From eaeb228e6c3c76bf6ff05cb0618d97ca808f915b Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 19 Jun 2018 23:01:44 +0200
Subject: [PATCH] new peptide column to display search engine
---
.../identificationpwizfile.cpp | 116 ++--
.../peptide_list_view/peptidetablemodel.cpp | 648 +++++++++++-------
src/gui/peptide_list_view/peptidetablemodel.h | 140 ++--
.../peptidetableproxymodel.cpp | 523 +++++++++-----
.../peptidetableproxymodel.h | 117 ++--
.../proteintableproxymodel.cpp | 532 +++++++++-----
.../proteintableproxymodel.h | 116 ++--
src/input/pepxmlsaxhandler.cpp | 10 +-
src/utils/utils.cpp | 231 +++++--
src/utils/utils.h | 60 +-
10 files changed, 1533 insertions(+), 960 deletions(-)
diff --git a/src/core/identification_sources/identificationpwizfile.cpp b/src/core/identification_sources/identificationpwizfile.cpp
index 6a7d0b83f..2ee2672f2 100644
--- a/src/core/identification_sources/identificationpwizfile.cpp
+++ b/src/core/identification_sources/identificationpwizfile.cpp
@@ -6,27 +6,27 @@
*/
/*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 "../../input/identificationpwizreader.h"
#include "../project.h"
@@ -34,61 +34,79 @@
#include <pappsomspp/pappsoexception.h>
IdentificationPwizFile::IdentificationPwizFile(const QFileInfo &ident_file)
- : IdentificationDataSource(ident_file.absoluteFilePath()),
- _ident_file(ident_file) {
+ : IdentificationDataSource(ident_file.absoluteFilePath())
+ , _ident_file(ident_file)
+{
//_engine = IdentificationEngine::XTandem;
_engine = IdentificationEngine::peptider;
}
IdentificationPwizFile::IdentificationPwizFile(
- const IdentificationPwizFile &other)
- : IdentificationDataSource(other), _ident_file(other._ident_file) {
+ const IdentificationPwizFile &other)
+ : IdentificationDataSource(other), _ident_file(other._ident_file)
+{
_engine = other._engine;
}
-IdentificationPwizFile::~IdentificationPwizFile() {}
+IdentificationPwizFile::~IdentificationPwizFile()
+{
+}
-bool IdentificationPwizFile::
-operator==(const IdentificationPwizFile &other) const {}
+bool
+IdentificationPwizFile::operator==(const IdentificationPwizFile &other) const
+{
+}
pappso::SpectrumSp
-IdentificationPwizFile::getSpectrumSp(unsigned int scan_number) const {
+IdentificationPwizFile::getSpectrumSp(unsigned int scan_number) const
+{
pappso::SpectrumSp spectrum_sp =
- IdentificationDataSource::getSpectrumSp(scan_number);
+ IdentificationDataSource::getSpectrumSp(scan_number);
return spectrum_sp;
}
-void IdentificationPwizFile::parseTo(Project *p_project) {
+void
+IdentificationPwizFile::parseTo(Project *p_project)
+{
qDebug() << "IdentificationPwizFile::parseTo begin";
IdentificationPwizReader pwiz_reader(_ident_file);
MsRunSp msrun_sp =
- p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
+ p_project->getMsRunStore().getInstance(pwiz_reader.getMsrunName());
_engine = pwiz_reader.getIdentificationEngine();
setMsRunSp(msrun_sp);
std::vector<IdentificationGroup *> identification_list =
- p_project->getIdentificationGroupList();
+ p_project->getIdentificationGroupList();
IdentificationGroup *identification_group_p = nullptr;
- if (p_project->getProjectMode() == ProjectMode::combined) {
- if (identification_list.size() == 0) {
- identification_group_p = p_project->newIdentificationGroup();
- } else {
- identification_group_p = identification_list[0];
- }
- } else {
- for (IdentificationGroup *identification_p_flist : identification_list) {
- if (identification_p_flist->containSample(
- msrun_sp.get()->getSampleName())) {
- identification_group_p = identification_p_flist;
- break;
- }
+ if(p_project->getProjectMode() == ProjectMode::combined)
+ {
+ if(identification_list.size() == 0)
+ {
+ identification_group_p = p_project->newIdentificationGroup();
+ }
+ else
+ {
+ identification_group_p = identification_list[0];
+ }
}
- if (identification_group_p == nullptr) {
- identification_group_p = p_project->newIdentificationGroup();
+ else
+ {
+ for(IdentificationGroup *identification_p_flist : identification_list)
+ {
+ if(identification_p_flist->containSample(
+ msrun_sp.get()->getSampleName()))
+ {
+ identification_group_p = identification_p_flist;
+ break;
+ }
+ }
+ if(identification_group_p == nullptr)
+ {
+ identification_group_p = p_project->newIdentificationGroup();
+ }
}
- }
identification_group_p->addIdentificationDataSourceP(this);
pwiz_reader.read(this, p_project, identification_group_p);
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 5f4ee6b9d..70cf209fc 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 "peptidetablemodel.h"
@@ -29,377 +30,526 @@
#include "peptidelistwindow.h"
#include <pappsomspp/grouping/grppeptide.h>
#include "../../core/labeling/label.h"
+#include "../../utils/utils.h"
-PeptideTableModel::PeptideTableModel(PeptideListWindow * parent)
- :QAbstractTableModel(parent)
+PeptideTableModel::PeptideTableModel(PeptideListWindow *parent)
+ : QAbstractTableModel(parent)
{
- _p_peptide_list_window = parent;
- //ui->tableView->show();
- // QModelIndex topLeft = createIndex(0,0);
- //emit a signal to make the view reread identified data
- //emit dataChanged(topLeft, topLeft);
+ _p_peptide_list_window = parent;
+ // ui->tableView->show();
+ // QModelIndex topLeft = createIndex(0,0);
+ // emit a signal to make the view reread identified data
+ // emit dataChanged(topLeft, topLeft);
}
-void PeptideTableModel::setProteinMatch(ProteinMatch * p_protein_match) {
- qDebug() << "PeptideTableModel::setProteinMatch begin " ;
+void
+PeptideTableModel::setProteinMatch(ProteinMatch *p_protein_match)
+{
+ qDebug() << "PeptideTableModel::setProteinMatch begin ";
- beginResetModel();
- _p_protein_match = p_protein_match;
- endResetModel();
- //QModelIndex topLeft = createIndex(0,0);
- //QModelIndex bottomRight = createIndex(rowCount(),columnCount());
+ beginResetModel();
+ _p_protein_match = p_protein_match;
+ endResetModel();
+ // QModelIndex topLeft = createIndex(0,0);
+ // QModelIndex bottomRight = createIndex(rowCount(),columnCount());
- _p_peptide_list_window->resizeColumnsToContents();
- //emit dataChanged(topLeft, topLeft);
- //emit headerDataChanged(Qt::Horizontal, 0,3);
- qDebug() << "PeptideTableModel::setProteinMatch end " ;
+ _p_peptide_list_window->resizeColumnsToContents();
+ // emit dataChanged(topLeft, topLeft);
+ // emit headerDataChanged(Qt::Horizontal, 0,3);
+ qDebug() << "PeptideTableModel::setProteinMatch end ";
}
-ProteinMatch * PeptideTableModel::getProteinMatch() {
- return _p_protein_match;
+ProteinMatch *
+PeptideTableModel::getProteinMatch()
+{
+ return _p_protein_match;
}
-int PeptideTableModel::rowCount(const QModelIndex &parent ) const {
- if (_p_protein_match != nullptr) {
- //qDebug() << "PeptideTableModel::rowCount(const QModelIndex &parent ) " << _p_protein_match->getPeptideMatchList().size();
- return (int) _p_protein_match->getPeptideMatchList().size();
+int
+PeptideTableModel::rowCount(const QModelIndex &parent) const
+{
+ if(_p_protein_match != nullptr)
+ {
+ // qDebug() << "PeptideTableModel::rowCount(const QModelIndex &parent ) "
+ // << _p_protein_match->getPeptideMatchList().size();
+ return (int)_p_protein_match->getPeptideMatchList().size();
}
- return 0;
+ return 0;
}
-int PeptideTableModel::columnCount(const QModelIndex &parent ) const {
- return 22;
+int
+PeptideTableModel::columnCount(const QModelIndex &parent) const
+{
+ return 23;
}
-QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
+QVariant
+PeptideTableModel::headerData(int section, Qt::Orientation orientation,
+ int role) const
{
- if (orientation == Qt::Horizontal) {
- switch (role) {
- case Qt::DisplayRole :
+ if(orientation == Qt::Horizontal)
+ {
+ switch(role)
+ {
+ case Qt::DisplayRole:
return QVariant(getTitle(section));
break;
- case Qt::ToolTipRole :
+ case Qt::ToolTipRole:
return QVariant(getDescription(section));
break;
-
}
}
-//if (_p_peptide_list_window->getProjectWindow()->getProjectP()->getLabelingMethodSp().get() == nullptr) {
