ptm group ok. trying to sort it

src/grouping/ptm/ptmgroupingexperiment.cpp

@@ -72,7 +72,23 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
 
 }
 
+void PtmGroupingExperiment::numbering() {
+  std::sort(_ptm_island_group_list.begin(), _ptm_island_group_list.end(),[](const PtmIslandGroupSp a, const PtmIslandGroupSp b)
+        {
+            return  a.get() < b.get();
+        });
+}
 void PtmGroupingExperiment::startGrouping() {
+    //we have a list of ptm island subgroups to group :
+    for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
+        if (std::none_of(_ptm_island_group_list.begin(), _ptm_island_group_list.end(), [ptm_island_subgroup](PtmIslandGroupSp element) {
+        return element.get()->mergePtmIslandSubgroupSp(ptm_island_subgroup);
+        })) {
+            //create a new group
+            _ptm_island_group_list.push_back(std::make_shared<PtmIslandGroup>(ptm_island_subgroup));
+        }
+    }
+    numbering();
 }
 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) {

src/grouping/ptm/ptmgroupingexperiment.h

@@ -50,6 +50,7 @@ private:
     
     std::vector< PtmIslandSp > mergePeptideMatchPtmIslandList(vector< PtmIslandSp > ptm_island_list);
     void addPtmIsland(PtmIslandSp ptm_island);
+    void numbering();
 private:
     std::list<pappso::AaModificationP> _modification_list;
     ValidationState _peptide_validation_state = ValidationState::validAndChecked;

src/grouping/ptm/ptmisland.cpp

@@ -44,6 +44,9 @@ PtmIsland::~PtmIsland()
 
 }
 
+const ProteinMatch * PtmIsland::getProteinMatch() const {
+    return _protein_match_p;
+}
 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) {

src/grouping/ptm/ptmisland.h

@@ -55,6 +55,7 @@ public:
     
     bool containsPeptideMatch(const PeptideMatch* element) const;
     std::vector<std::size_t> getSampleScanSet() const;
+    const ProteinMatch * getProteinMatch() const;
 private:
     const ProteinMatch * _protein_match_p;
     std::vector<const PeptideMatch *> _peptide_match_list;

src/grouping/ptm/ptmislandgroup.cpp

@@ -29,17 +29,45 @@
 
 #include "ptmislandgroup.h"
 
-PtmIslandGroup::PtmIslandGroup()
+PtmIslandGroup::PtmIslandGroup(PtmIslandSubgroupSp ptm_island_subgroup_sp)
 {
-
+    _ptm_island_subgroup_list.push_back(ptm_island_subgroup_sp);
 }
 
 PtmIslandGroup::PtmIslandGroup(const PtmIslandGroup& other)
 {
-
+    _ptm_island_subgroup_list = other._ptm_island_subgroup_list;
 }
 
 PtmIslandGroup::~PtmIslandGroup()
 {
 
 }
+
+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());
+        }
+    }
+    else {
+        return (_ptm_island_subgroup_list.size() < other._ptm_island_subgroup_list.size());
+    }
+}
+
+
+bool PtmIslandGroup::mergePtmIslandSubgroupSp(PtmIslandSubgroupSp ptm_island_subgroup_sp) {
+
+    //http://en.cppreference.com/w/cpp/algorithm/all_any_none_of
+    if (std::any_of(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [ptm_island_subgroup_sp](PtmIslandSubgroupSp element) {
+    return element.get()->containsProteinMatchFrom( ptm_island_subgroup_sp.get());
+    })) {
+        //accept this subgroup
+        _ptm_island_subgroup_list.push_back(ptm_island_subgroup_sp);
+        return true;
+    }
+    return false;
+}

src/grouping/ptm/ptmislandgroup.h

@@ -31,6 +31,7 @@
 #define PTMISLANDGROUP_H
 
 #include <memory>
+#include "ptmislandsubgroup.h"
 
 class PtmIslandGroup;
 
@@ -42,9 +43,16 @@ typedef std::shared_ptr<PtmIslandGroup> PtmIslandGroupSp;
 class PtmIslandGroup
 {
 public:
-    PtmIslandGroup();
+    PtmIslandGroup(PtmIslandSubgroupSp ptm_island_subgroup_sp);
     PtmIslandGroup(const PtmIslandGroup& other);
     ~PtmIslandGroup();
+    /** @brief merge with the given ptm island subgroup if at least one protein is shared
+    * */
+    bool mergePtmIslandSubgroupSp(PtmIslandSubgroupSp ptm_island_subgroup_sp);
+
+private :
+    std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
+    unsigned int _group_number;
 };
 
 #endif // PTMISLANDGROUP_H

src/grouping/ptm/ptmislandsubgroup.cpp

@@ -47,6 +47,18 @@ PtmIslandSubgroup::~PtmIslandSubgroup()
 
 }
 
+
+bool PtmIslandSubgroup::containsProteinMatchFrom(PtmIslandSubgroup* ptm_island_subgroup_p) {
+  for (PtmIslandSp ptm_island_sp :_ptm_island_list) {
+    if (std::any_of(ptm_island_subgroup_p->_ptm_island_list.begin(), ptm_island_subgroup_p->_ptm_island_list.end(), [ptm_island_sp](PtmIslandSp element) {
+        return (element.get()->getProteinMatch() == ptm_island_sp.get()->getProteinMatch());
+        })) {
+            return true;
+        }
+  }
+  return false;
+}
+
 bool PtmIslandSubgroup::mergePtmIslandSp(PtmIslandSp ptm_island_sp) {
     if (_sample_scan_set == ptm_island_sp.get()->getSampleScanSet()) {
         //merge

src/grouping/ptm/ptmislandsubgroup.h

@@ -50,6 +50,7 @@ public:
     /** @brief merge with the given ptm island if all sample scans are shared
     * */
     bool mergePtmIslandSp(PtmIslandSp ptm_island_sp);
+    bool containsProteinMatchFrom(PtmIslandSubgroup* ptm_island_subgroup_p);
 
 private:
     std::vector< PtmIslandSp > _ptm_island_list;