From 2051e21353a45bab05c04edf7230ce68a12d9b5c Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 17 Mar 2017 17:16:51 +0100
Subject: [PATCH] wip : lot of xpip features
---
src/CMakeLists.txt | 1 +
src/core/identificationgroup.cpp | 52 +++++++++
src/core/identificationgroup.h | 63 +++++++++++
src/core/peptidematch.cpp | 7 ++
src/core/peptidematch.h | 11 ++
src/core/project.cpp | 39 +++----
src/core/project.h | 17 +--
src/core/proteinmatch.cpp | 6 ++
src/core/proteinmatch.h | 9 ++
src/gui/mainwindow.cpp | 2 +-
.../protein_list_view/proteinlistwindow.cpp | 9 +-
src/gui/protein_list_view/proteinlistwindow.h | 2 +-
.../protein_list_view/proteintablemodel.cpp | 56 +++++++---
src/gui/protein_list_view/proteintablemodel.h | 10 +-
src/input/xpipsaxhandler.cpp | 100 ++++++++++++++++--
src/input/xpipsaxhandler.h | 7 ++
16 files changed, 317 insertions(+), 74 deletions(-)
create mode 100644 src/core/identificationgroup.cpp
create mode 100644 src/core/identificationgroup.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index bd4b9ebcd..462b946e2 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -53,6 +53,7 @@ configure_file (${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_SOURCE_DIR}/src/c
# File list
SET(CPP_FILES
+ core/identificationgroup.cpp
core/peptidematch.cpp
core/project.cpp
core/proteinmatch.cpp
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
new file mode 100644
index 000000000..0345b1f62
--- /dev/null
+++ b/src/core/identificationgroup.cpp
@@ -0,0 +1,52 @@
+
+/*******************************************************************************
+* 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 "identificationgroup.h"
+
+IdentificationGroup::IdentificationGroup(Project * project)
+{
+ _p_project = project;
+}
+
+IdentificationGroup::~IdentificationGroup()
+{
+ auto it = _protein_match_list.begin();
+ while (it != _protein_match_list.end()) {
+ delete (*it);
+ it++;
+ }
+}
+
+bool IdentificationGroup::isValid(ProteinMatch* p_protein_match) const {
+ return true;
+}
+
+void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
+ _protein_match_list.push_back(protein_match);
+}
+void IdentificationGroup::addMsRunIdSp(pappso::MsRunIdSp ms_run_sp) {
+ _ms_run_list.push_back(ms_run_sp);
+}
+std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
+ return _protein_match_list;
+}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
new file mode 100644
index 000000000..71d591286
--- /dev/null
+++ b/src/core/identificationgroup.h
@@ -0,0 +1,63 @@
+
+/*******************************************************************************
+* 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 <memory>
+#include <pappsomspp/grouping/grpexperiment.h>
+#include <QFileInfo>
+#include "proteinmatch.h"
+#include <pappsomspp/msrun/msrunid.h>
+
+
+#ifndef IDENTIFICATIONGROUP_H
+#define IDENTIFICATIONGROUP_H
+
+
+class Project;
+
+/** @brief an identification group contains one or more sample to consider for grouping
+ */
+class IdentificationGroup
+{
+
+public:
+ IdentificationGroup(Project * project);
+ ~IdentificationGroup();
+
+ void addProteinMatch(ProteinMatch * protein_match);
+ std::vector<ProteinMatch *> & getProteinMatchList();
+ void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
+
+
+ /** @brief is it valid regarding threshold and project rules
+ */
+ bool isValid(ProteinMatch* p_protein_match) const;
+
+ pappso::GrpExperiment * _p_grp_experiment= nullptr;
+private :
+ Project * _p_project;
+
+ std::vector<ProteinMatch *> _protein_match_list;
+
+ std::vector<pappso::MsRunIdSp> _ms_run_list;
+};
+
+#endif // IDENTIFICATIONGROUP_H
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 9981088c5..ba399e77e 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -48,3 +48,10 @@ void PeptideMatch::setCharge(unsigned int charge) {
void PeptideMatch::setPeptideSp (pappso::PeptideSp peptide) {