- return QVariant();
+ // if
+ // (_p_peptide_list_window->getProjectWindow()->getProjectP()->getLabelingMethodSp().get()
+ // == nullptr) {
+ return QVariant();
}
-QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
- // generate a log message when this method gets called
- int row = index.row();
- int col = index.column();
- //qDebug() << QString("row %1, col%2, role %3")
- // .arg(row).arg(col).arg(role);
+QVariant
+PeptideTableModel::data(const QModelIndex &index, int role) const
+{
+ // generate a log message when this method gets called
+ int row = index.row();
+ int col = index.column();
+ // qDebug() << QString("row %1, col%2, role %3")
+ // .arg(row).arg(col).arg(role);
- switch(role) {
- case Qt::CheckStateRole:
+ switch(role)
+ {
+ case Qt::CheckStateRole:
- if (col == 0) //add a checkbox to cell(1,0)
- {
- if ( _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->isChecked()) {
+ if(col == 0) // add a checkbox to cell(1,0)
+ {
+ if(_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->isChecked())
+ {
return Qt::Checked;
- }
- else {
+ }
+ else
+ {
return Qt::Unchecked;
- }
- }
- break;
- case Qt::BackgroundRole:
- if (_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->isValid() == false)
- {
+ }
+ }
+ break;
+ case Qt::BackgroundRole:
+ if(_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->isValid() == false)
+ {
return QVariant(QColor("grey"));
- }
- break;
- case Qt::SizeHintRole :
- //qDebug() << "ProteinTableModel::headerData " << ProteinTableModel::getColumnWidth(section);
- return QSize( PeptideTableModel::getColumnWidth(col), 30 );
- break;
- case Qt::DisplayRole:
- if (_p_protein_match == nullptr) {
- }
- else {
- pappso::GrpPeptide * p_grp_peptide;
- const Label * p_label;
- GroupingGroup * p_grp;
- switch (col) {
- case (std::int8_t)PeptideListColumn::checked:
- return QVariant();
- break;
+ }
+ break;
+ case Qt::SizeHintRole:
+ // qDebug() << "ProteinTableModel::headerData " <<
+ // ProteinTableModel::getColumnWidth(section);
+ return QSize(PeptideTableModel::getColumnWidth(col), 30);
+ break;
+ case Qt::DisplayRole:
+ if(_p_protein_match == nullptr)
+ {
+ }
+ else
+ {
+ pappso::GrpPeptide *p_grp_peptide;
+ const Label *p_label;
+ GroupingGroup *p_grp;
+ switch(col)
+ {
+ case(std::int8_t)PeptideListColumn::checked:
+ return QVariant();
+ break;
- case (std::int8_t)PeptideListColumn::peptide_grouping_id:
- p_grp_peptide = _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getGrpPeptideSp().get();
- if (p_grp_peptide != nullptr) return p_grp_peptide->getGroupingId();
- return QVariant();
- break;
- case (std::int8_t)PeptideListColumn::sample:
- return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getIdentificationDataSource()->getSampleName();
- break;
- case (std::int8_t)PeptideListColumn::scan:
- return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getScan());
- break;
- case (std::int8_t)PeptideListColumn::rtmin:
- return QVariant ((qreal) (_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getRetentionTime()/60));
- break;
- case (std::int8_t)PeptideListColumn::rt:
- return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getRetentionTime());
- break;
- case (std::int8_t)PeptideListColumn::charge:
- return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getCharge());
- break;
- case (std::int8_t)PeptideListColumn::experimental_mz:
- return QVariant (_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getExperimentalMz());
- break;
- case (std::int8_t)PeptideListColumn::sequence:
- return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getSequence();
- break;
- case (std::int8_t)PeptideListColumn::modifs:
- return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getModifString();
- break;
- case (std::int8_t)PeptideListColumn::label:
- p_label = _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getLabel();
- if (p_label != nullptr) {
- return QVariant(p_label->getXmlId());
- }
- else {
- return QVariant();
- }
- break;
- case (std::int8_t)PeptideListColumn::start:
- return QVariant((quint32) _p_protein_match->getPeptideMatchList().at(row).getStart()+1);
- break;
- case (std::int8_t)PeptideListColumn::length:
- return QVariant((quint32) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->size());
- break;
- case (std::int8_t)PeptideListColumn::used:
- p_grp = _p_protein_match->getGroupingGroupSp().get();
- if (p_grp != nullptr) return QVariant((qreal) p_grp->countSubgroupPresence(_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()));
- return QVariant();
- break;
- case (std::int8_t)PeptideListColumn::subgroups:
- p_grp = _p_protein_match->getGroupingGroupSp().get();
- if (p_grp != nullptr) return QVariant( p_grp->getSubgroupIdList(_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()).join(" "));
- return QVariant();
- break;
- case (std::int8_t)PeptideListColumn::Evalue:
- return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getEvalue());
- break;
- case (std::int8_t)PeptideListColumn::experimental_mhplus:
- return QVariant(_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getExperimentalMhplus());
- break;
- case (std::int8_t)PeptideListColumn::theoretical_mhplus:
- return QVariant(_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1));
- break;
- case (std::int8_t)PeptideListColumn::delta_mhplus:
- return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getDeltaMass());
- break;
- case (std::int8_t)PeptideListColumn::delta_ppm:
- return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPpmDeltaMass());
- break;
- case (std::int8_t)PeptideListColumn::hyperscore:
- return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore);
- break;
- case (std::int8_t)PeptideListColumn::mascot_score:
- return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideEvidenceParam::mascot_score);
- break;
- }
- }
+ case(std::int8_t)PeptideListColumn::peptide_grouping_id:
+ p_grp_peptide = _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getGrpPeptideSp()
+ .get();
+ if(p_grp_peptide != nullptr)
+ return p_grp_peptide->getGroupingId();
+ return QVariant();
+ break;
+ case(std::int8_t)PeptideListColumn::engine:
+ return Utils::getIdentificationEngineName(
+ _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getIdentificationEngine());
+ break;
+ case(std::int8_t)PeptideListColumn::sample:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getIdentificationDataSource()
+ ->getSampleName();
+ break;
+ case(std::int8_t)PeptideListColumn::scan:
+ return QVariant(
+ (quint32)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getScan());
+ break;
+ case(std::int8_t)PeptideListColumn::rtmin:
+ return QVariant(
+ (qreal)(_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getRetentionTime() /
+ 60));
+ break;
+ case(std::int8_t)PeptideListColumn::rt:
+ return QVariant((qreal)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getRetentionTime());
+ break;
+ case(std::int8_t)PeptideListColumn::charge:
+ return QVariant(
+ (quint32)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getCharge());
+ break;
+ case(std::int8_t)PeptideListColumn::experimental_mz:
+ return QVariant(_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getExperimentalMz());
+ break;
+ case(std::int8_t)PeptideListColumn::sequence:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequence();
+ break;
+ case(std::int8_t)PeptideListColumn::modifs:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getModifString();
+ break;
+ case(std::int8_t)PeptideListColumn::label:
+ p_label = _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getLabel();
+ if(p_label != nullptr)
+ {
+ return QVariant(p_label->getXmlId());
+ }
+ else
+ {
+ return QVariant();
+ }
+ break;
+ case(std::int8_t)PeptideListColumn::start:
+ return QVariant(
+ (quint32)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getStart() +
+ 1);
+ break;
+ case(std::int8_t)PeptideListColumn::length:
