work on PTM islands : new ptm subgroup

src/CMakeLists.txt

@@ -70,6 +70,7 @@ SET(CPP_FILES
   grouping/groupingpeptidemass.cpp
   grouping/ptm/ptmgroupingexperiment.cpp
   grouping/ptm/ptmisland.cpp
+  grouping/ptm/ptmislandsubgroup.cpp
   gui/peptide_detail_view/spectrum_widget/spectrumpainter.cpp
   input/xpipsaxhandler.cpp
   input/xtandemsaxhandler.cpp

src/grouping/ptm/ptmgroupingexperiment.cpp

@@ -72,6 +72,15 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
 
 }
 
+void PtmGroupingExperiment::addPtmIsland(PtmIslandSp ptm_island_sp) {
+    if (std::none_of(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [ptm_island_sp](PtmIslandSubgroupSp element) {
+    return element.get()->mergePtmIslandSp(ptm_island_sp);
+    })) {
+        //create a new subgroup
+        _ptm_island_subgroup_list.push_back(std::make_shared<PtmIslandSubgroup>(ptm_island_sp));
+    }
+
+}
 void PtmGroupingExperiment::addProteinMatch(const ProteinMatch* p_protein_match) {
     if (p_protein_match->getValidationState() >= _peptide_validation_state) {
         std::vector< unsigned int > ptm_position_list = getPtmPositions(p_protein_match);
@@ -86,7 +95,10 @@ void PtmGroupingExperiment::addProteinMatch(const ProteinMatch* p_protein_match)
         }
 
         std::vector< PtmIslandSp > protein_ptm_islands = mergePeptideMatchPtmIslandList(ptm_island_list);
-	//=> ptm island subgroups (same set of sample scan numbers)
+        //=> ptm island subgroups (same set of sample scan numbers)
+        for (PtmIslandSp ptm_island:protein_ptm_islands) {
+            addPtmIsland(ptm_island);
+        }
     }
 }
 
@@ -101,7 +113,7 @@ std::vector< PtmIslandSp > PtmGroupingExperiment::mergePeptideMatchPtmIslandList
             new_ptm_island_list.push_back(ptm_island_sp);
         }
     }
-    
+
     return new_ptm_island_list;
 
 }

src/grouping/ptm/ptmgroupingexperiment.h

@@ -33,6 +33,7 @@
 #include "../../core/proteinmatch.h"
 #include <pappsomspp/amino_acid/aamodification.h>
 #include "ptmisland.h"
+#include "ptmislandsubgroup.h"
 
 class PtmGroupingExperiment
 {
@@ -46,9 +47,11 @@ private:
     std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
     
     std::vector< PtmIslandSp > mergePeptideMatchPtmIslandList(vector< PtmIslandSp > ptm_island_list);
+    void addPtmIsland(PtmIslandSp ptm_island);
 private:
     std::list<pappso::AaModificationP> _modification_list;
     ValidationState _peptide_validation_state = ValidationState::validAndChecked;
+    std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
 };
 
 #endif // PTMGROUPINGEXPERIMENT_H

src/grouping/ptm/ptmisland.cpp

@@ -43,6 +43,17 @@ PtmIsland::~PtmIsland()
 {
 
 }
+
+std::vector<std::size_t> PtmIsland::getSampleScanSet() const {
+    std::vector<std::size_t> sample_scan_set;
+    for (const PeptideMatch * p_peptide_match:_peptide_match_list) {
+        sample_scan_set.push_back(p_peptide_match->getHashSampleScan());
+    }
+
+    std::sort(sample_scan_set.begin(), sample_scan_set.end());
+    sample_scan_set.erase(std::unique(sample_scan_set.begin(), sample_scan_set.end()), sample_scan_set.end());
+    return sample_scan_set;
+}
 bool PtmIsland::containsPeptideMatch(const PeptideMatch* peptide_match) const {
 
     return std::any_of(_peptide_match_list.begin(), _peptide_match_list.end(), [peptide_match](const PeptideMatch* element) {

src/grouping/ptm/ptmisland.h

@@ -54,6 +54,7 @@ public:
     bool merge(PtmIslandSp ptm_island_sp);
     
