start and size of ptm islands

src/grouping/ptm/ptmisland.cpp

@@ -48,6 +48,12 @@ PtmIsland::~PtmIsland()
 {
 
 }
+unsigned int PtmIsland::getStart() const {
+    return _protein_start;
+}
+unsigned int PtmIsland::size() const {
+    return _protein_stop - _protein_start;
+}
 
 unsigned int PtmIsland::countSampleScanMultiPtm(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
     std::set<std::size_t> sample_scan_list;
@@ -110,7 +116,16 @@ void PtmIsland::addPeptideMatch(const PeptideMatch* p_peptide_match) {
     if (_position_list.size()==1) {
         unsigned int position = _position_list[0];
         if (p_peptide_match->containsPosition(position)) {
+            if (_peptide_match_list.size() == 0) {
+                _protein_start = p_peptide_match->getStart();
+            }
             _peptide_match_list.push_back(p_peptide_match);
+	    if (p_peptide_match->getStart() < _protein_start) {
+	      _protein_start = p_peptide_match->getStart();
+	    }
+	    if (p_peptide_match->getStop() > _protein_stop) {
+	      _protein_stop = p_peptide_match->getStop();
+	    }
         }
     }
     else {

src/grouping/ptm/ptmisland.h

@@ -50,25 +50,28 @@ public:
     PtmIsland(const PtmIsland & other);
     ~PtmIsland();
     void addPeptideMatch(const PeptideMatch* p_peptide_match);
-    
+
     /** @brief merge with the given ptm island if there is at least one common peptide match
      * */
     bool merge(PtmIslandSp ptm_island_sp);
-    
+
     bool containsPeptideMatch(const PeptideMatch* element) const;
     std::vector<std::size_t> getSampleScanSet() const;
     const ProteinMatch * getProteinMatch() const;
     unsigned int getProteinStartPosition() const;
     void setPtmIslandSubgroup(PtmIslandSubgroup* p_ptm_island_subgroup);
     void setProteinNumber(unsigned int prot_number);
-    
-    
+
+
     const QString getGroupingId() const;
     const std::vector<unsigned int> & getPositionList() const;
     const PtmIslandSubgroup * getPtmIslandSubroup() const;
     unsigned int countSequence() const;
     unsigned int countSampleScanMultiPtm(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
-    
+
+    unsigned int getStart() const;
+    unsigned int size() const;
+
 private:
     const ProteinMatch * _protein_match_p;
     std::vector<const PeptideMatch *> _peptide_match_list;

src/grouping/ptm/ptmislandgroup.cpp

@@ -77,17 +77,17 @@ void PtmIslandGroup::setGroupNumber(unsigned int number) {
     }
 }
 bool PtmIslandGroup::operator<(const PtmIslandGroup& other) const {
-    if (_ptm_island_subgroup_list.size() == other._ptm_island_subgroup_list.size()) {
-        if (maxCountSampleScan() == other.maxCountSampleScan()) {
-            return (getFirstAccession() < other.getFirstAccession());
-        }
-        else {
-            return (maxCountSampleScan() < other.maxCountSampleScan());
-        }
+    //if (_ptm_island_subgroup_list.size() == other._ptm_island_subgroup_list.size()) {
+    if (maxCountSampleScan() == other.maxCountSampleScan()) {
+        return (getFirstAccession() < other.getFirstAccession());
     }
     else {
-        return (_ptm_island_subgroup_list.size() < other._ptm_island_subgroup_list.size());
+        return (maxCountSampleScan() > other.maxCountSampleScan());
     }
+    //}
+    //else {
+    //    return (_ptm_island_subgroup_list.size() < other._ptm_island_subgroup_list.size());
+    //}
 }
 unsigned int PtmIslandGroup::maxCountSampleScan() const {
     std::vector<PtmIslandSubgroupSp>::const_iterator it_result = std::max_element(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [](const PtmIslandSubgroupSp &  a, const PtmIslandSubgroupSp & b)

src/gui/ptm_island_list_view/ptmislandtablemodel.cpp

@@ -39,7 +39,9 @@ PtmIslandTableModel::columnMap PtmIslandTableModel::_column_assignment = {
     (std::int8_t)PtmIslandListColumn::spectrum,
     (std::int8_t)PtmIslandListColumn::sequence,
     (std::int8_t)PtmIslandListColumn::ptm_position_list,
-    (std::int8_t)PtmIslandListColumn::multiptm
+    (std::int8_t)PtmIslandListColumn::multiptm,
+    (std::int8_t)PtmIslandListColumn::ptm_island_start,
+    (std::int8_t)PtmIslandListColumn::ptm_island_length
 };
 
