Merge ElucidataInc#1340 from ElucidataInc/fix_ag_issues

Fixes related to storing correct RT bounds
saif-el · Mar 3, 2021 · 4a96785 · 4a96785
2 parents e0285be + e6df501
commit 4a96785
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Showing 4 changed files with 26 additions and 3 deletions.
diff --git a/src/core/libmaven/peakdetector.cpp b/src/core/libmaven/peakdetector.cpp
@@ -576,6 +576,13 @@ void PeakDetector::processSlices(vector<mzSlice*>& slices,
             make_move_iterator(peakgroups.end()));
     };
 
+    float minRtOverAllSamples = numeric_limits<float>::max();
+    for (auto sample : _mavenParameters->samples)
+        minRtOverAllSamples = min(minRtOverAllSamples, sample->minRt);
+    float maxRtOverAllSamples = numeric_limits<float>::min();
+    for (auto sample : _mavenParameters->samples)
+        maxRtOverAllSamples = max(maxRtOverAllSamples, sample->maxRt);
+
     if (!appendNewGroups)
         _mavenParameters->allgroups.clear();
 
@@ -587,6 +594,9 @@ void PeakDetector::processSlices(vector<mzSlice*>& slices,
         }
 
         mzSlice* slice = slices[s];
+        slice->rtmin = max(slice->rtmin, minRtOverAllSamples);
+        slice->rtmax = min(slice->rtmax, maxRtOverAllSamples);
+
         vector<EIC*> eics = pullEICs(slice,
                                      _mavenParameters->samples,
                                      _mavenParameters);
@@ -1063,6 +1073,7 @@ void PeakDetector::detectIsotopesForParent(PeakGroup& parentGroup,
             visibleSamples.push_back(sample);
         }
 
+        auto parentSlice = parentGroup.getSlice();
         MassSlicer massSlicer(_mavenParameters);
         massSlicer.generateIsotopeSlices({parentGroup.getCompound()},
                                          findBarplotIsotopes);
@@ -1073,6 +1084,8 @@ void PeakDetector::detectIsotopesForParent(PeakGroup& parentGroup,
             if (slice->isotope.isParent())
                 continue;
 
+            slice->rtmin = parentSlice.rtmin;
+            slice->rtmax = parentSlice.rtmax;
             auto eics = pullEICs(slice, visibleSamples, _mavenParameters);
             auto isotopeGroup = integrateEicRegion(eics,
                                                    parentGroup.minRt,
@@ -1092,6 +1105,7 @@ void PeakDetector::detectIsotopesForParent(PeakGroup& parentGroup,
                 parentGroup.addIsotopeChild(*isotopeGroup);
             }
         }
+        massSlicer.clearSlices();
     } else {
         processCompounds({parentGroup.getCompound()},
                          false,

diff --git a/src/gui/mzroll/eicwidget.cpp b/src/gui/mzroll/eicwidget.cpp
@@ -8,7 +8,6 @@
 #include "boxplot.h"
 #include "classifierNeuralNet.h"
 #include "datastructures/adduct.h"
-#include "datastructures/mzSlice.h"
 #include "eiclogic.h"
 #include "globals.h"
 #include "isotopeswidget.h"
@@ -201,11 +200,15 @@ void EicWidget::mouseDoubleClickEvent(QMouseEvent* event) {
 void EicWidget::integrateRegion(float rtMin, float rtMax)
 {
     const auto& visibleSamples = getMainWindow()->getVisibleSamples();
+    auto slice = eicParameters->_slice;
+    auto bounds = visibleSamplesBounds();
+    slice.rtmin = bounds.rtmin;
+    slice.rtmax = bounds.rtmax;
     auto integratedGroup = PeakDetector::integrateEicRegion(
         eicParameters->eics,
         rtMin,
         rtMax,
-        eicParameters->_slice,
+        slice,
         visibleSamples,
         getMainWindow()->mavenParameters,
         getMainWindow()->getClassifier(),

diff --git a/src/gui/mzroll/eicwidget.h b/src/gui/mzroll/eicwidget.h
@@ -6,6 +6,7 @@
 #include "stable.h"
 
 #include "datastructures/isotope.h"
+#include "datastructures/mzSlice.h"
 
 class EIC;
 class EICLogic;
@@ -37,6 +38,7 @@ Q_OBJECT
 	void addPeakPositions();
 	void setBarplotPosition(PeakGroup* group);
     void renderPdf(shared_ptr<PeakGroup> group, QPainter* painter);
+    mzSlice visibleSamplesBounds();
 
 public Q_SLOTS:
 	void setMzSlice(float mz1, float mz2 = 0.0);
@@ -255,7 +257,6 @@ public Q_SLOTS:
 	void cleanup();		//deallocate eics, fragments, peaks, peakgroups
 	void clearPlot();	//removes non permenent graphics objects
 	void findPlotBounds(); //find _minX, _maxX...etc
-	mzSlice visibleSamplesBounds();
 
 	float toX(float x);
 	float toY(float y);

diff --git a/src/gui/mzroll/point.cpp b/src/gui/mzroll/point.cpp
@@ -221,6 +221,11 @@ void EicPoint::mouseDoubleClickEvent(QGraphicsSceneMouseEvent*) {
     if (_group != nullptr) {
         _group = make_shared<PeakGroup>(*_group,
                                         PeakGroup::IntegrationType::Manual);
+        auto slice = _group->getSlice();
+        auto bounds = _mw->getEicWidget()->visibleSamplesBounds();
+        slice.rtmin = bounds.rtmin;
+        slice.rtmax = bounds.rtmax;
+        _group->setSlice(slice);
         _mw->isotopeWidget->setPeakGroupAndMore(_group, true);
     }