use peptide table model

src/gui/peptide_list_view/peptidetablemodel.cpp

@@ -29,6 +29,27 @@
 #include "../../core/labeling/label.h"
 
 
+PeptideTableModel::columnMap PeptideTableModel::_column_assignment = {
+    (std::int8_t)PeptideListColumn::checked,
+    (std::int8_t)PeptideListColumn::peptide_grouping_id,
+    (std::int8_t)PeptideListColumn::sample,
+    (std::int8_t)PeptideListColumn::scan,
+    (std::int8_t)PeptideListColumn::rt,
+    (std::int8_t)PeptideListColumn::charge,
+    (std::int8_t)PeptideListColumn::sequence,
+    (std::int8_t)PeptideListColumn::modifs,
+    (std::int8_t)PeptideListColumn::label,
+    (std::int8_t)PeptideListColumn::start,
+    (std::int8_t)PeptideListColumn::length,
+    (std::int8_t)PeptideListColumn::used,
+    (std::int8_t)PeptideListColumn::subgroups,
+    (std::int8_t)PeptideListColumn::Evalue,
+    (std::int8_t)PeptideListColumn::theoretical_mhplus,
+    (std::int8_t)PeptideListColumn::delta_mhplus,
+    (std::int8_t)PeptideListColumn::hyperscore
+};
+
+
 PeptideTableModel::PeptideTableModel(QObject *parent)
     :QAbstractTableModel(parent)
 {
@@ -70,48 +91,18 @@ int PeptideTableModel::columnCount(const QModelIndex &parent ) const {
 }
 QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
 {
-    if (role == Qt::DisplayRole)
-    {
-        if (orientation == Qt::Horizontal) {
-            switch (section)
-            {
-            case 0:
-                return QString("checked");
-            case 1:
-                return QString("peptide ID");
-            case 2:
-                return QString("sample");
-            case 3:
-                return QString("scan");
-            case 4:
-                return QString("RT");
-            case 5:
-                return QString("charge");
-            case 6:
-                return QString("sequence");
-            case 7:
-                return QString("modifs");
-            case 8:
-                return QString("label");
-            case 9:
-                return QString("start");
-            case 10:
-                return QString("length");
-            case 11:
-                return QString("used");
-            case 12:
-                return QString("subgroups");
-            case 13:
-                return QString("Evalue");
-            case 14:
-                return QString("theoretical MH+");
-            case 15:
-                return QString("delta MH+");
-            case 16:
-                return QString("hyperscore");
-            }
+    if (orientation == Qt::Horizontal) {
+        switch (role) {
+        case Qt::DisplayRole :
+            return QVariant(getTitle(_column_assignment [section]));
+            break;
+        case Qt::ToolTipRole :
+            return QVariant(getDescription(_column_assignment [section]));
+            break;
+
         }
     }
+//if (_p_peptide_list_window->getProjectWindow()->getProjectP()->getLabelingMethodSp().get() == nullptr) {
     return QVariant();
 }
 QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
@@ -144,73 +135,74 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
         if (_p_protein_match == nullptr) {
         }
         else {
-
-            if (col == 0) {
+            pappso::GrpPeptide * p_grp_peptide;
+            const Label * p_label;
+            GroupingGroup * p_grp;
+            switch (_column_assignment[col]) {
+            case (std::int8_t)PeptideListColumn::checked:
                 return QVariant();
-            }
-            if (col == 1) {
-                pappso::GrpPeptide * p_grp_peptide = _p_protein_match->getPeptideMatchList().at(row)->getGrpPeptideSp().get();
+                break;
+
+            case (std::int8_t)PeptideListColumn::peptide_grouping_id:
+                p_grp_peptide = _p_protein_match->getPeptideMatchList().at(row)->getGrpPeptideSp().get();
                 if (p_grp_peptide != nullptr) return p_grp_peptide->getGroupingId();
                 return QVariant();
-            }
-            if (col == 2) {
+                break;
+            case (std::int8_t)PeptideListColumn::sample:
                 return _p_protein_match->getPeptideMatchList().at(row)->getIdentificationDataSource()->getSampleName();