+ return QVariant(
+ (quint32)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->size());
+ break;
+ case(std::int8_t)PeptideListColumn::used:
+ p_grp = _p_protein_match->getGroupingGroupSp().get();
+ if(p_grp != nullptr)
+ return QVariant((qreal)p_grp->countSubgroupPresence(
+ _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()));
+ return QVariant();
+ break;
+ case(std::int8_t)PeptideListColumn::subgroups:
+ p_grp = _p_protein_match->getGroupingGroupSp().get();
+ if(p_grp != nullptr)
+ return QVariant(p_grp
+ ->getSubgroupIdList(
+ _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence())
+ .join(" "));
+ return QVariant();
+ break;
+ case(std::int8_t)PeptideListColumn::Evalue:
+ return QVariant((qreal)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getEvalue());
+ break;
+ case(std::int8_t)PeptideListColumn::experimental_mhplus:
+ return QVariant(_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getExperimentalMhplus());
+ break;
+ case(std::int8_t)PeptideListColumn::theoretical_mhplus:
+ return QVariant(_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getMz(1));
+ break;
+ case(std::int8_t)PeptideListColumn::delta_mhplus:
+ return QVariant((qreal)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getDeltaMass());
+ break;
+ case(std::int8_t)PeptideListColumn::delta_ppm:
+ return QVariant((qreal)_p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getPpmDeltaMass());
+ break;
+ case(std::int8_t)PeptideListColumn::hyperscore:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::tandem_hyperscore);
+ break;
+ case(std::int8_t)PeptideListColumn::mascot_score:
+ return _p_protein_match->getPeptideMatchList()
+ .at(row)
+ .getPeptideEvidence()
+ ->getParam(PeptideEvidenceParam::mascot_score);
+ break;
+ }
+ }
return QString("Row%1, Column%2")
- .arg(index.row() + 1)
- .arg(index.column() +1);
+ .arg(index.row() + 1)
+ .arg(index.column() + 1);
}
- return QVariant();
+ return QVariant();
}
-void PeptideTableModel::onPeptideDataChanged() {
- qDebug() << "PeptideTableModel::onPeptideDataChanged begin " << rowCount();
- emit layoutAboutToBeChanged();
- emit layoutChanged();
+void
+PeptideTableModel::onPeptideDataChanged()
+{
+ qDebug() << "PeptideTableModel::onPeptideDataChanged begin " << rowCount();
+ emit layoutAboutToBeChanged();
+ emit layoutChanged();
}
-
-PeptideListColumn PeptideTableModel::getPeptideListColumn(std::int8_t column) {
- return static_cast<PeptideListColumn>(column);
+PeptideListColumn
+PeptideTableModel::getPeptideListColumn(std::int8_t column)
+{
+ return static_cast<PeptideListColumn>(column);
}
-const QString PeptideTableModel::getTitle(PeptideListColumn column) {
- qDebug() << "PeptideTableModel::getTitle begin ";
- return PeptideTableModel::getTitle((std::int8_t) column);
- //qDebug() << "ProteinTableModel::getTitle end ";
+const QString
+PeptideTableModel::getTitle(PeptideListColumn column)
+{
+ qDebug() << "PeptideTableModel::getTitle begin ";
+ return PeptideTableModel::getTitle((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::getTitle end ";
}
-const QString PeptideTableModel::getDescription(PeptideListColumn column) {
- qDebug() << "PeptideTableModel::columnCount begin ";
- return PeptideTableModel::getDescription((std::int8_t) column);
- //qDebug() << "ProteinTableModel::columnCount end ";
+const QString
+PeptideTableModel::getDescription(PeptideListColumn column)
+{
+ qDebug() << "PeptideTableModel::columnCount begin ";
+ return PeptideTableModel::getDescription((std::int8_t)column);
+ // qDebug() << "ProteinTableModel::columnCount end ";
}
-const QString PeptideTableModel::getTitle(std::int8_t column) {
+const QString
+PeptideTableModel::getTitle(std::int8_t column)
+{
- qDebug() << "PeptideTableModel::getTitle begin " << column;
- switch (column) {
+ qDebug() << "PeptideTableModel::getTitle begin " << column;
+ switch(column)
+ {
- case (std::int8_t) PeptideListColumn::checked:
+ case(std::int8_t)PeptideListColumn::checked:
return "checked";
break;
- case (std::int8_t) PeptideListColumn::peptide_grouping_id:
+ case(std::int8_t)PeptideListColumn::peptide_grouping_id:
return "peptide ID";
break;
- case (std::int8_t) PeptideListColumn::sample:
+ case(std::int8_t)PeptideListColumn::engine:
+ return "engine";
+ break;
+ case(std::int8_t)PeptideListColumn::sample:
return "sample";
break;
- case (std::int8_t) PeptideListColumn::scan:
+ case(std::int8_t)PeptideListColumn::scan:
return "scan";
break;
- case (std::int8_t) PeptideListColumn::rtmin:
+ case(std::int8_t)PeptideListColumn::rtmin:
return "RT min";
break;
- case (std::int8_t) PeptideListColumn::rt:
+ case(std::int8_t)PeptideListColumn::rt:
return "RT";
break;
- case (std::int8_t) PeptideListColumn::charge:
+ case(std::int8_t)PeptideListColumn::charge:
return "charge";
break;
- case (std::int8_t) PeptideListColumn::experimental_mz:
+ case(std::int8_t)PeptideListColumn::experimental_mz:
return "observed m/z";
break;
- case (std::int8_t) PeptideListColumn::sequence:
+ case(std::int8_t)PeptideListColumn::sequence:
return "sequence";
break;
- case (std::int8_t) PeptideListColumn::modifs:
+ case(std::int8_t)PeptideListColumn::modifs:
return "modifs";
break;
- case (std::int8_t) PeptideListColumn::label:
+ case(std::int8_t)PeptideListColumn::label:
return "label";
break;
- case (std::int8_t) PeptideListColumn::start:
+ case(std::int8_t)PeptideListColumn::start:
return "start";
break;
- case (std::int8_t) PeptideListColumn::length:
+ case(std::int8_t)PeptideListColumn::length:
return "length";
break;
- case (std::int8_t) PeptideListColumn::used:
+ case(std::int8_t)PeptideListColumn::used:
return "used";
break;
- case (std::int8_t) PeptideListColumn::subgroups:
+ case(std::int8_t)PeptideListColumn::subgroups:
return "subgroups";
break;
- case (std::int8_t) PeptideListColumn::Evalue:
+ case(std::int8_t)PeptideListColumn::Evalue:
return "Evalue";
break;
- case (std::int8_t) PeptideListColumn::experimental_mhplus:
+ case(std::int8_t)PeptideListColumn::experimental_mhplus:
return "observed MH+";
break;
- case (std::int8_t) PeptideListColumn::theoretical_mhplus:
+ case(std::int8_t)PeptideListColumn::theoretical_mhplus:
return "theoretical MH+";
break;
- case (std::int8_t) PeptideListColumn::delta_mhplus:
+ case(std::int8_t)PeptideListColumn::delta_mhplus:
return "delta MH+";
break;
- case (std::int8_t) PeptideListColumn::delta_ppm:
+ case(std::int8_t)PeptideListColumn::delta_ppm:
return "delta ppm";
break;
- case (std::int8_t) PeptideListColumn::hyperscore:
+ case(std::int8_t)PeptideListColumn::hyperscore:
return "hyperscore";
break;
- case (std::int8_t) PeptideListColumn::mascot_score:
+ case(std::int8_t)PeptideListColumn::mascot_score:
return "mascot score";
}
- return "";
+ return "";
}
-const QString PeptideTableModel::getDescription(std::int8_t column) {
+const QString
+PeptideTableModel::getDescription(std::int8_t column)
+{
- qDebug() << "ProteinTableModel::getDescription begin " << column;
- switch (column) {
+ qDebug() << "ProteinTableModel::getDescription begin " << column;
+ switch(column)
+ {
- case (std::int8_t) PeptideListColumn::checked:
+ case(std::int8_t)PeptideListColumn::checked:
return "manual protein check";
break;
- case (std::int8_t) PeptideListColumn::peptide_grouping_id:
+ case(std::int8_t)PeptideListColumn::peptide_grouping_id:
return "unique peptide identifier within this grouping experiment";
break;
- case (std::int8_t) PeptideListColumn::sample:
+ case(std::int8_t)PeptideListColumn::engine:
+ return "search engine";
+ break;
+ case(std::int8_t)PeptideListColumn::sample:
return "MS sample name";
break;
- case (std::int8_t) PeptideListColumn::scan:
+ case(std::int8_t)PeptideListColumn::scan:
return "scan number";
break;
- case (std::int8_t) PeptideListColumn::rtmin:
+ case(std::int8_t)PeptideListColumn::rtmin:
return "retention time in minutes";
break;
- case (std::int8_t) PeptideListColumn::rt:
+ case(std::int8_t)PeptideListColumn::rt:
return "retention time in seconds";
break;
- case (std::int8_t) PeptideListColumn::charge:
+ case(std::int8_t)PeptideListColumn::charge:
return "peptide charge";
break;
- case (std::int8_t) PeptideListColumn::experimental_mz:
+ case(std::int8_t)PeptideListColumn::experimental_mz:
return "observed m/z (experimental m/z of precursor)";
break;
- case (std::int8_t) PeptideListColumn::sequence:
+ case(std::int8_t)PeptideListColumn::sequence:
return "peptide sequence";
break;
- case (std::int8_t) PeptideListColumn::modifs:
+ case(std::int8_t)PeptideListColumn::modifs:
return "peptide modifications";
break;
- case (std::int8_t) PeptideListColumn::label:
+ case(std::int8_t)PeptideListColumn::label:
return "peptide label";
break;
- case (std::int8_t) PeptideListColumn::start:
+ case(std::int8_t)PeptideListColumn::start:
return "peptide start position on protein";
break;
- case (std::int8_t) PeptideListColumn::length:
+ case(std::int8_t)PeptideListColumn::length:
return "peptide length";
break;
- case (std::int8_t) PeptideListColumn::used:
+ case(std::int8_t)PeptideListColumn::used:
return "number of subgroups in which this peptide is used";
break;
- case (std::int8_t) PeptideListColumn::subgroups:
+ case(std::int8_t)PeptideListColumn::subgroups:
return "list of subgroups in which this peptide is used";
break;
- case (std::int8_t) PeptideListColumn::Evalue:
+ case(std::int8_t)PeptideListColumn::Evalue:
return "peptide Evalue";
break;
- case (std::int8_t) PeptideListColumn::experimental_mhplus:
+ case(std::int8_t)PeptideListColumn::experimental_mhplus:
return "observed peptide mass + H+";
break;
- case (std::int8_t) PeptideListColumn::theoretical_mhplus:
+ case(std::int8_t)PeptideListColumn::theoretical_mhplus:
return "peptide theoretical MH+";
break;
- case (std::int8_t) PeptideListColumn::delta_mhplus:
- return "peptide mass difference in dalton between observed mass and theoretical mass (observed - theoretical)";
+ case(std::int8_t)PeptideListColumn::delta_mhplus:
+ return "peptide mass difference in dalton between observed mass and "
+ "theoretical mass (observed - theoretical)";
break;
- case (std::int8_t) PeptideListColumn::delta_ppm:
- return "peptide mass difference in ppm between observed mass and theoretical mass";
+ case(std::int8_t)PeptideListColumn::delta_ppm:
+ return "peptide mass difference in ppm between observed mass and "
+ "theoretical mass";
break;
- case (std::int8_t) PeptideListColumn::hyperscore:
+ case(std::int8_t)PeptideListColumn::hyperscore:
return "X!Tandem hyperscore";
break;
- case (std::int8_t) PeptideListColumn::mascot_score:
+ case(std::int8_t)PeptideListColumn::mascot_score:
return "Mascot ion score";
-
}
- return "";
+ return "";
}
-int PeptideTableModel::getColumnWidth(int column) {
- qDebug() << "PeptideTableModel::getColumnWidth " << column;
- switch (column) {
+int
+PeptideTableModel::getColumnWidth(int column)
+{
+ qDebug() << "PeptideTableModel::getColumnWidth " << column;
+ switch(column)
+ {
- case (int) PeptideListColumn::checked:
+ case(int)PeptideListColumn::checked:
break;
- case (int) PeptideListColumn::peptide_grouping_id:
+ case(int)PeptideListColumn::peptide_grouping_id:
return 120;
break;
- case (int) PeptideListColumn::sample:
+ case(int)PeptideListColumn::sample:
return 250;
break;
- case (int) PeptideListColumn::sequence:
+ case(int)PeptideListColumn::sequence:
return 250;
break;
}
- return 100;
+ return 100;
}
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index cde92b475..85c719227 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 PEPTIDETABLEMODEL_H
#define PEPTIDETABLEMODEL_H
@@ -31,62 +32,67 @@
*
*/
-enum class PeptideListColumn: std::int8_t {
- checked=0, ///< manual checked
- peptide_grouping_id=1, ///< manual checked
- sample=2,
- scan=3,
- rtmin=4,
- rt=5,
- charge=6,
- experimental_mz=7,
- sequence=8,
- modifs=9,
- label=10,
- start=11,
- length=12,
- used=13,
- subgroups=14,
- Evalue=15,
- experimental_mhplus=16,
- theoretical_mhplus=17,
- delta_mhplus=18,
- delta_ppm=19,
- hyperscore=20,
- mascot_score=21
+enum class PeptideListColumn : std::int8_t
+{
+ checked = 0, ///< manual checked
+ peptide_grouping_id = 1, ///< manual checked
+ engine = 2,
+ sample = 3,
+ scan = 4,
+ rtmin = 5,
+ rt = 6,
+ charge = 7,
+ experimental_mz = 8,
+ sequence = 9,
+ modifs = 10,
+ label = 11,
+ start = 12,
+ length = 13,
+ used = 14,
+ subgroups = 15,
+ Evalue = 16,
+ experimental_mhplus = 17,
+ theoretical_mhplus = 18,
+ delta_mhplus = 19,
+ delta_ppm = 20,
+ hyperscore = 21,
+ mascot_score = 22
};
class PeptideListWindow;
-class PeptideTableModel: public QAbstractTableModel
+class PeptideTableModel : public QAbstractTableModel
{
- Q_OBJECT
-public:
- PeptideTableModel(PeptideListWindow *parent);
- int rowCount(const QModelIndex &parent = QModelIndex()) const override;
- int columnCount(const QModelIndex &parent = QModelIndex()) const override;
- QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
- QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+ Q_OBJECT
+ public:
+ PeptideTableModel(PeptideListWindow *parent);
+ int rowCount(const QModelIndex &parent = QModelIndex()) const override;
+ int columnCount(const QModelIndex &parent = QModelIndex()) const override;
+ QVariant headerData(int section, Qt::Orientation orientation,
+ int role) const override;
+ QVariant data(const QModelIndex &index,
+ int role = Qt::DisplayRole) const override;
+
+ static const QString getTitle(PeptideListColumn column);
+ static const QString getDescription(PeptideListColumn column);
+ static PeptideListColumn getPeptideListColumn(std::int8_t column);
- static const QString getTitle(PeptideListColumn column);
- static const QString getDescription(PeptideListColumn column);
- static PeptideListColumn getPeptideListColumn(std::int8_t column);
+ void setProteinMatch(ProteinMatch *p_protein_match);
+ ProteinMatch *getProteinMatch();
+ signals:
+ void peptideEvidenceClicked(PeptideEvidence *p_peptide_evidence);
- void setProteinMatch(ProteinMatch * p_protein_match);
- ProteinMatch * getProteinMatch();
-signals:
- void peptideEvidenceClicked(PeptideEvidence * p_peptide_evidence);
+ public slots:
+ void onPeptideDataChanged();
-public slots:
- void onPeptideDataChanged();
+ private:
+ static const QString getTitle(std::int8_t column);
+ static const QString getDescription(std::int8_t column);
+ static int getColumnWidth(int column);
-private :
- static const QString getTitle(std::int8_t column);
- static const QString getDescription(std::int8_t column);
- static int getColumnWidth(int column);
-private :
- ProteinMatch * _p_protein_match= nullptr;
- PeptideListWindow * _p_peptide_list_window=nullptr;
+ private:
+ ProteinMatch *_p_protein_match = nullptr;
+ PeptideListWindow *_p_peptide_list_window = nullptr;
};
#endif // PEPTIDETABLEMODEL_H
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.cpp b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
index b43cbb2f9..b2920c374 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.cpp
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 <QDebug>
#include <QSettings>
@@ -29,264 +30,408 @@
#include "peptidelistwindow.h"
#include "../project_view/projectwindow.h"
-PeptideTableProxyModel::PeptideTableProxyModel(PeptideListWindow * p_peptide_list_window, PeptideTableModel * peptide_table_model_p): QSortFilterProxyModel(peptide_table_model_p)
+PeptideTableProxyModel::PeptideTableProxyModel(
+ PeptideListWindow *p_peptide_list_window,
+ PeptideTableModel *peptide_table_model_p)
+ : QSortFilterProxyModel(peptide_table_model_p)
{
- _peptide_table_model_p = peptide_table_model_p;
- _p_peptide_list_window = p_peptide_list_window;
- _column_display.resize(30);
- QSettings settings;
+ _peptide_table_model_p = peptide_table_model_p;
+ _p_peptide_list_window = p_peptide_list_window;
+ _column_display.resize(30);
+ QSettings settings;