_peptide_sp = peptide;
}
+
+void PeptideMatch::setChecked(bool arg1) {
+ _checked = arg1;
+}
+void PeptideMatch::setIdentificationDataSource(IdentificationDataSource* identification_source) {
+ _p_identification_source = identification_source;
+}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 738962240..1bcfe877d 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -39,6 +39,8 @@ public :
void setStart(unsigned int start);
void setCharge(unsigned int charge);
void setPeptideSp (pappso::PeptideSp peptide);
+ void setIdentificationDataSource(IdentificationDataSource* identification_source);
+ void setChecked(bool arg1);
private :
@@ -50,6 +52,15 @@ private :
pappso::pappso_double _exp_mass;
unsigned int _start;
unsigned int _charge;
+ IdentificationDataSource* _p_identification_source = nullptr;
+
+ /** @brief manually checked by user (true by default)
+ */
+ bool _checked = true;
+
+ /** @brief automatic filter result (false by default)
+ */
+ bool _proxy_valid = false;
};
#endif // PEPTIDEMATCH_H
diff --git a/src/core/project.cpp b/src/core/project.cpp
index d4f5b6597..bf7bf5094 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -30,8 +30,8 @@ Project::Project()
Project::~Project()
{
- auto it = _protein_match_list.begin();
- while (it != _protein_match_list.end()) {
+ auto it = _identification_goup_list.begin();
+ while (it != _identification_goup_list.end()) {
delete (*it);
it++;
}
@@ -42,6 +42,11 @@ ProjectSp Project::makeProjectSp() const {
}
+IdentificationGroup* Project::newIdentificationGroup() {
+ _p_current_identification_group = new IdentificationGroup(this);
+ _identification_goup_list.push_back(_p_current_identification_group);
+ return _p_current_identification_group;
+}
void Project::readXpipFile(QFileInfo xpip_fileinfo) {
@@ -57,37 +62,21 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
QXmlInputSource xmlInputSource(&qfile);
if (simplereader.parse(xmlInputSource)) {
+
+ qfile.close();
} else {
qDebug() << parser->errorString();
// throw PappsoException(
// QObject::tr("error reading tandem XML result file :\n").append(
// parser->errorString()));
- }
- qfile.close();
-
- /*
- GrpGroupingMonitor monitor;
- GrpExperiment grpExperiment(monitor);
- PeptideReader peptideReader(grpExperiment);
- FastaReader reader(peptideReader);
- reader.parse(&fastaFile);
- fastaFile.close();
- grpExperiment.startGrouping();
+ qfile.close();
- std::list<GrpProteinSp> protein_list;
- grpExperiment.getGroupedProteinSpList(protein_list);
- */
+ throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(xpip_fileinfo.absoluteFilePath()).arg(parser->errorString()));
+ }
}
-
-void Project::addProteinMatch(ProteinMatch * protein_match) {
- _protein_match_list.push_back(protein_match);
-}
-void Project::addMsRunIdSp(pappso::MsRunIdSp ms_run_sp) {
- _ms_run_list.push_back(ms_run_sp);
-}
-std::vector<ProteinMatch *> & Project::getProteinMatchList() {
- return _protein_match_list;
+IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
+ return _p_current_identification_group;
}
diff --git a/src/core/project.h b/src/core/project.h
index a04c73a4e..997d75030 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -24,10 +24,7 @@
#define PROJECT_H
#include<memory>
-#include <pappsomspp/grouping/grpexperiment.h>
-#include <QFileInfo>
-#include "proteinmatch.h"
-#include <pappsomspp/msrun/msrunid.h>
+#include "identificationgroup.h"
class Project;
typedef std::shared_ptr<Project> ProjectSp;
@@ -40,15 +37,11 @@ public:
ProjectSp makeProjectSp() const;
void readXpipFile(QFileInfo xpip_source);
- void addProteinMatch(ProteinMatch * protein_match);
- std::vector<ProteinMatch *> & getProteinMatchList();
- void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
-
- pappso::GrpExperiment * _p_grp_experiment= nullptr;
+ IdentificationGroup* newIdentificationGroup();
+ IdentificationGroup* getCurrentIdentificationGroupP() const;
