diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 3c1b5405a4db9ace4e50444416d77f82d3460eef..22cc58a4dc5c0260ca564a9aa27232a4da064025 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/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 :
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 8bf6b8ff8aeb9959b76d6b31fb7fb3dd1b6e477d..2bb27540ef11fa6b716ba4b713956da44843443a 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/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);
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index 713ab5bbd93b8ef6941df5173d18f045de62269a..619e6572a1d01dc7d2748fa619c9ec26e0a69853 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/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;
diff --git a/src/grouping/ptm/ptmislandgroup.cpp b/src/grouping/ptm/ptmislandgroup.cpp
index 599eb66e27c2510a772ebbeccabae98481469334..b4abe62f9c51aed727ffe831abb79b1e0ba1743b 100644
--- a/src/grouping/ptm/ptmislandgroup.cpp
+++ b/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) {
diff --git a/src/grouping/ptm/ptmislandgroup.h b/src/grouping/ptm/ptmislandgroup.h
index 1507afd7bbc102c9359e9ddb1f9f4c02092f3d67..18038220e5f610a00a68fbdeb4893d90af4028b6 100644
--- a/src/grouping/ptm/ptmislandgroup.h
+++ b/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;
diff --git a/src/grouping/ptm/ptmislandsubgroup.cpp b/src/grouping/ptm/ptmislandsubgroup.cpp
index 423fa50e0a1913bfca405eade61b89f630dfb615..6a0d99e5f53e1605cfffcfee3a59ba8162952f83 100644
--- a/src/grouping/ptm/ptmislandsubgroup.cpp
+++ b/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) {
diff --git a/src/grouping/ptm/ptmislandsubgroup.h b/src/grouping/ptm/ptmislandsubgroup.h
index 862e71ae6d8a1f3b05370fa1fa1e63767fa3477f..4148fa31f83c5a55c8ec51a7888bab9b11f4bc6a 100644
--- a/src/grouping/ptm/ptmislandsubgroup.h
+++ b/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;
};