-            }
-            if (col == 3) {
+                break;
+            case (std::int8_t)PeptideListColumn::scan:
                 return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row)->getScan());
-            }
-            if (col == 4) {
+                break;
+            case (std::int8_t)PeptideListColumn::rt:
                 return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getRetentionTime());
-            }
-            if (col == 5) {
+                break;
+            case (std::int8_t)PeptideListColumn::charge:
                 return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getCharge());
-            }
-            if (col ==6) {
+                break;
+            case (std::int8_t)PeptideListColumn::sequence:
                 return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getSequence();
-            }
-            if (col ==7) {
+                break;
+            case (std::int8_t)PeptideListColumn::modifs:
                 return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getModifString();
-            }
-            if (col ==8) {//label
-                const Label * p_label = _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getLabel();
+                break;
+            case (std::int8_t)PeptideListColumn::label:
+                p_label = _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getLabel();
                 if (p_label != nullptr) {
                     return QVariant(p_label->getXmlId());
                 }
                 else {
                     return QVariant();
                 }
-            }
-            if (col ==9) {
+                break;
+            case (std::int8_t)PeptideListColumn::start:
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getStart()+1);
-            }
-            if (col ==10) {
+                break;
+            case (std::int8_t)PeptideListColumn::length:
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->size());
-            }
-            if (col ==11) {
-                GroupingGroup * p_grp = _p_protein_match->getGroupingGroupSp().get();
+                break;
+            case (std::int8_t)PeptideListColumn::used:
+                p_grp = _p_protein_match->getGroupingGroupSp().get();
                 if (p_grp != nullptr) return QVariant((qreal)  p_grp->countSubgroupPresence(_p_protein_match->getPeptideMatchList().at(row)));
                 return QVariant();
-            }
-            if (col ==12) {
-                GroupingGroup * p_grp = _p_protein_match->getGroupingGroupSp().get();
+                break;
+            case (std::int8_t)PeptideListColumn::subgroups:
+                p_grp = _p_protein_match->getGroupingGroupSp().get();
                 if (p_grp != nullptr) return QVariant( p_grp->getSubgroupIdList(_p_protein_match->getPeptideMatchList().at(row)).join(" "));
                 return QVariant();
-            }
-            if (col ==13) {
+                break;
+            case (std::int8_t)PeptideListColumn::Evalue:
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getEvalue());
-            }
-
-            if (col ==14) {
+                break;
+            case (std::int8_t)PeptideListColumn::theoretical_mhplus:
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getMz(1));
-
-            }
-            if (col ==15) {
+                break;
+            case (std::int8_t)PeptideListColumn::delta_mhplus:
                 return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row)->getDeltaMass());
-
-            }
-            if (col ==16) {
+                break;
+            case (std::int8_t)PeptideListColumn::hyperscore:
                 return _p_protein_match->getPeptideMatchList().at(row)->getParam(PeptideMatchParam::tandem_hyperscore);
-
+                break;
             }
         }
         return QString("Row%1, Column%2")
@@ -244,3 +236,136 @@ void PeptideTableModel::onPeptideDataChanged() {
     emit layoutAboutToBeChanged();
     emit layoutChanged();
 }
+
+
+
+const QString PeptideTableModel::getTitle(PeptideListColumn column) {
+    qDebug() << "PeptideTableModel::getTitle begin ";
+    return PeptideTableModel::getTitle((std::int8_t) column);