private :
- std::vector<ProteinMatch *> _protein_match_list;
-
- std::vector<pappso::MsRunIdSp> _ms_run_list;
+ std::vector<IdentificationGroup *> _identification_goup_list;
+ IdentificationGroup* _p_current_identification_group = nullptr;
};
#endif // PROJECT_H
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 8294cc6e7..c0e056930 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -48,6 +48,12 @@ void ProteinMatch::setProteinSp(pappso::ProteinSp protein_sp) {
_protein_sp = protein_sp;
}
+bool ProteinMatch::isChecked() const {
+ return _checked;
+}
+void ProteinMatch::setChecked(bool arg1) {
+ _checked = arg1;
+}
void ProteinMatch::addPeptideMatch(PeptideMatch * peptide_match) {
_peptide_match_list.push_back(peptide_match);
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 5ae01df3a..ffe62a7ef 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -40,10 +40,19 @@ public:
void setProteinSp(pappso::ProteinSp protein_sp);
void addPeptideMatch(PeptideMatch * peptide_match);
std::vector<PeptideMatch *> & getPeptideMatchList();
+ void setChecked(bool arg1);
+ bool isChecked() const;
private:
std::vector<PeptideMatch *> _peptide_match_list;
pappso::ProteinSp _protein_sp = nullptr;
pappso::pappso_double _evalue=0;
+ /** @brief manually checked by user (true by default)
+ */
+ bool _checked = true;
+
+ /** @brief automatic filter result (false by default)
+ */
+ bool _proxy_valid = false;
};
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 1bf9b7dd8..487df39db 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -92,6 +92,6 @@ void MainWindow::selectXpipFile() {
XpipFile xpip_file(new_xpip_file);
_project_sp = xpip_file.getProjectSp();
- _protein_list_window->setProject(_project_sp.get());
+ _protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
}
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 4069a4660..71ae18a08 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -53,7 +53,7 @@ ProteinListWindow::ProteinListWindow(QWidget *parent):
_protein_table_model_p = new ProteinTableModel(0);
- _p_proxy_model = new ProteinTableProxyModel(this);
+ _p_proxy_model = new ProteinTableProxyModel(this, _protein_table_model_p);
_p_proxy_model->setSourceModel(_protein_table_model_p);
_p_proxy_model->setDynamicSortFilter(true);
ui->tableView->setModel( _p_proxy_model );
@@ -68,8 +68,9 @@ ProteinListWindow::~ProteinListWindow()
}
-void ProteinListWindow::setProject(Project* project_p) {
- _protein_table_model_p->setProject(project_p);
- _p_proxy_model->setSourceModel(_protein_table_model_p);
+void ProteinListWindow::setIdentificationGroup(IdentificationGroup * p_identification_group) {
+ _protein_table_model_p->setIdentificationGroup(p_identification_group);
+ _p_proxy_model->setSourceModel(_protein_table_model_p);
}
+
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index f4e337dc3..e30f7aabe 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -40,7 +40,7 @@ public:
explicit ProteinListWindow(QWidget * parent = 0);
~ProteinListWindow();
- void setProject(Project* project_p);
+ void setIdentificationGroup(IdentificationGroup * p_identification_group);
public slots:
//void peptideEdited(QString peptideStr);
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 525861366..697cb11e7 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -26,14 +26,16 @@
#include <QDebug>
-ProteinTableProxyModel::ProteinTableProxyModel(QObject *parent): QSortFilterProxyModel(parent),
+ProteinTableProxyModel::ProteinTableProxyModel(QObject *parent,ProteinTableModel* protein_table_model_p): QSortFilterProxyModel(parent),
m_minGravity(0.0), m_minDensity(0.0)
{
+ _protein_table_model_p = protein_table_model_p;
}
bool ProteinTableProxyModel::filterAcceptsRow(int source_row,
const QModelIndex &source_parent) const {
- return true;
+ //return _protein_table_model_p->acceptRow(source_row);
+ return true;
}