- for (std::size_t i=0; i < _column_display.size(); i++) {
- _column_display[i] = settings.value(QString("peptide_list_columns/%1").arg(_peptide_table_model_p->getTitle((PeptideListColumn)i)), "true").toBool();
+ for(std::size_t i = 0; i < _column_display.size(); i++)
+ {
+ _column_display[i] =
+ settings
+ .value(QString("peptide_list_columns/%1")
+ .arg(_peptide_table_model_p->getTitle((PeptideListColumn)i)),
+ "true")
+ .toBool();
}
- _mass_delegate = new MassItemDelegate(_p_peptide_list_window);
- _minute_delegate = new MinuteItemDelegate(_p_peptide_list_window);
- _second_delegate = new SecondItemDelegate(_p_peptide_list_window);
+ _mass_delegate = new MassItemDelegate(_p_peptide_list_window);
+ _minute_delegate = new MinuteItemDelegate(_p_peptide_list_window);
+ _second_delegate = new SecondItemDelegate(_p_peptide_list_window);
}
PeptideTableProxyModel::~PeptideTableProxyModel()
{
- // delete _mass_delegate ;
- // delete _minute_delegate ;
- // delete _second_delegate ;
+ // delete _mass_delegate ;
+ // delete _minute_delegate ;
+ // delete _second_delegate ;
}
-bool PeptideTableProxyModel::filterAcceptsColumn(int source_column, const QModelIndex & source_parent) const {
- if (_peptide_table_model_p->getPeptideListColumn(source_column) == PeptideListColumn::label) {
- if (_p_peptide_list_window->getProjectWindow()->getProjectP()->getLabelingMethodSp().get() == nullptr) {
- return false;
+bool
+PeptideTableProxyModel::filterAcceptsColumn(
+ int source_column, const QModelIndex &source_parent) const
+{
+ if(_peptide_table_model_p->getPeptideListColumn(source_column) ==
+ PeptideListColumn::label)
+ {
+ if(_p_peptide_list_window->getProjectWindow()
+ ->getProjectP()
+ ->getLabelingMethodSp()
+ .get() == nullptr)
+ {
+ return false;
}
}
- return _column_display[source_column];
+ return _column_display[source_column];
}
-bool PeptideTableProxyModel::filterAcceptsRow(int source_row,
- const QModelIndex &source_parent) const {
- try {
- qDebug() << "PeptideTableProxyModel::filterAcceptsRow begin " << source_row;
- PeptideEvidence * peptide_evidence = _peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(source_row).getPeptideEvidence();
- qDebug() << "PeptideTableProxyModel::filterAcceptsRow protein_match " << source_row;
-
- qDebug() << "PeptideTableProxyModel::filterAcceptsRow valid ";
- if (_hide_not_valid) {
- if (! peptide_evidence->isValid()) {
- return false;
+bool
+PeptideTableProxyModel::filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const
+{
+ try
+ {
+ qDebug() << "PeptideTableProxyModel::filterAcceptsRow begin "
+ << source_row;
+ PeptideEvidence *peptide_evidence =
+ _peptide_table_model_p->getProteinMatch()
+ ->getPeptideMatchList()
+ .at(source_row)
+ .getPeptideEvidence();
+ qDebug() << "PeptideTableProxyModel::filterAcceptsRow protein_match "
+ << source_row;
+
+ qDebug() << "PeptideTableProxyModel::filterAcceptsRow valid ";
+ if(_hide_not_valid)
+ {
+ if(!peptide_evidence->isValid())
+ {
+ return false;
}
}
- qDebug() << "PeptideTableProxyModel::filterAcceptsRow checked ";
- if (_hide_not_checked) {
- if (! peptide_evidence->isChecked()) {
- return false;
+ qDebug() << "PeptideTableProxyModel::filterAcceptsRow checked ";
+ if(_hide_not_checked)
+ {
+ if(!peptide_evidence->isChecked())
+ {
+ return false;
}
}
- qDebug() << "PeptideTableProxyModel::filterAcceptsRow grouped ";
- if (_hide_not_grouped) {
- if (! peptide_evidence->isGrouped()) {
- return false;
+ qDebug() << "PeptideTableProxyModel::filterAcceptsRow grouped ";
+ if(_hide_not_grouped)
+ {
+ if(!peptide_evidence->isGrouped())
+ {
+ return false;
}
-
}
- if (_search_on == "msrun/scan") {
- unsigned int scan_num = this->_p_peptide_list_window->ui->scan_number_edit->value();
- QString file_search_string = this->_p_peptide_list_window->ui->msrun_auto_completion->text().toLower();
- qDebug() << "PeptideTableProxyModel::filterAcceptsRow msrun/scan " << file_search_string << " " << scan_num;
- bool scan_ok = true;
- if (scan_num > 0) {
- scan_ok = false;
- if (peptide_evidence->getScan() == scan_num) {
- scan_ok = true;
+ if(_search_on == "msrun/scan")
+ {
+ unsigned int scan_num =
+ this->_p_peptide_list_window->ui->scan_number_edit->value();
+ QString file_search_string =
+ this->_p_peptide_list_window->ui->msrun_auto_completion->text()
+ .toLower();
+ qDebug() << "PeptideTableProxyModel::filterAcceptsRow msrun/scan "
+ << file_search_string << " " << scan_num;
+ bool scan_ok = true;
+ if(scan_num > 0)
+ {
+ scan_ok = false;
+ if(peptide_evidence->getScan() == scan_num)
+ {
+ scan_ok = true;
}
}
- bool msrun_ok = true;
- if (!file_search_string.isEmpty()) {
- msrun_ok = false;
- if (peptide_evidence->getMsRunP()->getFilename().toLower().contains(file_search_string)) {
- msrun_ok = true;
+ bool msrun_ok = true;
+ if(!file_search_string.isEmpty())
+ {
+ msrun_ok = false;
+ if(peptide_evidence->getMsRunP()
+ ->getFilename()
+ .toLower()
+ .contains(file_search_string))
+ {
+ msrun_ok = true;
}
}
- if (msrun_ok && scan_ok ) {
- return true;
+ if(msrun_ok && scan_ok)
+ {
+ return true;
}
- return false;
+ return false;
}
- if (!_peptide_search_string.isEmpty()) {
- if (_search_on == "peptide") {
- if (!peptide_evidence->getPeptideXtpSp().get()->getSequence().contains(_peptide_search_string)) {
- return false;
+ if(!_peptide_search_string.isEmpty())
+ {
+ if(_search_on == "peptide")
+ {
+ if(!peptide_evidence->getPeptideXtpSp()
+ .get()
+ ->getSequence()
+ .contains(_peptide_search_string))
+ {
+ return false;
}
}
- else if (_search_on == "sample") {
- if (!peptide_evidence->getMsRunP()->getSampleName().contains(_peptide_search_string)) {
- return false;
+ else if(_search_on == "sample")
+ {
+ if(!peptide_evidence->getMsRunP()->getSampleName().contains(
+ _peptide_search_string))
+ {
+ return false;
}
- } else if (_search_on == "subgroup") {
- if (peptide_evidence->getValidationState() != ValidationState::grouped) {
- return false;
+ }
+ else if(_search_on == "subgroup")
+ {
+ if(peptide_evidence->getValidationState() !=
+ ValidationState::grouped)
+ {
+ return false;
}
- unsigned int subgroup = _peptide_search_string.toUInt();
- return false;
- } else if (_search_on == "modification") {
- return false;
+ unsigned int subgroup = _peptide_search_string.toUInt();
+ return false;
+ }
+ else if(_search_on == "modification")
+ {
+ return false;
}
}
- if (_search_on == "modifications") {
- QString mod_search_string = this->_p_peptide_list_window->ui->mod_auto_completion->text();
-
- std::vector<pappso::AaModificationP> mod_list;
- for (pappso::AaModificationP mod :_p_peptide_list_window->getProjectWindow()->getProjectP()->getPeptideStore().getModificationCollection()) {
- if (QString("[%1] %2 %3").arg(mod->getAccession()).arg(mod->getName()).arg(mod->getMass()).contains(mod_search_string)) {
- mod_list.push_back(mod);
+ if(_search_on == "modifications")
+ {
+ QString mod_search_string =
+ this->_p_peptide_list_window->ui->mod_auto_completion->text();
+
+ std::vector<pappso::AaModificationP> mod_list;
+ for(pappso::AaModificationP mod :
+ _p_peptide_list_window->getProjectWindow()
+ ->getProjectP()
+ ->getPeptideStore()
+ .getModificationCollection())
+ {
+ if(QString("[%1] %2 %3")
+ .arg(mod->getAccession())
+ .arg(mod->getName())
+ .arg(mod->getMass())
+ .contains(mod_search_string))
+ {
+ mod_list.push_back(mod);
}
- //qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+ // qDebug() << "ProteinListWindow::setIdentificationGroup " <<
+ // msrun_sp.get()->getFilename();
}
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow msrun/scan " << file_search_string << " " << scan_num;
- for (pappso::AaModificationP mod :mod_list) {
- if (peptide_evidence->getPeptideXtpSp().get()->getNumberOfModification(mod) > 0) {
- return true;
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow msrun/scan "
+ // << file_search_string << " " << scan_num;
+ for(pappso::AaModificationP mod : mod_list)
