look for modifications in peptide list

src/gui/peptide_list_view/peptide_view.ui

@@ -86,6 +86,11 @@
           <string>peptide</string>
          </property>
         </item>
+        <item>
+         <property name="text">
+          <string>modifications</string>
+         </property>
+        </item>
         <item>
          <property name="text">
           <string>msrun/scan</string>
@@ -101,6 +106,9 @@
       <item>
        <widget class="QLineEdit" name="peptide_search_edit"/>
       </item>
+      <item>
+       <widget class="QLineEdit" name="mod_auto_completion"/>
+      </item>
       <item>
        <widget class="QLineEdit" name="msrun_auto_completion"/>
       </item>
@@ -241,6 +249,22 @@
     </hint>
    </hints>
   </connection>
+  <connection>
+   <sender>mod_auto_completion</sender>
+   <signal>textChanged(QString)</signal>
+   <receiver>PeptideView</receiver>
+   <slot>doModificationSearch(QString)</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>436</x>
+     <y>360</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>699</x>
+     <y>506</y>
+    </hint>
+   </hints>
+  </connection>
  </connections>
  <slots>
   <slot>doNotValidHide(bool)</slot>
@@ -250,5 +274,6 @@
   <slot>doSearchOn(QString)</slot>
   <slot>doMsrunFileSearch(QString)</slot>
   <slot>doScanNumberSearch(int)</slot>
+  <slot>doModificationSearch(QString)</slot>
  </slots>
 </ui>

src/gui/peptide_list_view/peptidelistwindow.cpp

@@ -103,6 +103,7 @@ PeptideListWindow::PeptideListWindow(ProjectWindow *parent):
 
     ui->scan_number_edit->setVisible(false);
     ui->msrun_auto_completion->setVisible(false);
+    ui->mod_auto_completion->setVisible(false);
     ui->peptide_search_edit->setVisible(true);
 
 #if QT_VERSION >= 0x050000
@@ -172,6 +173,19 @@ void PeptideListWindow::setProteinMatch(IdentificationGroup * p_identification_g
         completer->setFilterMode(Qt::MatchContains);
         ui->msrun_auto_completion->setCompleter(completer);
 
+        QStringList mod_list;
+        for (pappso::AaModificationP mod :_project_window->getProjectP()->getPeptideStore().getModificationCollection()) {
+            mod_list << QString("[%1] %2 %3").arg(mod->getAccession()).arg(mod->getName()).arg(mod->getMass());
+            //qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+        }
+        completer = new QCompleter(mod_list, this);
+        completer->setCaseSensitivity(Qt::CaseInsensitive);
+
+        completer->setCompletionMode(QCompleter::PopupCompletion);
+        completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
+        completer->setFilterMode(Qt::MatchContains);
+        ui->mod_auto_completion->setCompleter(completer);
+
     }
 
 }
@@ -227,6 +241,10 @@ void PeptideListWindow::doPeptideSearchEdit(QString protein_search_string) {
     emit peptideDataChanged();
 }
 
+void PeptideListWindow::doModificationSearch(QString mod_search) {
+    //_p_proxy_model->setMsrunFileSearch(msr_run_file_search);
+    emit peptideDataChanged();
+}
 void PeptideListWindow::doMsrunFileSearch(QString msr_run_file_search) {
     qDebug() << "PeptideListWindow::doMsrunFileSearch begin " << msr_run_file_search;
     emit peptideDataChanged();
@@ -239,17 +257,22 @@ void PeptideListWindow::doSearchOn(QString search_on) {
     qDebug() << "PeptideListWindow::doSearchOn begin " << search_on;
     _p_proxy_model->setSearchOn( search_on);
 