bool ProteinTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
@@ -81,9 +83,9 @@ ProteinTableModel::ProteinTableModel(QObject *parent)
}
-void ProteinTableModel::setProject(Project * p_project) {
- qDebug() << "ProteinTableModel::setProject begin " << p_project->getProteinMatchList().size();
- _p_project = p_project;
+void ProteinTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
+ qDebug() << "ProteinTableModel::setIdentificationGroup begin " << p_identification_group->getProteinMatchList().size();
+ _p_identification_group = p_identification_group;
QModelIndex topLeft = createIndex(0,0);
QModelIndex bottomRight = createIndex(rowCount(),columnCount());
@@ -92,9 +94,9 @@ void ProteinTableModel::setProject(Project * p_project) {
}
int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
- if (_p_project != nullptr) {
- qDebug() << "ProteinTableModel::rowCount(const QModelIndex &parent ) " << _p_project->getProteinMatchList().size();
- return _p_project->getProteinMatchList().size();
+ if (_p_identification_group != nullptr) {
+ qDebug() << "ProteinTableModel::rowCount(const QModelIndex &parent ) " << _p_identification_group->getProteinMatchList().size();
+ return _p_identification_group->getProteinMatchList().size();
}
return 0;
}
@@ -125,21 +127,35 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
int col = index.column();
qDebug() << QString("row %1, col%2, role %3")
.arg(row).arg(col).arg(role);
- if (role == Qt::DisplayRole)
- {
+
+ switch(role) {
+ case Qt::CheckStateRole:
+
+ if (col == 0) //add a checkbox to cell(1,0)
+ {
+ if ( _p_identification_group->getProteinMatchList().at(row)->isChecked()) {
+ return Qt::Checked;
+ }
+ else {
+ return Qt::Unchecked;
+ }
+ }
+ break;
+ case Qt::DisplayRole:
if (col == 0) {
- if (_p_project != nullptr) {
- return QVariant ((quint16) _p_project->getProteinMatchList().at(row)->getPeptideMatchList().size());
+ if (_p_identification_group != nullptr) {
+
+ return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->getPeptideMatchList().size());
}
}
if (col == 1) {
- if (_p_project != nullptr) {
- return _p_project->getProteinMatchList().at(row)->getProteinSp().get()->getAccession();
+ if (_p_identification_group != nullptr) {
+ return _p_identification_group->getProteinMatchList().at(row)->getProteinSp().get()->getAccession();
}
}
if (col == 2) {
- if (_p_project != nullptr) {
- return _p_project->getProteinMatchList().at(row)->getProteinSp().get()->getDescription();
+ if (_p_identification_group != nullptr) {
+ return _p_identification_group->getProteinMatchList().at(row)->getProteinSp().get()->getDescription();
}
}
return QString("Row%1, Column%2")
@@ -148,3 +164,11 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
}
return QVariant();
}
+
+
+bool ProteinTableModel::acceptRow(int source_row) {
+ if (_p_identification_group->isValid(_p_identification_group->getProteinMatchList().at(source_row))) {
+ return true;
+ }
+ return false;
+}
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index 7b11abe6d..2d58c8793 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -28,12 +28,12 @@
#include <QSortFilterProxyModel>
#include "../../core/project.h"
-
+class ProteinTableModel;
class ProteinTableProxyModel : public QSortFilterProxyModel
{
Q_OBJECT
public:
- ProteinTableProxyModel(QObject* parent = 0);
+ ProteinTableProxyModel(QObject* parent,ProteinTableModel* protein_table_model_p);
bool filterAcceptsRow(int source_row,
const QModelIndex &source_parent) const override;
QVariant headerData(int section, Qt::Orientation orientation,
@@ -46,6 +46,7 @@ public slots:
private:
double m_minGravity;
double m_minDensity;
+ ProteinTableModel* _protein_table_model_p;
};
class ProteinTableModel: public QAbstractTableModel
@@ -59,10 +60,11 @@ public:
QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
- void setProject(Project * p_project);
+ void setIdentificationGroup(IdentificationGroup * p_identification_group);