+ {
+ if(peptide_evidence->getPeptideXtpSp()
+ .get()
+ ->getNumberOfModification(mod) > 0)
+ {
+ return true;
}
}
- return false;
+ return false;
}
- return true;
+ return true;
}
- catch (pappso::PappsoException exception_pappso) {
- //QMessageBox::warning(this,
- // tr("Error in ProteinTableModel::acceptRow :"), exception_pappso.qwhat());
- qDebug() << "Error in PeptideTableProxyModel::acceptRow :" << exception_pappso.qwhat();
+ catch(pappso::PappsoException exception_pappso)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error in ProteinTableModel::acceptRow :"),
+ // exception_pappso.qwhat());
+ qDebug() << "Error in PeptideTableProxyModel::acceptRow :"
+ << exception_pappso.qwhat();
}
- catch (std::exception exception_std) {
- //QMessageBox::warning(this,
- // tr("Error in ProteinTableModel::acceptRow :"), exception_std.what());
- qDebug() << "Error in PeptideTableProxyModel::acceptRow :" << exception_std.what();
+ catch(std::exception exception_std)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error in ProteinTableModel::acceptRow :"),
+ // exception_std.what());
+ qDebug() << "Error in PeptideTableProxyModel::acceptRow :"
+ << exception_std.what();
}
- return true;
+ return true;
- //return true;
+ // return true;
}
-
-void PeptideTableProxyModel::onTableClicked(const QModelIndex &index)
+void
+PeptideTableProxyModel::onTableClicked(const QModelIndex &index)
{
- qDebug() << "PeptideTableProxyModel::onTableClicked begin " << index.row();
- qDebug() << "PeptideTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
-
- //_protein_table_model_p->onTableClicked(this->mapToSource(index));
- QModelIndex source_index(this->mapToSource(index));
- int row = source_index.row();
- PeptideListColumn col = (PeptideListColumn) source_index.column();
- PeptideMatch * peptide_match = &_peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(row);
- if (col == PeptideListColumn::checked) //add a checkbox to cell(1,0)
+ qDebug() << "PeptideTableProxyModel::onTableClicked begin " << index.row();
+ qDebug() << "PeptideTableProxyModel::onTableClicked begin "
+ << this->mapToSource(index).row();
+
+ //_protein_table_model_p->onTableClicked(this->mapToSource(index));
+ QModelIndex source_index(this->mapToSource(index));
+ int row = source_index.row();
+ PeptideListColumn col = (PeptideListColumn)source_index.column();
+ PeptideMatch *peptide_match =
+ &_peptide_table_model_p->getProteinMatch()->getPeptideMatchList().at(row);
+ if(col == PeptideListColumn::checked) // add a checkbox to cell(1,0)
{
- if ( peptide_match->getPeptideEvidence()->isChecked()) {
- peptide_match->getPeptideEvidence()->setChecked(false);
+ if(peptide_match->getPeptideEvidence()->isChecked())
+ {
+ peptide_match->getPeptideEvidence()->setChecked(false);
}
- else {
- peptide_match->getPeptideEvidence()->setChecked(true);
+ else
+ {
+ peptide_match->getPeptideEvidence()->setChecked(true);
}
- _p_peptide_list_window->edited();
+ _p_peptide_list_window->edited();
}
- else {
- _p_peptide_list_window->askPeptideDetailView(peptide_match->getPeptideEvidence());
+ else
+ {
+ _p_peptide_list_window->askPeptideDetailView(
+ peptide_match->getPeptideEvidence());
}
- qDebug() << "PeptideTableProxyModel::onTableClicked end " << index.row();
-
+ qDebug() << "PeptideTableProxyModel::onTableClicked end " << index.row();
}
-bool PeptideTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
- QVariant leftData = sourceModel()->data(left);
- QVariant rightData = sourceModel()->data(right);
- if (leftData.type() == QVariant::UInt) {
- return leftData.toUInt() < rightData.toUInt();
+bool
+PeptideTableProxyModel::lessThan(const QModelIndex &left,
+ const QModelIndex &right) const
+{
+ QVariant leftData = sourceModel()->data(left);
+ QVariant rightData = sourceModel()->data(right);
+ if(leftData.type() == QVariant::UInt)
+ {
+ return leftData.toUInt() < rightData.toUInt();
}
- if (leftData.type() == QVariant::UInt) {
- return leftData.toUInt() < rightData.toUInt();
+ if(leftData.type() == QVariant::UInt)
+ {
+ return leftData.toUInt() < rightData.toUInt();
}
- if (leftData.type() == QVariant::Double) {
- return leftData.toDouble() < rightData.toDouble();
+ if(leftData.type() == QVariant::Double)
+ {
+ return leftData.toDouble() < rightData.toDouble();
}
- return leftData.toString() < rightData.toString();
+ return leftData.toString() < rightData.toString();
}
-QVariant PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation, int role) const
+QVariant
+PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation,
+ int role) const
{
- int col = mapToSource(index(0,section)).column();
+ int col = mapToSource(index(0, section)).column();
- return sourceModel()->headerData(col, orientation,
- role);
+ return sourceModel()->headerData(col, orientation, role);
}
-void PeptideTableProxyModel::hideNotValid(bool hide) {
- _hide_not_valid = hide;
+QVariant
+PeptideTableProxyModel::data(const QModelIndex &index, int role) const
+{
+
+ //auto new_index = this->index(index.row(), mapToSource(index).column());
+ return sourceModel()->data(mapToSource(index), role);
}
-void PeptideTableProxyModel::hideNotChecked(bool hide) {
- qDebug() << "PeptideTableProxyModel::hideNotChecked begin ";
- _hide_not_checked = hide;
- qDebug() << "PeptideTableProxyModel::hideNotChecked end ";
+void
+PeptideTableProxyModel::hideNotValid(bool hide)
+{
+ _hide_not_valid = hide;
}
-void PeptideTableProxyModel::hideNotGrouped(bool hide) {
- _hide_not_grouped = hide;
+
+void
+PeptideTableProxyModel::hideNotChecked(bool hide)
+{
+ qDebug() << "PeptideTableProxyModel::hideNotChecked begin ";
+ _hide_not_checked = hide;
+ qDebug() << "PeptideTableProxyModel::hideNotChecked end ";
+}
+void
+PeptideTableProxyModel::hideNotGrouped(bool hide)
+{
+ _hide_not_grouped = hide;
}
-void PeptideTableProxyModel::setSearchOn(QString search_on) {
- _search_on = search_on;
+void
+PeptideTableProxyModel::setSearchOn(QString search_on)
+{
+ _search_on = search_on;
}
-void PeptideTableProxyModel::setPeptideSearchString(QString peptide_search_string) {
- _peptide_search_string = peptide_search_string;
+void
+PeptideTableProxyModel::setPeptideSearchString(QString peptide_search_string)
+{
+ _peptide_search_string = peptide_search_string;
}
-bool PeptideTableProxyModel::getPeptideListColumnDisplay(PeptideListColumn column) const {
- return _column_display[(std::int8_t) column];
+bool
+PeptideTableProxyModel::getPeptideListColumnDisplay(
+ PeptideListColumn column) const
+{
+ return _column_display[(std::int8_t)column];
}
-void PeptideTableProxyModel::setPeptideListColumnDisplay(PeptideListColumn column, bool toggled) {
- qDebug() << "PeptideTableProxyModel::setPeptideListColumnDisplay begin " << toggled;
- beginResetModel();
- QSettings settings;
- settings.setValue(QString("peptide_list_columns/%1").arg(_peptide_table_model_p->getTitle(column)),toggled);
- _column_display[(std::int8_t) column] = toggled;
+void
+PeptideTableProxyModel::setPeptideListColumnDisplay(PeptideListColumn column,
+ bool toggled)
+{
+ qDebug() << "PeptideTableProxyModel::setPeptideListColumnDisplay begin "
+ << toggled;
+ beginResetModel();
+ QSettings settings;
+ settings.setValue(QString("peptide_list_columns/%1")
+ .arg(_peptide_table_model_p->getTitle(column)),
+ toggled);
+ _column_display[(std::int8_t)column] = toggled;
- endResetModel();
+ endResetModel();
- resteItemDelegates();
+ resteItemDelegates();
- //emit columnsRemoved(createIndex(1, 2), (int) column, (int) column)
+ // emit columnsRemoved(createIndex(1, 2), (int) column, (int) column)
}
-void PeptideTableProxyModel::resteItemDelegates() const {
+void
+PeptideTableProxyModel::resteItemDelegates() const
+{
- for (int i = 0; i < columnCount(); ++i) {
- _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(i, _p_peptide_list_window->ui->tableView->itemDelegate());
