From 252e3a2f5001781dd3b547b7d0d7af59f6dcf2be Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 28 Mar 2017 11:11:25 +0200
Subject: [PATCH] count specific and specific unique
---
src/CMakeLists.txt | 2 +
src/core/identificationgroup.cpp | 15 ++-
src/core/proteinmatch.cpp | 18 +++
src/core/proteinmatch.h | 17 ++-
src/grouping/groupinggroup.cpp | 109 ++++++++++++++++++
src/grouping/groupinggroup.h | 51 ++++++++
.../protein_list_view/proteintablemodel.cpp | 32 +++--
src/utils/groupstore.cpp | 58 ++++++++++
src/utils/groupstore.h | 48 ++++++++
9 files changed, 333 insertions(+), 17 deletions(-)
create mode 100644 src/grouping/groupinggroup.cpp
create mode 100644 src/grouping/groupinggroup.h
create mode 100644 src/utils/groupstore.cpp
create mode 100644 src/utils/groupstore.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 15653c620..9bc5d36a9 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -65,8 +65,10 @@ SET(CPP_FILES
core/identification_sources/identificationxtandemfile.cpp
files/xpipfile.cpp
grouping/groupingexperiment.cpp
+ grouping/groupinggroup.cpp
grouping/groupingpeptidemass.cpp
input/xpipsaxhandler.cpp
+ utils/groupstore.cpp
utils/peptidestore.cpp
utils/proteinstore.cpp
utils/readspectrum.cpp
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index c4717b3ef..059fc9d65 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -23,6 +23,7 @@
#include "identificationgroup.h"
#include "project.h"
+#include "../utils/groupstore.h"
IdentificationGroup::IdentificationGroup(Project * project)
@@ -55,7 +56,7 @@ void IdentificationGroup::addMsRunIdSp(pappso::MsRunIdSp ms_run_sp) {
_ms_run_list.push_back(ms_run_sp);
}
const std::vector<pappso::MsRunIdSp> & IdentificationGroup::getMsRunIdSpList() const {
- return _ms_run_list;
+ return _ms_run_list;
}
std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
return _protein_match_list;
@@ -87,11 +88,13 @@ void IdentificationGroup::startGrouping (const GroupingType & grouping_type) {
}
_p_grp_experiment = GroupingExperiment::newInstance(grouping_type);
for (auto & p_protein_match : _protein_match_list) {
- p_protein_match->setGroupingExperiment(_p_grp_experiment);
+ p_protein_match->setGroupingExperiment(_p_grp_experiment);
}
-
+
_p_grp_experiment->startGrouping();
-
- //remove contaminant groups
- // renumbering
+ GroupStore group_store;
+ for (auto & p_protein_match : _protein_match_list) {
+ p_protein_match->setGroupInstance(group_store);
+ }
+
}
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 83871216e..ae009c04d 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -113,6 +113,10 @@ std::vector<PeptideMatch *> & ProteinMatch::getPeptideMatchList() {
return _peptide_match_list;
}
+const std::vector<PeptideMatch *> & ProteinMatch::getPeptideMatchList() const {
+ return _peptide_match_list;
+}
+
void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment) {
_sp_grp_protein = nullptr;
if (isValidAndChecked()) {
@@ -181,3 +185,17 @@ pappso::pappso_double ProteinMatch::getCoverage() const {
//qDebug() << "ProteinMatch::getCoverage count=" << count << " prot_size=" << prot_size;
return (((pappso::pappso_double)count)/ ((pappso::pappso_double)prot_size));
}
+const GroupingGroupSp & ProteinMatch::getGroupingGroupSp() const {
+ return _sp_group;
+}
+
+void ProteinMatch::setGroupInstance(GroupStore & group_store) {
+ _sp_group = nullptr;
+ if (_sp_grp_protein != nullptr) {
+ unsigned int group_number = _sp_grp_protein.get()->getGroupNumber();
+ if (group_number > 0) {
+ _sp_group = group_store.getInstance(group_number);
+ _sp_group.get()->add(this);
+ }
+ }
+}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index ea42eba33..b473d43e6 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -27,12 +27,17 @@
#include "peptidematch.h"
#include "automaticfilterparameters.h"
#include "../grouping/groupingexperiment.h"
+#include "../utils/groupstore.h"
+#include "../grouping/groupinggroup.h"
#ifndef PROTEINMATCH_H
#define PROTEINMATCH_H
+class IdentificationGroup;
+
class ProteinMatch
{
+ friend IdentificationGroup;
public:
ProteinMatch();
~ProteinMatch();
@@ -44,6 +49,7 @@ public:
void setProteinXtpSp(ProteinXtpSp protein_sp);
void addPeptideMatch(PeptideMatch * peptide_match);
