Merge branch 'beta_fixes' into develop

.appveyor.yml

@@ -27,7 +27,7 @@ cache:
     - C:\msys64\var\cache\pacman\pkg
 
 install:
-    - SET "PATH=C:\Qt\5.12.2\mingw73_64\bin;C:\%MSYS2_DIR%\%MSYSTEM%\bin;C:\%MSYS2_DIR%\usr\bin;%PATH%"
+    - SET "PATH=C:\Qt\5.12.4\mingw73_64\bin;C:\%MSYS2_DIR%\%MSYSTEM%\bin;C:\%MSYS2_DIR%\usr\bin;%PATH%"
 
     - bash -lc "pacman -S --needed --noconfirm mingw64/mingw-w64-x86_64-hdf5 mingw64/mingw-w64-x86_64-netcdf mingw64/mingw-w64-x86_64-boost"
 

.travis.yml

@@ -106,9 +106,12 @@ after_success:
       bash <(curl -s https://codecov.io/bash)
     fi
 
-
-before_deploy:
   - |
+    if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
+      echo "This build is for a PR. Not proceeding with installer creation."
+      exit 0
+    fi
+
     export ELMAVEN_TAG=`git describe --tags`
     SUBSTRING=$(echo $ELMAVEN_TAG| cut -d'-' -f 1)
     export ELMAVEN_VERSION=${SUBSTRING[@]:1}

src/core/libmaven/mavenparameters.cpp

@@ -13,8 +13,7 @@ MavenParameters::MavenParameters(string settingsPath):lastUsedSettingsPath(setti
 {
 
     clsf = NULL;
-    alignWrtExpectedRt=false;
-	alignSamplesFlag = false;
+    alignSamplesFlag = false;
         processAllSlices = false;
         pullIsotopesFlag = false;
         matchRtFlag = false;

src/core/libmaven/mavenparameters.h

@@ -105,7 +105,6 @@ class MavenParameters
         bool pullIsotopesFlag;
         bool showProgressFlag;
         bool matchRtFlag;
-        bool alignWrtExpectedRt;
 
         /**
         * default ionization mode used by mass spec

src/gui/mzroll/alignmentdialog.cpp

@@ -23,7 +23,6 @@ AlignmentDialog::AlignmentDialog(QWidget *parent) : QDialog(parent) {
         connect(alignAlgo, SIGNAL(currentIndexChanged(int)), this, SLOT(algoChanged()));
 	connect(peakDetectionAlgo, SIGNAL(currentIndexChanged(int)), this, SLOT(algoChanged()));
         connect(cancelButton, &QPushButton::clicked, this, &AlignmentDialog::cancel);
-        connect(alignWrtExpectedRt,SIGNAL(toggled(bool)),SLOT(setAlignWrtExpectedRt(bool)));
         connect(local, SIGNAL(toggled(bool)),this, SLOT(setInitPenalty(bool)));
         connect(restoreDefaultObiWarpParams, SIGNAL(clicked(bool)), this, SLOT(restorDefaultValues(bool)));
         connect(showAdvanceParams, SIGNAL(toggled(bool)), this, SLOT(showAdvanceParameters(bool)));
@@ -73,11 +72,6 @@ void AlignmentDialog::refSampleChanged()
     emit changeRefSample(sample);
 }
 
-void AlignmentDialog::setAlignWrtExpectedRt(bool checked)
-{
-	_mw->mavenParameters->alignWrtExpectedRt = checked;
-}
-
 void AlignmentDialog::setInitPenalty(bool checked)
 {
         initPenalty->setEnabled(checked);

src/gui/mzroll/alignmentdialog.h

@@ -35,7 +35,6 @@ class AlignmentDialog : public QDialog, public Ui_AlignmentDialog {
 		void setDatabase(QString db);
 		void setProgressBar(QString text, int progress, int totalSteps);
 		void showInfo(QString text);
-		void setAlignWrtExpectedRt(bool checked);
 		void setInitPenalty(bool checked);
 		void restorDefaultValues(bool checked);
 		void showAdvanceParameters(bool checked);

src/gui/mzroll/database.cpp

@@ -226,6 +226,17 @@ vector<Compound*> Database::findSpeciesByName(string name, string dbname) {
 		return set;
 }
 
+vector<Compound*> Database::findSpeciesById(string id, string dbName) {
+    vector<Compound*> matches;
+    for (auto compound : compoundsDB) {
+        if (compound->id == id && compound->db == dbName) {
+            matches.push_back(compound);
+        }
+    }
+
+    return matches;
+}
+
 void Database::loadReactions(string db) {
 
 		map<string, Reaction*> seenReactions;

src/gui/mzroll/database.h

@@ -92,6 +92,7 @@ class Database {
 	deque<Compound*> getCompoundsDB(){ 	return compoundsDB;}
 	set<Compound*> findSpeciesByMass(float mz, MassCutoff *massCutoff);
 	vector<Compound*> findSpeciesByName(string name, string dbname);
+	vector<Compound*> findSpeciesById(string id, string dbName);
 
