sorting and numbering ptm islands

src/grouping/ptm/ptmgroupingexperiment.cpp

@@ -75,8 +75,14 @@ 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();
+            return  *(a.get()) < *(b.get());
         });
+  
+  unsigned int number=0;
+  for (PtmIslandGroupSp ptm_island_group:_ptm_island_group_list) {
+      number ++;
+      ptm_island_group.get()->setGroupNumber(number);
+  }
 }
 void PtmGroupingExperiment::startGrouping() {
     //we have a list of ptm island subgroups to group :

src/grouping/ptm/ptmisland.cpp

@@ -76,6 +76,10 @@ void PtmIsland::addPeptideMatch(const PeptideMatch* p_peptide_match) {
     }
 }
 
+unsigned int PtmIsland::getProteinStartPosition() const {
+    return _protein_start;
+}
+
 bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
     if (std::none_of(_peptide_match_list.begin(), _peptide_match_list.end(), [ptm_island_sp](const PeptideMatch* element) {
     return ptm_island_sp.get()->containsPeptideMatch(element);

src/grouping/ptm/ptmisland.h

@@ -56,6 +56,8 @@ public:
     bool containsPeptideMatch(const PeptideMatch* element) const;
     std::vector<std::size_t> getSampleScanSet() const;
     const ProteinMatch * getProteinMatch() const;
+    unsigned int getProteinStartPosition() const;
+    
 private:
     const ProteinMatch * _protein_match_p;
     std::vector<const PeptideMatch *> _peptide_match_list;

src/grouping/ptm/ptmislandgroup.cpp

@@ -44,6 +44,35 @@ PtmIslandGroup::~PtmIslandGroup()
 
 }
 
+QString PtmIslandGroup::getFirstAccession() const {
+    if (_ptm_island_subgroup_list.size() == 0) return QString();
+    QStringList accession_list;
+    for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
+        for (PtmIslandSp ptm_island: ptm_island_subgroup.get()->getPtmIslandList()) {
+            accession_list << ptm_island.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession();
+        }
+    }
+    accession_list.sort();
+
+    return accession_list[0];
+}
+
+void PtmIslandGroup::setGroupNumber(unsigned int number) {
+    _group_number = number;
+    for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
+        ptm_island_subgroup.get()->setPtmIslandGroup(this);
+    }
+    std::sort(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [](const PtmIslandSubgroupSp& a, const PtmIslandSubgroupSp& b)
+    {
+        return  (a.get()->getFirstPtmIsland()->getProteinStartPosition() < b.get()->getFirstPtmIsland()->getProteinStartPosition());
+    });
+
+    unsigned int sg_number=0;
+    for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
+        sg_number ++;
+        ptm_island_subgroup.get()->setSubgroupNumber(sg_number);
+    }
+}
 bool PtmIslandGroup::operator<(const PtmIslandGroup& other) const {
     if (_ptm_island_subgroup_list.size() == other._ptm_island_subgroup_list.size()) {
         if (maxCountSampleScan() == other.maxCountSampleScan()) {
@@ -57,7 +86,13 @@ bool PtmIslandGroup::operator<(const PtmIslandGroup& other) const {
         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)
+    {
+        return  (a.get()->countSampleScan() < b.get()->countSampleScan());
+    });
+    return it_result->get()->countSampleScan();
+}
 
 bool PtmIslandGroup::mergePtmIslandSubgroupSp(PtmIslandSubgroupSp ptm_island_subgroup_sp) {
 

src/grouping/ptm/ptmislandgroup.h

@@ -46,9 +46,14 @@ public:
     PtmIslandGroup(PtmIslandSubgroupSp ptm_island_subgroup_sp);
     PtmIslandGroup(const PtmIslandGroup& other);
     ~PtmIslandGroup();
+    bool operator<(const PtmIslandGroup& other) const;
     /** @brief merge with the given ptm island subgroup if at least one protein is shared
     * */
     bool mergePtmIslandSubgroupSp(PtmIslandSubgroupSp ptm_island_subgroup_sp);
+    
+    unsigned int maxCountSampleScan() const;
+    QString getFirstAccession() const;
+    void setGroupNumber(unsigned int number);
 
 private :
     std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;

src/grouping/ptm/ptmislandsubgroup.cpp

@@ -46,17 +46,35 @@ PtmIslandSubgroup::~PtmIslandSubgroup()
 {
 
 }
+const PtmIsland * PtmIslandSubgroup::getFirstPtmIsland() const {
+    return _ptm_island_list.begin()->get();
+}
 
-
+void PtmIslandSubgroup::setSubgroupNumber(unsigned int number) {
+    _subgroup_number = number;
+}
+void PtmIslandSubgroup::setPtmIslandGroup(PtmIslandGroup * p_ptm_island_group) {
+    _ptm_island_group_p = p_ptm_island_group;
+    std::sort(_ptm_island_list.begin(), _ptm_island_list.end(), [](const PtmIslandSp& a, const PtmIslandSp& b)
+    {
+        return  (a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() < b.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
+    });
+}
+const std::vector< PtmIslandSp > & PtmIslandSubgroup::getPtmIslandList() const {
+    return _ptm_island_list;
+}
+unsigned int PtmIslandSubgroup::countSampleScan() const {
+    return _sample_scan_set.size();
+}
 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) {
+    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;
+    }
+    return false;
 }
 
 bool PtmIslandSubgroup::mergePtmIslandSp(PtmIslandSp ptm_island_sp) {

src/grouping/ptm/ptmislandsubgroup.h

@@ -39,6 +39,7 @@ class PtmIslandSubgroup;
  */
 typedef std::shared_ptr<PtmIslandSubgroup> PtmIslandSubgroupSp;
 
+class PtmIslandGroup;
 
 class PtmIslandSubgroup
 {
@@ -51,10 +52,21 @@ public:
     * */
     bool mergePtmIslandSp(PtmIslandSp ptm_island_sp);
     bool containsProteinMatchFrom(PtmIslandSubgroup* ptm_island_subgroup_p);
+    
+    unsigned int countSampleScan() const;
+    
+    const std::vector< PtmIslandSp > & getPtmIslandList() const;
+    
+    void setPtmIslandGroup(PtmIslandGroup * p_ptm_island_group);
+    
+    const PtmIsland * getFirstPtmIsland() const;
+    void setSubgroupNumber(unsigned int number);
 
 private:
     std::vector< PtmIslandSp > _ptm_island_list;
     std::vector<std::size_t> _sample_scan_set;
+    PtmIslandGroup * _ptm_island_group_p = nullptr;
+    unsigned int _subgroup_number;
 
 };