std::vector<PeptideMatch *> & getPeptideMatchList();
+ const std::vector<PeptideMatch *> & getPeptideMatchList() const;
void setChecked(bool arg1);
bool isChecked() const;
@@ -62,17 +68,22 @@ public:
size_t countUniqueSequence()const;
-
+ const pappso::GrpProteinSp & getGrpProteinSp() const;
+ const GroupingGroupSp & getGroupingGroupSp() const;
+
+protected :
+
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
void setGroupingExperiment(GroupingExperiment * p_grp_experiment);
-
- const pappso::GrpProteinSp & getGrpProteinSp() const;
+
+ void setGroupInstance(GroupStore & group_store);
private:
pappso::GrpProteinSp _sp_grp_protein;
+ GroupingGroupSp _sp_group;
std::vector<PeptideMatch *> _peptide_match_list;
ProteinXtpSp _protein_sp = nullptr;
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
new file mode 100644
index 000000000..cd030733c
--- /dev/null
+++ b/src/grouping/groupinggroup.cpp
@@ -0,0 +1,109 @@
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "groupinggroup.h"
+#include <core/proteinmatch.h>
+#include <core/peptidematch.h>
+#include <set>
+
+GroupingGroup::GroupingGroup()
+{
+
+}
+
+GroupingGroup::~GroupingGroup()
+{
+
+}
+
+
+std::size_t GroupingGroup::countSpecificSpectrum(const ProteinMatch * p_protein_match) const {
+ if (_number_of_subgroup == 1) {
+ return p_protein_match->countValidAndCheckedSpectrum();
+ }
+ std::set<QString> spectrum_list_in;
+ for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
+ if (p_peptide_match->isValidAndChecked()) {
+ spectrum_list_in.insert(QString("%1-%2").arg(p_peptide_match->getMsRunIdSp().get()->getXmlId()).arg(p_peptide_match->getScan()));
+ }
+ }
+ std::set<QString> spectrum_list_out;
+ unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
+ for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
+ if (pair_peptide_match.first != sg_number) {
+ spectrum_list_out.insert(QString("%1-%2").arg(pair_peptide_match.second->getMsRunIdSp().get()->getXmlId()).arg(pair_peptide_match.second->getScan()));
+ }
+ }
+
+ std::size_t count = 0;
+ for (const QString & spectrum: spectrum_list_in) {
+ std::set<QString>::const_iterator it = spectrum_list_out.find(spectrum);
+ if (it == spectrum_list_out.end()) {
+ count++;
+ }
+ }
+ return count;
+}
+
+std::size_t GroupingGroup::countSpecificSequence(const ProteinMatch * p_protein_match) const {
+ if (_number_of_subgroup == 1) {
+ return p_protein_match->countUniqueSequence();
+ }
+ std::set<QString> sequence_list_in;
+ for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
+ if (p_peptide_match->isValidAndChecked()) {
+ sequence_list_in.insert(p_peptide_match->getPeptideXtpSp().get()->getSequence());
+ }
+ }
+ std::set<QString> sequence_list_out;
+ unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
+ for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
+ if (pair_peptide_match.first != sg_number) {
+ sequence_list_out.insert(pair_peptide_match.second->getPeptideXtpSp().get()->getSequence());
+ }
+ }
+
+ std::size_t count = 0;
+ for (const QString & sequence: sequence_list_in) {
+ std::set<QString>::const_iterator it = sequence_list_out.find(sequence);
+ if (it == sequence_list_out.end()) {
+ count++;
+ }
+ }
+ return count;
+}
+
+void GroupingGroup::add(const ProteinMatch * p_protein_match) {
+
+ if (p_protein_match->getGrpProteinSp().get()->getRank() == 1) {
+ _number_of_subgroup++;
+ unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
+
+ for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
+ if (p_peptide_match->isValidAndChecked()) {
+ _pair_sg_number_peptide_match_list.push_back(std::pair<unsigned int, const PeptideMatch * >(sg_number, p_peptide_match));
+ }
+ }
+ }
+}
+
diff --git a/src/grouping/groupinggroup.h b/src/grouping/groupinggroup.h
new file mode 100644
index 000000000..983996c7d
--- /dev/null
+++ b/src/grouping/groupinggroup.h
@@ -0,0 +1,51 @@
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef GROUPINGGROUP_H
+#define GROUPINGGROUP_H
+
+#include <memory>
+#include <vector>
+
+class ProteinMatch;
+class PeptideMatch;
+
+class GroupingGroup;
+typedef std::shared_ptr<GroupingGroup> GroupingGroupSp;
+
+class GroupingGroup
+{
+public:
+
+ GroupingGroup();
+ ~GroupingGroup();
+
+ void add(const ProteinMatch * p_protein_match);
