 +41,7 @@ class BackgroundDirectInfusionUpdate : public QThread {
 
 signals:
     void updateProgressBar(QString, int, int);
-    void newDirectInfusionAnnotation(DirectInfusionAnnotation*);
+    void newDirectInfusionAnnotation(DirectInfusionAnnotation*, int);
     void closeDialog();
 
 };

diff --git a/src/maven/directinfusiondialog.cpp b/src/maven/directinfusiondialog.cpp
@@ -50,7 +50,7 @@ void DirectInfusionDialog::analyze() {
     TableDockWidget* resultsTable = mainwindow->addPeaksTable(title.toLatin1().data());
     resultsTable->setWindowTitle(title.toLatin1().data());
 
-    connect(directInfusionUpdate, SIGNAL(newDirectInfusionAnnotation(DirectInfusionAnnotation*)), resultsTable, SLOT(addDirectInfusionAnnotation(DirectInfusionAnnotation*)));
+    connect(directInfusionUpdate, SIGNAL(newDirectInfusionAnnotation(DirectInfusionAnnotation*, int)), resultsTable, SLOT(addDirectInfusionAnnotation(DirectInfusionAnnotation*, int)));
 
     connect(directInfusionUpdate, SIGNAL(updateProgressBar(QString,int,int)), SLOT(setProgressBar(QString, int,int)));
     connect(directInfusionUpdate, SIGNAL(closeDialog()), SLOT(hide()));

diff --git a/src/maven/tabledockwidget.cpp b/src/maven/tabledockwidget.cpp
@@ -458,16 +458,14 @@ PeakGroup* TableDockWidget::addPeakGroup(PeakGroup *group, bool updateTable, boo
     return g;
 }
 
-void TableDockWidget::addDirectInfusionAnnotation(DirectInfusionAnnotation* directInfusionAnnotation){
-
-    directInfusionClusterNum++;
+void TableDockWidget::addDirectInfusionAnnotation(DirectInfusionAnnotation* directInfusionAnnotation, int clusterNum) {
 
     float meanMz = 0.5f*(directInfusionAnnotation->precMzMin + directInfusionAnnotation->precMzMax);
 
     for (auto tuple : directInfusionAnnotation->compounds){
 
         PeakGroup pg;
-        pg.metaGroupId = directInfusionClusterNum;
+        pg.metaGroupId = clusterNum;
 
         //TODO: much of the information needs to be stuffed into Peak, b/c
         //when opening a file it all gets re-derived from PeakGroup::groupStatistics()

diff --git a/src/maven/tabledockwidget.h b/src/maven/tabledockwidget.h
@@ -35,7 +35,7 @@ public slots:
 	  //void showInfo(PeakGroup* group);
       PeakGroup* addPeakGroup(PeakGroup* group, bool updateTable);
       PeakGroup* addPeakGroup(PeakGroup* group, bool updateTable, bool isDeletePeakGroupPtr);
-      void addDirectInfusionAnnotation(DirectInfusionAnnotation* directInfusionAnnotation);
+      void addDirectInfusionAnnotation(DirectInfusionAnnotation* directInfusionAnnotation, int clusterNum);
       void setupPeakTable();
       PeakGroup* getSelectedGroup();
       PeakGroup* getLastBookmarkedGroup();
@@ -120,7 +120,6 @@ protected slots:
           tableViewType viewType;
 
           PeakGroup *lastSelectedGroup;
-          int directInfusionClusterNum = 0;
 };
 
 #endif
diff --git a/src/maven_core b/src/maven_core