 	void loadRetentionTimes(QString method);
 	void saveRetentionTime(Compound* c, float rt, QString method);

src/gui/mzroll/forms/alignmentdialog.ui

@@ -643,22 +643,6 @@
        <property name="rightMargin">
         <number>9</number>
        </property>
-       <item row="3" column="0">
-        <widget class="QLabel" name="label_13">
-         <property name="sizePolicy">
-          <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
-           <horstretch>0</horstretch>
-           <verstretch>0</verstretch>
-          </sizepolicy>
-         </property>
-         <property name="text">
-          <string>Alignment w.r.t Expected Rt</string>
-         </property>
-         <property name="alignment">
-          <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
-         </property>
-        </widget>
-       </item>
        <item row="1" column="1">
         <widget class="QSpinBox" name="limitGroupCount">
          <property name="sizePolicy">
@@ -770,19 +754,6 @@
          </property>
         </widget>
        </item>
-       <item row="3" column="1">
-        <widget class="QCheckBox" name="alignWrtExpectedRt">
-         <property name="sizePolicy">
-          <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
-           <horstretch>0</horstretch>
-           <verstretch>0</verstretch>
-          </sizepolicy>
-         </property>
-         <property name="text">
-          <string/>
-         </property>
-        </widget>
-       </item>
       </layout>
      </widget>
     </widget>

src/gui/mzroll/masscalcgui.cpp

@@ -219,6 +219,7 @@ void MassCalcWidget::setFragmentationScan(Scan* scan) {
 
     Fragment f(scan, 0, 0, 1024);
     _mz = scan->precursorMz;
+    precursorMz->setText(QString(to_string(_mz).c_str()));
     getMatches();
 
     for(auto& m : matches ) {

src/gui/mzroll/mzfileio.cpp

@@ -1175,9 +1175,18 @@ PeakGroup* mzFileIO::readGroupXML(QXmlStreamReader& xml, PeakGroup* parent)
         if (matches.size() > 0)
             group->compound = matches[0];
     } else if (!compoundId.empty()) {
-        Compound* c = DB.findSpeciesByIdAndName(compoundId,
-                                                group->compound->name,
-                                                DB.ANYDATABASE);
+        Compound* c = nullptr;
+
+        if (group->compound && !group->compound->name.empty()) {
+            c = DB.findSpeciesByIdAndName(compoundId,
+                                          group->compound->name,
+                                          DB.ANYDATABASE);
+        } else if (!compoundDB.empty()) {
+            vector<Compound*> matches = DB.findSpeciesById(compoundId, compoundDB);
+            if (matches.size())
+                c = matches[0];
+        }
+
         if (c)
             group->compound = c;
     }

src/gui/mzroll/numeric_treewidgetitem.cpp

@@ -8,18 +8,18 @@ bool NumericTreeWidgetItem::operator<( const QTreeWidgetItem & other ) const{
     QCollator collator;
     collator.setNumericMode(true);
 
-    QRegExp exp1("^[-+]?([0-9]*\\.?[0-9]+)[eE][-+]?([0-9]+)$");
-    QRegExp exp2("^[-+]?([0-9]*\\.?[0-9]+)[eE][-+]?([0-9]+)$");
-    if (thisText.contains(exp1) && otherText.contains(exp2)) {
-        QString thisMantissa = exp1.cap(1);
-        QString thisExponent = exp1.cap(2);
-        QString otherMantissa = exp2.cap(1);
-        QString otherExponent = exp2.cap(2);
-
-        if (collator.compare(thisExponent, otherExponent) == 0) {
-            return collator.compare(thisMantissa, otherMantissa) < 0;
-        }
-        return collator.compare(thisExponent, otherExponent) < 0;
+    QRegExp exp("^[-+]?([0-9]*\\.?[0-9]+)[eE][-+]?([0-9]+)$");
+    if (thisText.contains(exp)) {
+        double mantissa = exp.cap(1).toDouble();
+        double exponent = exp.cap(2).toDouble();
+        double trueValue = mantissa * (pow(10, exponent));
+        thisText = QString::fromStdString(to_string(trueValue).c_str());
+    }
+    if (otherText.contains(exp)) {
+        double mantissa = exp.cap(1).toDouble();
+        double exponent = exp.cap(2).toDouble();
+        double trueValue = mantissa * (pow(10, exponent));
+        otherText = QString::fromStdString(to_string(trueValue).c_str());
     }
 
     return collator.compare(thisText , otherText) < 0;

src/gui/mzroll/spectrawidget.cpp

@@ -877,12 +877,18 @@ float SpectraWidget::invY(float y)
 
 void SpectraWidget::mousePressEvent(QMouseEvent *event)
 {
+    if (_currentScan == nullptr)
+        return;
+
     QGraphicsView::mousePressEvent(event);
     _mouseStartPos = event->pos();
 }
 
 void SpectraWidget::mouseReleaseEvent(QMouseEvent *event)
 {
+    if (_currentScan == nullptr)
+        return;
+
     QGraphicsView::mouseReleaseEvent(event);
 
     _mouseEndPos = event->pos();