+ std::size_t countSpecificSpectrum(const ProteinMatch * p_protein_match) const;
+ std::size_t countSpecificSequence(const ProteinMatch * p_protein_match) const;
+private :
+ unsigned int _number_of_subgroup=0;
+ std::vector<std::pair<unsigned int, const PeptideMatch *>> _pair_sg_number_peptide_match_list;
+};
+
+#endif // GROUPINGGROUP_H
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 932391ea8..041e9efc2 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -24,6 +24,7 @@
#include "proteintablemodel.h"
#include "proteinlistwindow.h"
#include <pappsomspp/grouping/grpprotein.h>
+#include "../../grouping/groupinggroup.h"
#include <QDebug>
@@ -146,7 +147,7 @@ int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
return 0;
}
int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
- return 8;
+ return 10;
}
QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
@@ -168,8 +169,12 @@ QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation,
case 5:
return QString("spectrum");
case 6:
- return QString("unique");
+ return QString("specific");
case 7:
+ return QString("sequence");
+ case 8:
+ return QString("specific sequence");
+ case 9:
return QString("coverage");
}
}
@@ -183,6 +188,7 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
qDebug() << QString("row %1, col%2, role %3")
.arg(row).arg(col).arg(role);
+
switch(role) {
case Qt::CheckStateRole:
@@ -237,19 +243,29 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
}
- if (col == 5) {
+ if (col == 5) {//spectrum
return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countValidAndCheckedSpectrum());
}
- if (col == 6) {
+ if (col == 6) {//specific
+ GroupingGroup * p_groupin_group = _p_identification_group->getProteinMatchList().at(row)->getGroupingGroupSp().get();
+ if (p_groupin_group != nullptr) {
+ return QVariant ((qreal) p_groupin_group->countSpecificSpectrum(_p_identification_group->getProteinMatchList().at(row)));
+ }
+ }
+ if (col == 7) {//sequence
return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countUniqueSequence());
}
- if (col == 7) {
+ if (col == 8) {//specific sequence
+ GroupingGroup * p_groupin_group = _p_identification_group->getProteinMatchList().at(row)->getGroupingGroupSp().get();
+ if (p_groupin_group != nullptr) {
+ return QVariant ((qreal) p_groupin_group->countSpecificSequence(_p_identification_group->getProteinMatchList().at(row)));
+ }
+ }
+ if (col == 9) {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getCoverage());
}
- return QString("Row%1, Column%2")
- .arg(index.row() + 1)
- .arg(index.column() +1);
+ return QVariant();
}
return QVariant();
}
diff --git a/src/utils/groupstore.cpp b/src/utils/groupstore.cpp
new file mode 100644
index 000000000..7f5f0ffa9
--- /dev/null
+++ b/src/utils/groupstore.cpp
@@ -0,0 +1,58 @@
+/**
+ * \file utils/groupstore.cpp
+ * \date 28/3/2017
+ * \author Olivier Langella
+ * \brief store unique version of groups
+ */
+
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "groupstore.h"
+
+GroupStore::GroupStore()
+{
+
+}
+
+GroupStore::~GroupStore()
+{
+
+}
+
+GroupingGroupSp GroupStore::getInstance(unsigned int group_number) {
+
+ GroupingGroupSp sp_group;
+ if (group_number > 0) {
+ std::map< unsigned int, GroupingGroupSp>::iterator it = _map_group.find(group_number);
+ if (it != _map_group.end()) {
+ sp_group = it->second;
+ }
+ else {
+ sp_group = std::make_shared<GroupingGroup>();
+ _map_group.insert(std::pair<unsigned int, GroupingGroupSp>(group_number,sp_group));
+ }
+ }
+ return (sp_group);
+
+}
diff --git a/src/utils/groupstore.h b/src/utils/groupstore.h
new file mode 100644
index 000000000..051918cd4
--- /dev/null
+++ b/src/utils/groupstore.h
@@ -0,0 +1,48 @@
+/**
+ * \file utils/groupstore.h
+ * \date 28/3/2017
+ * \author Olivier Langella
+ * \brief store unique version of groups
+ */
+
+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "../grouping/groupinggroup.h"
+
+#ifndef GROUPSTORE_H
+#define GROUPSTORE_H
+
+#include <map>
+
+class GroupStore
+{
+public:
+ GroupStore();
+ ~GroupStore();
+ GroupingGroupSp getInstance(unsigned int group_number);
+private :
+ std::map<unsigned int, GroupingGroupSp> _map_group;
+};
+
+#endif // GROUPSTORE_H
--
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