+ bool acceptRow(int source_row);
private :
- Project * _p_project = nullptr;
+ IdentificationGroup * _p_identification_group = nullptr;
};
#endif // PROTEINTABLEMODEL_H
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 23deada7c..1afa8677c 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -43,9 +43,12 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
try {
//startElement_group
- if (qName == "protein")
- {
+ if (qName == "match") {
+ is_ok = startElement_match(attributes);
+ } else if (qName == "protein") {
is_ok = startElement_protein(attributes);
+ } else if (qName == "identification") {
+ is_ok = startElement_identification(attributes);
}
//<sample value="P6_08_10"/>
else if (qName == "sample") {
@@ -56,7 +59,12 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
is_ok = startElement_modifs_mass(attributes);
} else if (qName == "modif") {
is_ok = startElement_modif(attributes);
+ } else if (qName == "filter_params") {
+ is_ok = startElement_filter_params(attributes);
+ } else if (qName == "information") {
+ is_ok = startElement_information(attributes);
}
+
_current_text.clear();
}
catch (pappso::PappsoException exception_pappso) {
@@ -80,12 +88,18 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
{
is_ok = endElement_protein();
}
+ else if (qName == "identification") {
+ is_ok = endElement_identification();
+ }
else if (qName == "peptide") {
is_ok = endElement_peptide();
}
else if (qName == "sequence") {
is_ok = endElement_sequence();
}
+ else if (qName == "match") {
+ is_ok = endElement_match();
+ }
// end of detection_moulon
// else if ((_tag_stack.size() > 1) &&
@@ -106,6 +120,31 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
return is_ok;
}
+bool XpipSaxHandler::startElement_identification(QXmlAttributes attributes) {
+
+ qDebug() << "startElement_identification ";
+ _map_massstr_aamod.clear();
+ _current_identification_group_p = _p_project->newIdentificationGroup();
+ qDebug() << "startElement_identification end" ;
+ return true;
+}
+
+bool XpipSaxHandler::startElement_filter_params(QXmlAttributes attributes) {
+
+//<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="1" filter_to_all="false" database_filter="contaminants_standarts.fasta"/>
+ qDebug() << "startElement_filter_params ";
+ qDebug() << "startElement_filter_params end" ;
+ return true;
+}
+
+bool XpipSaxHandler::startElement_information(QXmlAttributes attributes) {
+
+//<information Data_Type="indiv" match_number="223"/>
+ qDebug() << "startElement_information ";
+ qDebug() << "startElement_information end" ;
+ return true;
+}
+
bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
/*
@@ -120,9 +159,9 @@ bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
qDebug() << "startElement_modifs_mass ";
QString mass_str(attributes.value("modvalue").simplified());
pappso::mz mass = mass_str.toDouble();
-
+
pappso::AaModificationP mod = getAaModificationP(mass);
-
+
_map_massstr_aamod[mass_str] = mod;
qDebug() << "startElement_modifs_mass end" ;
return true;
@@ -137,25 +176,40 @@ bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
ms_run.setFilename(attributes.value("value").simplified());
pappso::MsRunIdSp msrunid_sp = ms_run.makeMsRunIdSp();
- _p_project->addMsRunIdSp(msrunid_sp);
-
+ _current_identification_group_p->addMsRunIdSp(msrunid_sp);
+
_map_msrunid[ms_run.getXmlId()] = msrunid_sp;
qDebug() << "startElement_sample end" ;
return true;
}
+bool XpipSaxHandler::startElement_match(QXmlAttributes attributes) {
+
+ qDebug() << "startElement_match ";
+ /*
+ * <match_list><match validate="true">
+ */
+ _p_protein_match = new ProteinMatch();
+ _p_protein_match->setChecked(false);
+ if (attributes.value("validate").simplified().toLower() == "true") {
+ _p_protein_match->setChecked(true);
+ }
+ qDebug() << "startElement_match end" ;
+ return true;
+}
bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
+ qDebug() << "startElement_protein ";
/*
- * <protein peptide_number="268" evalue="-432.77353" URL="Genome_Z_mays_5a.fasta" description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
+ * <protein peptide_number="268" evalue="-432.77353" URL="Genome_Z_mays_5a.fasta"
+ * description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31)
+ * seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
<protein_evalue evalue="-399.36093" sample="20120906_balliau_extract_1_A02_urzb-1"/>
<protein_evalue evalue="-384.54382" sample="20120906_balliau_extract_1_A01_urnb-1"/>
<sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
</protein>
*/
- _p_protein_match = new ProteinMatch();
_p_protein_match->setEvalue(attributes.value("evalue").toDouble());
- qDebug() << "startElement_protein ";
_current_protein.setDescription(attributes.value("description").simplified());
_current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
qDebug() << "startElement_protein end" ;
@@ -181,7 +235,21 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
_p_peptide_match->setExperimentalMass(exp_mass);
_p_peptide_match->setStart(attributes.value("start").simplified().toUInt());
_p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
-
+
+ _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
+
+ IdentificationDataSource* p_identification_data_source = IdentificationDataSource::getInstance(attributes.value("sample_file").simplified());
+ _p_peptide_match->setIdentificationDataSource( p_identification_data_source);
+ if (p_identification_data_source->getMsRunSp().get() == nullptr) {
+ p_identification_data_source->setMsRunSp(ms_run_id);
+ }
+ if (p_identification_data_source->getMsRunSp().get() != ms_run_id.get()) {
+ throw pappso::PappsoException(QObject::tr("p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
+ }
+ _p_peptide_match->setChecked(false);
+ if (attributes.value("validate").simplified().toLower() == "true") {
+ _p_peptide_match->setChecked(true);
+ }
_p_protein_match->addPeptideMatch(_p_peptide_match);
qDebug() << "startElement_peptide end" ;
return true;
@@ -217,10 +285,20 @@ bool XpipSaxHandler::endElement_sequence() {
}
bool XpipSaxHandler::endElement_protein() {
_p_protein_match->setProteinSp(_current_protein.makeProteinSp());
- _p_project->addProteinMatch(_p_protein_match);
+
+ return true;
+}
+
+bool XpipSaxHandler::endElement_identification() {
+
return true;
}
+bool XpipSaxHandler::endElement_match() {
+ _current_identification_group_p->addProteinMatch(_p_protein_match);
+ _p_protein_match = nullptr;
+ return true;
+}
bool XpipSaxHandler::error(const QXmlParseException &exception) {
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index 55e2a2b1c..ae9e8ff12 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -57,14 +57,20 @@ public:
private:
+ bool startElement_filter_params(QXmlAttributes attributes);
+ bool startElement_information(QXmlAttributes attributes);
+ bool startElement_identification(QXmlAttributes attributes);
+ bool startElement_match(QXmlAttributes attributes);
bool startElement_peptide(QXmlAttributes attributes);
bool startElement_protein(QXmlAttributes attributes);
bool startElement_sample(QXmlAttributes attributes);
bool startElement_modifs_mass(QXmlAttributes attributes);
bool startElement_modif(QXmlAttributes attributes);
+ bool endElement_identification();
bool endElement_sequence();
bool endElement_protein();
bool endElement_peptide();
+ bool endElement_match();
pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
@@ -78,6 +84,7 @@ private:
PeptideMatch * _p_peptide_match;
pappso::Protein _current_protein;
pappso::NoConstPeptideSp _current_peptide_sp;
+ IdentificationGroup * _current_identification_group_p;
PeptideStore _peptide_store;
QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
--
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