 
@@ -54,30 +56,36 @@ PtmIslandTableModel::~PtmIslandTableModel()
 }
 const QString PtmIslandTableModel::getTitle(std::int8_t column) const {
     switch (column) {
-            
-      case (std::int8_t) PtmIslandListColumn::spectrum:
-	    return "spectrum";
-	break;
-    
-	  case (std::int8_t) PtmIslandListColumn::description:
-            return "description";
-	break; 
-	  case (std::int8_t) PtmIslandListColumn::multiptm:
-            return "multi PTM";
-	break; 
-      case (std::int8_t) PtmIslandListColumn::sequence:
-	    return "sequence";
-	break;
-	  case (std::int8_t) PtmIslandListColumn::ptm_island_id:
-            return "PTM island ID";
-	break;
-	  case (std::int8_t) PtmIslandListColumn::accession:
-            return "accession";
-	break; 
-	  case (std::int8_t) PtmIslandListColumn::ptm_position_list:
-	    return "ptm positions";
-
-	}
+
+    case (std::int8_t) PtmIslandListColumn::spectrum:
+        return "spectrum";
+        break;
+
+    case (std::int8_t) PtmIslandListColumn::description:
+        return "description";
+        break;
+    case (std::int8_t) PtmIslandListColumn::multiptm:
+        return "multi PTM";
+        break;
+    case (std::int8_t) PtmIslandListColumn::sequence:
+        return "sequence";
+        break;
+    case (std::int8_t) PtmIslandListColumn::ptm_island_id:
+        return "PTM island ID";
+        break;
+    case (std::int8_t) PtmIslandListColumn::accession:
+        return "accession";
+        break;
+    case (std::int8_t) PtmIslandListColumn::ptm_position_list:
+        return "ptm positions";
+        break;
+    case (std::int8_t) PtmIslandListColumn::ptm_island_start:
+        return "start";
+        break;
+    case (std::int8_t) PtmIslandListColumn::ptm_island_length:
+        return "length";
+
+    }
     return "";
 }
 void PtmIslandTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
@@ -91,9 +99,10 @@ void PtmIslandTableModel::setIdentificationGroup(IdentificationGroup * p_identif
     endResetModel();
 }
 const PtmGroupingExperiment * PtmIslandTableModel::getPtmGroupingExperiment() const {
-  if (_p_identification_group == nullptr) {return nullptr;
-  }
-  return _p_identification_group->getPtmGroupingExperiment();
+    if (_p_identification_group == nullptr) {
+        return nullptr;
+    }
+    return _p_identification_group->getPtmGroupingExperiment();
 }
 int PtmIslandTableModel::rowCount(const QModelIndex &parent ) const {
     //qDebug() << "ProteinTableModel::rowCount begin ";
@@ -106,7 +115,7 @@ int PtmIslandTableModel::rowCount(const QModelIndex &parent ) const {
 int PtmIslandTableModel::columnCount(const QModelIndex &parent ) const {
     //qDebug() << "ProteinTableModel::columnCount begin ";
     if (getPtmGroupingExperiment() != nullptr) {
-        return 7;
+        return 9;
     }
     return 0;
 }
@@ -116,9 +125,9 @@ QVariant PtmIslandTableModel::headerData(int section, Qt::Orientation orientatio
     if (orientation == Qt::Horizontal)
     {
         if (role == Qt::DisplayRole)
-            {
-                return QVariant(getTitle(_column_assignment [section]));
-            }
+        {
+            return QVariant(getTitle(_column_assignment [section]));
+        }
     }
     return QVariant();
 }
@@ -127,39 +136,45 @@ QVariant PtmIslandTableModel::data(const QModelIndex &index, int role ) const {
     if (getPtmGroupingExperiment() == nullptr) return QVariant();
     int row = index.row();
     int col = index.column();
-     switch(role) {
-        case Qt::DisplayRole:
+    switch(role) {
+    case Qt::DisplayRole:
         if (_p_identification_group == nullptr) {
             return QVariant();
         }
         switch (_column_assignment [col]) {
-            
-      case (std::int8_t) PtmIslandListColumn::spectrum:
-	    return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getPtmIslandSubroup()->countSampleScan());
-	break;
 