+    //qDebug() << "ProteinTableModel::getTitle end ";
+}
+const QString PeptideTableModel::getDescription(PeptideListColumn column) {
+    qDebug() << "PeptideTableModel::columnCount begin ";
+    return PeptideTableModel::getDescription((std::int8_t) column);
+    //qDebug() << "ProteinTableModel::columnCount end ";
+}
+
+const QString PeptideTableModel::getTitle(std::int8_t column) {
+
+    qDebug() << "PeptideTableModel::getTitle begin " << column;
+    switch (column) {
+
+    case (std::int8_t) PeptideListColumn::checked:
+        return "checked";
+        break;
+    case (std::int8_t) PeptideListColumn::peptide_grouping_id:
+        return "peptide ID";
+        break;
+    case (std::int8_t) PeptideListColumn::sample:
+        return "sample";
+        break;
+    case (std::int8_t) PeptideListColumn::scan:
+        return "scan";
+        break;
+    case (std::int8_t) PeptideListColumn::rt:
+        return "RT";
+        break;
+    case (std::int8_t) PeptideListColumn::charge:
+        return "charge";
+        break;
+    case (std::int8_t) PeptideListColumn::sequence:
+        return "sequence";
+        break;
+    case (std::int8_t) PeptideListColumn::modifs:
+        return "modifs";
+        break;
+    case (std::int8_t) PeptideListColumn::label:
+        return "label";
+        break;
+    case (std::int8_t) PeptideListColumn::start:
+        return "start";
+        break;
+    case (std::int8_t) PeptideListColumn::length:
+        return "length";
+        break;
+    case (std::int8_t) PeptideListColumn::used:
+        return "used";
+        break;
+    case (std::int8_t) PeptideListColumn::subgroups:
+        return "subgroups";
+        break;
+    case (std::int8_t) PeptideListColumn::Evalue:
+        return "Evalue";
+        break;
+    case (std::int8_t) PeptideListColumn::theoretical_mhplus:
+        return "theoretical MH+";
+        break;
+    case (std::int8_t) PeptideListColumn::delta_mhplus:
+        return "delta MH+";
+        break;
+    case (std::int8_t) PeptideListColumn::hyperscore:
+        return "hyperscore";
+    }
+    return "";
+}
+
+const QString PeptideTableModel::getDescription(std::int8_t column) {
+
+    qDebug() << "ProteinTableModel::getDescription begin " << column;
+    switch (column) {
+
+    case (std::int8_t) PeptideListColumn::checked:
+        return "manual protein check";
+        break;
+
+    case (std::int8_t) PeptideListColumn::peptide_grouping_id:
+        return "unique peptide identifier within this grouping experiment";
+        break;
+    case (std::int8_t) PeptideListColumn::sample:
+        return "MS sample name";
+        break;
+    case (std::int8_t) PeptideListColumn::scan:
+        return "scan number";
+        break;
+    case (std::int8_t) PeptideListColumn::rt:
+        return "retention time in seconds";
+        break;
+    case (std::int8_t) PeptideListColumn::charge:
+        return "peptide charge";
+        break;
+    case (std::int8_t) PeptideListColumn::sequence:
+        return "peptide sequence";
+        break;
+    case (std::int8_t) PeptideListColumn::modifs:
+        return "peptide modifications";
+        break;
+    case (std::int8_t) PeptideListColumn::label:
+        return "peptide label";
+        break;
+    case (std::int8_t) PeptideListColumn::start:
+        return "peptide start position on protein";
+        break;
+    case (std::int8_t) PeptideListColumn::length:
+        return "peptide length";
+        break;
+    case (std::int8_t) PeptideListColumn::used:
+        return "used";
+        break;
+    case (std::int8_t) PeptideListColumn::subgroups:
+        return "subgroups";
+        break;
+    case (std::int8_t) PeptideListColumn::Evalue:
+        return "peptide Evalue";
+        break;
+    case (std::int8_t) PeptideListColumn::theoretical_mhplus:
+        return "peptide theoretical MH+";
+        break;
+    case (std::int8_t) PeptideListColumn::delta_mhplus:
+        return "peptide mass difference betwenn observed mass and theoretical mass";
+        break;
+    case (std::int8_t) PeptideListColumn::hyperscore:
+        return "X!Tandem hyperscore";
+
+    }
+    return "";
+}

