diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 732c69e2653c974554d4ac3287e6283db4d560a7..215df8a89631f13f6c6a31d3cf65712e774fa3b8 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/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 {
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index f811f016e0d7aa270a57487ba6e4f19ddfbda754..2c29d0383b69591da4a12b62bb51912feda1b9b2 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/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;
diff --git a/src/grouping/ptm/ptmislandgroup.cpp b/src/grouping/ptm/ptmislandgroup.cpp
index c7cc921d3a7a7603e00d4a30c1e0d508db6a84b3..cf79ed89d7249fa83658a3bcec6ff0d13ea543ae 100644
--- a/src/grouping/ptm/ptmislandgroup.cpp
+++ b/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)
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index 97102a3a9261ed9b5d30d4dfbb40e142a422c021..52259a14f27fbdd3e2e18c89aab74b9ed877921f 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ 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();
}
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 808cca8d593ffc74c8a49653fb9a3161e7e52cce..c6eeda9b84df1bf86c2e4a1fa55e1af7a8b2ecc9 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/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
diff --git a/src/utils/types.h b/src/utils/types.h
index 38491498fdea23ae9979d9955e40313ebf177c3c..9bf617565658a83712b894d44a73cc3ed75252ad 100644
--- a/src/utils/types.h
+++ b/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_ */