- if (mapToSource(index(0, i)).column() == (std::int8_t) PeptideListColumn::experimental_mhplus) {
- _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(i, _mass_delegate);
+ for(int i = 0; i < columnCount(); ++i)
+ {
+ _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _p_peptide_list_window->ui->tableView->itemDelegate());
+ if(mapToSource(index(0, i)).column() ==
+ (std::int8_t)PeptideListColumn::experimental_mhplus)
+ {
+ _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _mass_delegate);
}
- if (mapToSource(index(0, i)).column() == (std::int8_t) PeptideListColumn::theoretical_mhplus) {
- _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(i, _mass_delegate);
+ if(mapToSource(index(0, i)).column() ==
+ (std::int8_t)PeptideListColumn::theoretical_mhplus)
+ {
+ _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _mass_delegate);
}
- if (mapToSource(index(0, i)).column() == (std::int8_t) PeptideListColumn::experimental_mz) {
- _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(i, _mass_delegate);
+ if(mapToSource(index(0, i)).column() ==
+ (std::int8_t)PeptideListColumn::experimental_mz)
+ {
+ _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _mass_delegate);
}
- if (mapToSource(index(0, i)).column() == (std::int8_t) PeptideListColumn::rtmin) {
- _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(i, _minute_delegate);
+ if(mapToSource(index(0, i)).column() ==
+ (std::int8_t)PeptideListColumn::rtmin)
+ {
+ _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _minute_delegate);
}
- if (mapToSource(index(0, i)).column() == (std::int8_t) PeptideListColumn::rt) {
- _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(i, _second_delegate);
+ if(mapToSource(index(0, i)).column() ==
+ (std::int8_t)PeptideListColumn::rt)
+ {
+ _p_peptide_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _second_delegate);
}
}
- /*
- MinuteItemDelegate * minute_delegate = new MinuteItemDelegate(ui->tableView);
- ui->tableView->setItemDelegateForColumn((std::int8_t) PeptideListColumn::rtmin, minute_delegate);
- SecondItemDelegate * second_delegate = new SecondItemDelegate(ui->tableView);
- ui->tableView->setItemDelegateForColumn((std::int8_t) PeptideListColumn::rt, second_delegate);
- */
+ /*
+ MinuteItemDelegate * minute_delegate = new MinuteItemDelegate(ui->tableView);
+ ui->tableView->setItemDelegateForColumn((std::int8_t)
+ PeptideListColumn::rtmin, minute_delegate); SecondItemDelegate *
+ second_delegate = new SecondItemDelegate(ui->tableView);
+ ui->tableView->setItemDelegateForColumn((std::int8_t) PeptideListColumn::rt,
+ second_delegate);
+ */
}
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.h b/src/gui/peptide_list_view/peptidetableproxymodel.h
index d8bd68652..569bc2016 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.h
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 PEPTIDETABLEPROXYMODEL_H
#define PEPTIDETABLEPROXYMODEL_H
@@ -36,42 +37,48 @@ class PeptideTableModel;
class PeptideTableProxyModel : public QSortFilterProxyModel
{
- Q_OBJECT
-public:
- PeptideTableProxyModel(PeptideListWindow * p_peptide_list_window, PeptideTableModel* peptide_table_model_p);
- virtual ~PeptideTableProxyModel();
- bool filterAcceptsRow(int source_row,
- const QModelIndex &source_parent) const override;
- bool filterAcceptsColumn(int source_column, const QModelIndex & source_parent) const override;
-
- QVariant headerData(int section, Qt::Orientation orientation,
- int role) const override;
- bool lessThan(const QModelIndex & left, const QModelIndex & right) const override;
-
- void hideNotValid(bool hide);
- void hideNotChecked(bool hide);
- void hideNotGrouped(bool hide);
- void setPeptideSearchString(QString peptide_search_string);
- void setSearchOn(QString search_on);
- void setPeptideListColumnDisplay(PeptideListColumn column, bool toggled);
- bool getPeptideListColumnDisplay(PeptideListColumn column) const;
+ Q_OBJECT
+ public:
+ PeptideTableProxyModel(PeptideListWindow *p_peptide_list_window,
+ PeptideTableModel *peptide_table_model_p);
+ virtual ~PeptideTableProxyModel();
+ bool filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const override;
+ bool filterAcceptsColumn(int source_column,
+ const QModelIndex &source_parent) const override;
- void resteItemDelegates() const;
-public slots:
- void onTableClicked(const QModelIndex &index);
-private :
-private:
- PeptideTableModel* _peptide_table_model_p;
- PeptideListWindow * _p_peptide_list_window;
- QString _peptide_search_string;
- bool _hide_not_valid = true;
- bool _hide_not_checked = true;
- bool _hide_not_grouped = true;
- QString _search_on = "peptide";
- std::vector<bool> _column_display;
- MassItemDelegate * _mass_delegate;
- MinuteItemDelegate * _minute_delegate;
- SecondItemDelegate * _second_delegate;
+ QVariant headerData(int section, Qt::Orientation orientation,
+ int role) const override;
+ QVariant data(const QModelIndex &index,
+ int role = Qt::DisplayRole) const override;
+ bool lessThan(const QModelIndex &left,
+ const QModelIndex &right) const override;
+
+ void hideNotValid(bool hide);
+ void hideNotChecked(bool hide);
+ void hideNotGrouped(bool hide);
+ void setPeptideSearchString(QString peptide_search_string);
+ void setSearchOn(QString search_on);
+ void setPeptideListColumnDisplay(PeptideListColumn column, bool toggled);
+ bool getPeptideListColumnDisplay(PeptideListColumn column) const;
+
+ void resteItemDelegates() const;
+ public slots:
+ void onTableClicked(const QModelIndex &index);
+
+ private:
+ private:
+ PeptideTableModel *_peptide_table_model_p;
+ PeptideListWindow *_p_peptide_list_window;
+ QString _peptide_search_string;
+ bool _hide_not_valid = true;
+ bool _hide_not_checked = true;
+ bool _hide_not_grouped = true;
+ QString _search_on = "peptide";
+ std::vector<bool> _column_display;
+ MassItemDelegate *_mass_delegate;
+ MinuteItemDelegate *_minute_delegate;
+ SecondItemDelegate *_second_delegate;
};
#endif // PEPTIDETABLEPROXYMODEL_H
diff --git a/src/gui/protein_list_view/proteintableproxymodel.cpp b/src/gui/protein_list_view/proteintableproxymodel.cpp
index 08806350a..7aa1d8ec3 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.cpp
+++ b/src/gui/protein_list_view/proteintableproxymodel.cpp
@@ -1,25 +1,26 @@
/*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 <QDebug>
#include <QSettings>
@@ -30,269 +31,420 @@
#include "proteinlistwindow.h"
#include "../project_view/projectwindow.h"
-ProteinTableProxyModel::ProteinTableProxyModel(ProteinListWindow * p_protein_list_window, ProteinTableModel* protein_table_model_p): QSortFilterProxyModel(protein_table_model_p)
+ProteinTableProxyModel::ProteinTableProxyModel(
+ ProteinListWindow *p_protein_list_window,
+ ProteinTableModel *protein_table_model_p)
+ : QSortFilterProxyModel(protein_table_model_p)
{
- _protein_table_model_p = protein_table_model_p;
- _p_protein_list_window = p_protein_list_window;
- _column_display.resize(30);
- QSettings settings;
- for (std::size_t i=0; i < _column_display.size(); i++) {
+ _protein_table_model_p = protein_table_model_p;
+ _p_protein_list_window = p_protein_list_window;
+ _column_display.resize(30);
+ QSettings settings;
+ for(std::size_t i = 0; i < _column_display.size(); i++)
+ {
- _column_display[i] = settings.value(QString("protein_list_columns/%1").arg(_protein_table_model_p->getTitle((ProteinListColumn)i)), "true").toBool();
+ _column_display[i] =
+ settings
+ .value(QString("protein_list_columns/%1")
+ .arg(_protein_table_model_p->getTitle((ProteinListColumn)i)),
+ "true")
+ .toBool();
}
-
- _percent_delegate = new PercentItemDelegate(p_protein_list_window->ui->tableView);
+ _percent_delegate =
+ new PercentItemDelegate(p_protein_list_window->ui->tableView);
}
ProteinTableProxyModel::~ProteinTableProxyModel()
{
- //delete _percent_delegate;
+ // delete _percent_delegate;
}
-bool ProteinTableProxyModel::filterAcceptsColumn(int source_column, const QModelIndex & source_parent) const {