src/gui/peptide_list_view/peptidetablemodel.h

@@ -26,6 +26,31 @@
 #include <QAbstractTableModel>
 #include "../../core/project.h"
 
+
+/** \def PeptideListColumn list of available fields to display in peptide list
+ *
+ */
+
+enum class PeptideListColumn {
+    checked, ///< manual checked
+    peptide_grouping_id, ///< manual checked
+    sample,
+    scan,
+    rt,
+    charge,
+    sequence,
+    modifs,
+    label,
+    start,
+    length,
+    used,
+    subgroups,
+    Evalue,
+    theoretical_mhplus,
+    delta_mhplus,
+    hyperscore
+};
+
 class PeptideTableModel;
 
 class PeptideTableModel: public QAbstractTableModel
@@ -38,9 +63,12 @@ public:
     QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
     QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
 
+    static const QString getTitle(PeptideListColumn column);
+    static const QString getDescription(PeptideListColumn column);
 
     void setProteinMatch(ProteinMatch * p_protein_match);
     ProteinMatch * getProteinMatch();
+    using columnMap = std::int8_t[30];
 signals:
     void peptideMatchClicked(PeptideMatch * p_peptide_match);
 
@@ -49,8 +77,12 @@ public slots:
 public slots:
     void onTableClicked(const QModelIndex &index);
 
+private :
+    static const QString getTitle(std::int8_t column);
+    static const QString getDescription(std::int8_t column);
 private :
     ProteinMatch * _p_protein_match= nullptr;
+    static columnMap _column_assignment;
 };
 
 #endif // PEPTIDETABLEMODEL_H

src/gui/peptide_list_view/peptidetableproxymodel.cpp

@@ -35,7 +35,7 @@ PeptideTableProxyModel::PeptideTableProxyModel(PeptideListWindow * p_peptide_lis
 }
 
 bool PeptideTableProxyModel::filterAcceptsColumn(int source_column, const QModelIndex & source_parent) const {
-    if (source_column == 8) {
+    if (source_column == (std::int8_t)PeptideListColumn::label) {
         if (_p_peptide_list_window->getProjectWindow()->getProjectP()->getLabelingMethodSp().get() == nullptr) {
             return false;
         }
@@ -157,21 +157,10 @@ bool PeptideTableProxyModel::lessThan(const QModelIndex & left, const QModelInde
 
 QVariant PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation, int role) const
 {
-    if (role == Qt::DisplayRole)
-    {
-        if (orientation == Qt::Horizontal) {
-            if (_p_peptide_list_window->getProjectWindow()->getProjectP()->getLabelingMethodSp().get() == nullptr) {
-                if (section > 7) {
-                    section = section+1;
-                }
-                return sourceModel()->headerData(section, orientation, role);
-        }
-            else {
-                return sourceModel()->headerData(section, orientation, role);
-            }
-        }
-    }
-    return QVariant();
+    int col = mapToSource(index(0,section)).column();
+    
+    return sourceModel()->headerData(col, orientation,
+                                     role);
 }
 
 void PeptideTableProxyModel::hideNotValid(bool hide) {
@@ -193,3 +182,4 @@ void PeptideTableProxyModel::setSearchOn(QString search_on) {
 void PeptideTableProxyModel::setPeptideSearchString(QString peptide_search_string) {
     _peptide_search_string = peptide_search_string;
 }
+

src/gui/protein_list_view/proteintablemodel.h

@@ -66,7 +66,7 @@ public:
 
     void setIdentificationGroup(IdentificationGroup * p_identification_group);
     IdentificationGroup * getIdentificationGroup();
-    using columnMap = std::int8_t[20];
+    using columnMap = std::int8_t[30];
     
 public slots:
     void onProteinDataChanged();

src/resources/catalog_label.xml

@@ -12,4 +12,5 @@
     		<mod at="Nter" value="36.0" acc="MOD:00638"/>
     		<mod at="K" value="36.0" acc="MOD:00638"/>
     	</isotope_label>
+    </isotope_label_list>
 </catalog>

src/utils/identificationdatasourcestore.cpp

@@ -54,7 +54,7 @@ IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QStr
         QFileInfo location_file(location);
         QString ext = location_file.suffix();
         //QString sample_name = location_file.baseName();
-        IdentificationDataSourceSp p_identfile;
+        IdentificationDataSourceSp p_identfile = nullptr;
         if (ext.toLower() == "xml") {
             //X!Tandem result file
             p_identfile = std::make_shared<IdentificationXtandemFile>(location_file);