+    ui->scan_number_edit->setVisible(false);
+    ui->msrun_auto_completion->setVisible(false);
+    ui->peptide_search_edit->setVisible(false);
+    ui->mod_auto_completion->setVisible(false);
     if (search_on == "msrun/scan" ) {
 
         qDebug() << "PeptideListWindow::doSearchOn visible " << search_on;
         ui->scan_number_edit->setVisible(true);
         ui->msrun_auto_completion->setVisible(true);
-        ui->peptide_search_edit->setVisible(false);
+    } else if (search_on == "modifications" ) {
+
+        qDebug() << "PeptideListWindow::doSearchOn visible " << search_on;
+        ui->mod_auto_completion->setVisible(true);
     }
     else {
         qDebug() << "PeptideListWindow::doSearchOn hidden " << search_on;
-        ui->scan_number_edit->setVisible(false);
-        ui->msrun_auto_completion->setVisible(false);
         ui->peptide_search_edit->setVisible(true);
     }
     //emit proteinDataChanged();

src/gui/peptide_list_view/peptidelistwindow.h

@@ -95,6 +95,7 @@ protected slots:
     void doNotGroupedHide(bool hide);
     void doPeptideSearchEdit(QString peptide_search_string);
     void doMsrunFileSearch(QString msr_run_file_search);
+    void doModificationSearch(QString mod_search);
     void doScanNumberSearch(int scan_num);
     void doSearchOn(QString search_on);
     void updateStatusBar();

src/gui/peptide_list_view/peptidetableproxymodel.cpp

@@ -56,6 +56,27 @@ bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
         PeptideEvidence * peptide_evidence = _peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(source_row).getPeptideEvidence();
         qDebug() << "PeptideTableProxyModel::filterAcceptsRow protein_match " << source_row;
 
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow valid ";
+        if (_hide_not_valid) {
+            if (! peptide_evidence->isValid()) {
+                return false;
+            }
+        }
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow checked ";
+        if (_hide_not_checked) {
+            if (! peptide_evidence->isChecked()) {
+                return false;
+            }
+        }
+
+        qDebug() << "PeptideTableProxyModel::filterAcceptsRow grouped ";
+        if (_hide_not_grouped) {
+            if (! peptide_evidence->isGrouped()) {
+                return false;
+            }
+
+        }
+
         if (_search_on == "msrun/scan") {
             unsigned int scan_num = this->_p_peptide_list_window->ui->scan_number_edit->value();
             QString file_search_string = this->_p_peptide_list_window->ui->msrun_auto_completion->text().toLower();
@@ -102,25 +123,24 @@ bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
             }
         }
 
-        qDebug() << "PeptideTableProxyModel::filterAcceptsRow valid ";
-        if (_hide_not_valid) {
-            if (! peptide_evidence->isValid()) {
-                return false;
-            }
-        }
-        qDebug() << "PeptideTableProxyModel::filterAcceptsRow checked ";
-        if (_hide_not_checked) {
-            if (! peptide_evidence->isChecked()) {
-                return false;
-            }
-        }
 
-        qDebug() << "PeptideTableProxyModel::filterAcceptsRow grouped ";
-        if (_hide_not_grouped) {
-            if (! peptide_evidence->isGrouped()) {
-                return false;
-            }
+        if (_search_on == "modifications") {
+            QString mod_search_string = this->_p_peptide_list_window->ui->mod_auto_completion->text();
 
+            std::vector<pappso::AaModificationP> mod_list;
+            for (pappso::AaModificationP mod :_p_peptide_list_window->getProjectWindow()->getProjectP()->getPeptideStore().getModificationCollection()) {
+                if (QString("[%1] %2 %3").arg(mod->getAccession()).arg(mod->getName()).arg(mod->getMass()).contains(mod_search_string)) {
+                    mod_list.push_back(mod);
+                }
+                //qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+            }
+            //qDebug() << "ProteinTableProxyModel::filterAcceptsRow msrun/scan " << file_search_string << " " << scan_num;
+            for (pappso::AaModificationP mod :mod_list) {
+                if (peptide_evidence->getPeptideXtpSp().get()->getNumberOfModification(mod) > 0) {
+                    return true;
+                }
+            }
+            return false;
         }
         return true;
     }

src/gui/protein_list_view/proteintableproxymodel.cpp

@@ -146,7 +146,6 @@ bool ProteinTableProxyModel::filterAcceptsRow(int source_row,
 
 
         if (_search_on == "modifications") {
-            unsigned int scan_num = this->_p_protein_list_window->ui->scan_number_edit->value();
             QString mod_search_string = this->_p_protein_list_window->ui->mod_auto_completion->text();
 
             std::vector<pappso::AaModificationP> mod_list;