     bool containsPeptideMatch(const PeptideMatch* element) const;
+    std::vector<std::size_t> getSampleScanSet() const;
 private:
     const ProteinMatch * _protein_match_p;
     std::vector<const PeptideMatch *> _peptide_match_list;

src/grouping/ptm/ptmprotein.cpp → src/grouping/ptm/ptmislandsubgroup.cpp

 /**
- * \file grouping/ptm/ptmprotein.cpp
- * \date 24/5/2017
+ * \file grouping/ptm/ptmislandsubgroup.cpp
+ * \date 29/5/2017
  * \author Olivier Langella
- * \brief PTM protein
+ * \brief object to group ptm islands sharing the same set of sample scans with different proteins
  */
 
 /*******************************************************************************
@@ -27,9 +27,31 @@
 *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
 ******************************************************************************/
 
-#include "ptmprotein.h"
+#include "ptmislandsubgroup.h"
 
-PtmProtein::PtmProtein(PtmGroupingExperiment * experiment, ProteinMatch * protein_match) {
-    _ptm_position_list = experiment->getPtmPositions(protein_match);
-    
+PtmIslandSubgroup::PtmIslandSubgroup(PtmIslandSp ptm_island_sp)
+{
+    _ptm_island_list.push_back(ptm_island_sp);
+    _sample_scan_set = ptm_island_sp.get()->getSampleScanSet();
+}
+
+PtmIslandSubgroup::PtmIslandSubgroup(const PtmIslandSubgroup& other)
+{
+    _ptm_island_list = other._ptm_island_list;
+    _sample_scan_set = other._sample_scan_set;
+
+}
+
+PtmIslandSubgroup::~PtmIslandSubgroup()
+{
+
+}
+
+bool PtmIslandSubgroup::mergePtmIslandSp(PtmIslandSp ptm_island_sp) {
+    if (_sample_scan_set == ptm_island_sp.get()->getSampleScanSet()) {
+        //merge
+        _ptm_island_list.push_back(ptm_island_sp);
+        return true;
+    }
+    return false;
 }

src/grouping/ptm/ptmprotein.h → src/grouping/ptm/ptmislandsubgroup.h

 /**
- * \file grouping/ptm/ptmprotein.h
- * \date 24/5/2017
+ * \file grouping/ptm/ptmislandsubgroup.h
+ * \date 29/5/2017
  * \author Olivier Langella
- * \brief PTM protein
+ * \brief object to group ptm islands sharing the same set of sample scans with different proteins
  */
 
 /*******************************************************************************
@@ -27,20 +27,34 @@
 *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
 ******************************************************************************/
 
-#ifndef PTMPROTEIN_H
-#define PTMPROTEIN_H
-
-#include "../../core/proteinmatch.h"
+#ifndef PTMISLANDSUBGROUP_H
+#define PTMISLANDSUBGROUP_H
+#include <memory>
 #include "ptmisland.h"
-#include "ptmgroupingexperiment.h"
 
-class PtmProtein
+
+class PtmIslandSubgroup;
+
+/** \brief shared pointer on a Peptide object
+ */
+typedef std::shared_ptr<PtmIslandSubgroup> PtmIslandSubgroupSp;
+
+
+class PtmIslandSubgroup
 {
 public:
-    PtmProtein(PtmGroupingExperiment * experiment, ProteinMatch * protein_match);
-    
+    PtmIslandSubgroup(PtmIslandSp ptm_island_sp);
+    PtmIslandSubgroup(const PtmIslandSubgroup& other);
+    ~PtmIslandSubgroup();
+
+    /** @brief merge with the given ptm island if all sample scans are shared
+    * */
+    bool mergePtmIslandSp(PtmIslandSp ptm_island_sp);
+
 private:
-    std::vector<unsigned int> _ptm_position_list;
+    std::vector< PtmIslandSp > _ptm_island_list;
+    std::vector<std::size_t> _sample_scan_set;
+
 };
 
-#endif // PTMPROTEIN_H
+#endif // PTMISLANDSUBGROUP_H