-	  case (std::int8_t) PtmIslandListColumn::description:
+        case (std::int8_t) PtmIslandListColumn::spectrum:
+            return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getPtmIslandSubroup()->countSampleScan());
+            break;
+
+        case (std::int8_t) PtmIslandListColumn::description:
             return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getProteinMatch()->getProteinXtpSp().get()->getDescription());
-	break; 
-	  case (std::int8_t) PtmIslandListColumn::multiptm:
+            break;
+        case (std::int8_t) PtmIslandListColumn::multiptm:
             return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->countSampleScanMultiPtm(getPtmGroupingExperiment()));
-	break; 
-      case (std::int8_t) PtmIslandListColumn::sequence:
-	    return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->countSequence());
-	break;
-	  case (std::int8_t) PtmIslandListColumn::ptm_island_id:
+            break;
+        case (std::int8_t) PtmIslandListColumn::sequence:
+            return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->countSequence());
+            break;
+        case (std::int8_t) PtmIslandListColumn::ptm_island_id:
             return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getGroupingId());
-	break;
-	  case (std::int8_t) PtmIslandListColumn::accession:
+            break;
+        case (std::int8_t) PtmIslandListColumn::accession:
             return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
-	break; 
-	  case (std::int8_t) PtmIslandListColumn::ptm_position_list:
-	    QStringList position_list;
-	    for (unsigned int position :getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getPositionList()) {
-	      position_list << QString("%1").arg(position+1);
-	    }
+            break;
+        case (std::int8_t) PtmIslandListColumn::ptm_island_start:
+            return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getStart());
+            break;
+        case (std::int8_t) PtmIslandListColumn::ptm_island_length:
+            return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->size());
+            break;
+        case (std::int8_t) PtmIslandListColumn::ptm_position_list:
+            QStringList position_list;
+            for (unsigned int position :getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getPositionList()) {
+                position_list << QString("%1").arg(position+1);
+            }
             return QVariant(position_list.join(" "));
-	}
+        }
     }
     return QVariant();
 }

src/gui/ptm_island_list_view/ptmislandtablemodel.h

@@ -33,7 +33,26 @@
 #include <QAbstractTableModel>
 #include "../../core/identificationgroup.h"
 #include "../../grouping/ptm/ptmgroupingexperiment.h"
-#include "../../utils/types.h"
+
+
+
+/** \def PtmIslandListColumn list of available fields to display in ptm island list
+ *
+ */
+
+enum class PtmIslandListColumn {
+     ptm_island_id, ///< ptm_island_id
+     accession, ///< protein accession
+     description, ///< protein description
+     ptm_position_list, ///< ptm position list
+     spectrum, ///< count sample scans
+     sequence, ///< unique sequence count
+     multiptm, ///< count multi ptm peptide match
+     ptm_island_start, ///< start position of the ptm island on the protein
+     ptm_island_length, ///< length of the ptm island
+     
+};
+
 
 class PtmIslandListWindow;
 class PtmIslandTableModel: public QAbstractTableModel

src/utils/types.h

@@ -113,20 +113,4 @@ enum class ProteinListColumn {
      pai, ///< PAI
 };
 
-
-/** \def PtmIslandListColumn list of available fields to display in ptm island list
- *
- */
-
-enum class PtmIslandListColumn {
-     ptm_island_id, ///< ptm_island_id
-     accession, ///< protein accession
-     description, ///< protein description
-     ptm_position_list, ///< ptm position list
-     spectrum, ///< count sample scans
-     sequence, ///< unique sequence count
-     multiptm, ///< count multi ptm peptide match
-     
-};
-
 #endif /* _TYPES_H_ */