- return _column_display[source_column];
+bool
+ProteinTableProxyModel::filterAcceptsColumn(
+ int source_column, const QModelIndex &source_parent) const
+{
+ return _column_display[source_column];
}
-bool ProteinTableProxyModel::filterAcceptsRow(int source_row,
- const QModelIndex &source_parent) const {
- try {
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow begin " << source_row;
- ProteinMatch * protein_match = _protein_table_model_p->getIdentificationGroup()->getProteinMatchList().at(source_row);
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match " << source_row;
-
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow valid ";
- if (_hide_not_valid) {
- if (! protein_match->isValid()) {
- return false;
+bool
+ProteinTableProxyModel::filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const
+{
+ try
+ {
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow begin " <<
+ // source_row;
+ ProteinMatch *protein_match =
+ _protein_table_model_p->getIdentificationGroup()
+ ->getProteinMatchList()
+ .at(source_row);
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match "
+ // << source_row;
+
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow valid ";
+ if(_hide_not_valid)
+ {
+ if(!protein_match->isValid())
+ {
+ return false;
}
}
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow checked ";
- if (_hide_not_checked) {
- if (! protein_match->isChecked()) {
- return false;
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow checked ";
+ if(_hide_not_checked)
+ {
+ if(!protein_match->isChecked())
+ {
+ return false;
}
}
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow grouped ";
- pappso::GrpProtein * p_grp_prot = protein_match->getGrpProteinSp().get();
- if (_hide_not_grouped) {
- if (p_grp_prot == nullptr) {
- return false;
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow grouped ";
+ pappso::GrpProtein *p_grp_prot = protein_match->getGrpProteinSp().get();
+ if(_hide_not_grouped)
+ {
+ if(p_grp_prot == nullptr)
+ {
+ return false;
}
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow grouped 2";
- if (p_grp_prot->getGroupingId().isEmpty()) {
- return false;
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow grouped 2";
+ if(p_grp_prot->getGroupingId().isEmpty())
+ {
+ return false;
}
}
- if (_search_on == "msrun/scan") {
- unsigned int scan_num = this->_p_protein_list_window->ui->scan_number_edit->value();
- QString file_search_string = this->_p_protein_list_window->ui->msrun_auto_completion->text().toLower();
- qDebug() << "ProteinTableProxyModel::filterAcceptsRow msrun/scan " << file_search_string << " " << scan_num;
- for (const PeptideMatch & p_peptide_match: protein_match->getPeptideMatchList()) {
- bool scan_ok = true;
- if (scan_num > 0) {
- scan_ok = false;
- if (p_peptide_match.getPeptideEvidence()->getScan() == scan_num) {
- scan_ok = true;
+ if(_search_on == "msrun/scan")
+ {
+ unsigned int scan_num =
+ this->_p_protein_list_window->ui->scan_number_edit->value();
+ QString file_search_string =
+ this->_p_protein_list_window->ui->msrun_auto_completion->text()
+ .toLower();
+ qDebug() << "ProteinTableProxyModel::filterAcceptsRow msrun/scan "
+ << file_search_string << " " << scan_num;
+ for(const PeptideMatch &p_peptide_match :
+ protein_match->getPeptideMatchList())
+ {
+ bool scan_ok = true;
+ if(scan_num > 0)
+ {
+ scan_ok = false;
+ if(p_peptide_match.getPeptideEvidence()->getScan() ==
+ scan_num)
+ {
+ scan_ok = true;
}
}
- bool msrun_ok = true;
- if (!file_search_string.isEmpty()) {
- msrun_ok = false;
- if (p_peptide_match.getPeptideEvidence()->getMsRunP()->getFilename().toLower().contains(file_search_string)) {
- msrun_ok = true;
+ bool msrun_ok = true;
+ if(!file_search_string.isEmpty())
+ {
+ msrun_ok = false;
+ if(p_peptide_match.getPeptideEvidence()
+ ->getMsRunP()
+ ->getFilename()
+ .toLower()
+ .contains(file_search_string))
+ {
+ msrun_ok = true;
}
}
- if (msrun_ok && scan_ok ) {
- return true;
+ if(msrun_ok && scan_ok)
+ {
+ return true;
}
}
- return false;
+ return false;
}
- if (!_protein_search_string.isEmpty()) {
- if (_search_on == "accession") {
- if (!protein_match->getProteinXtpSp().get()->getAccession().contains(_protein_search_string)) {
- return false;
+ if(!_protein_search_string.isEmpty())
+ {
+ if(_search_on == "accession")
+ {
+ if(!protein_match->getProteinXtpSp()
+ .get()
+ ->getAccession()
+ .contains(_protein_search_string))
+ {
+ return false;
}
}
- else if (_search_on == "group") {
- pappso::GrpProtein * p_grp_prot = protein_match->getGrpProteinSp().get();
- if (p_grp_prot == nullptr) {
- return false;
+ else if(_search_on == "group")
+ {
+ pappso::GrpProtein *p_grp_prot =
+ protein_match->getGrpProteinSp().get();
+ if(p_grp_prot == nullptr)
+ {
+ return false;
}
- else {
- p_grp_prot->getGroupingId();
- if (!p_grp_prot->getGroupingId().startsWith(_protein_search_string)) {
- return false;
+ else
+ {
+ p_grp_prot->getGroupingId();
+ if(!p_grp_prot->getGroupingId().startsWith(
+ _protein_search_string))
+ {
+ return false;
}
}
}
- else if (_search_on == "sequence") {
- if (!protein_match->getProteinXtpSp().get()->getSequence().contains(_protein_search_string)) {
- return false;
+ else if(_search_on == "sequence")
+ {
+ if(!protein_match->getProteinXtpSp()
+ .get()
+ ->getSequence()
+ .contains(_protein_search_string))
+ {
+ return false;
}
}
- else if (_search_on == "peptide") {
- QString peptide_search_string = QString(_protein_search_string).replace("L","I");
- for (const PeptideMatch & p_peptide_match: protein_match->getPeptideMatchList()) {
- if (p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequenceLi().contains(peptide_search_string)) {
- return true;
+ else if(_search_on == "peptide")
+ {
+ QString peptide_search_string =
+ QString(_protein_search_string).replace("L", "I");
+ for(const PeptideMatch &p_peptide_match :
+ protein_match->getPeptideMatchList())
+ {
+ if(p_peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi()
+ .contains(peptide_search_string))
+ {
+ return true;
}
}
- return false;
+ return false;
}
- else {
- if (!protein_match->getProteinXtpSp().get()->getDescription().contains(_protein_search_string)) {
- return false;
+ else
+ {
+ if(!protein_match->getProteinXtpSp()
+ .get()
+ ->getDescription()
+ .contains(_protein_search_string))
+ {
+ return false;
}
}
}
- if (_search_on == "modifications") {
- QString mod_search_string = this->_p_protein_list_window->ui->mod_auto_completion->text();
-
- std::vector<pappso::AaModificationP> mod_list;
- for (pappso::AaModificationP mod :_p_protein_list_window->getProjectWindow()->getProjectP()->getPeptideStore().getModificationCollection()) {
- if (QString("[%1] %2 %3").arg(mod->getAccession()).arg(mod->getName()).arg(mod->getMass()).contains(mod_search_string)) {
- mod_list.push_back(mod);
+ if(_search_on == "modifications")
+ {
+ QString mod_search_string =
+ this->_p_protein_list_window->ui->mod_auto_completion->text();
+
+ std::vector<pappso::AaModificationP> mod_list;
+ for(pappso::AaModificationP mod :
+ _p_protein_list_window->getProjectWindow()
+ ->getProjectP()
+ ->getPeptideStore()
+ .getModificationCollection())
+ {
+ if(QString("[%1] %2 %3")
+ .arg(mod->getAccession())
+ .arg(mod->getName())
+ .arg(mod->getMass())
+ .contains(mod_search_string))
+ {
+ mod_list.push_back(mod);
}
- //qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+ // qDebug() << "ProteinListWindow::setIdentificationGroup " <<
+ // msrun_sp.get()->getFilename();
}
- //qDebug() << "ProteinTableProxyModel::filterAcceptsRow msrun/scan " << file_search_string << " " << scan_num;
- for (const PeptideMatch & p_peptide_match: protein_match->getPeptideMatchList()) {
- for (pappso::AaModificationP mod :mod_list) {
- if (p_peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getNumberOfModification(mod) > 0) {
- return true;
+ // qDebug() << "ProteinTableProxyModel::filterAcceptsRow msrun/scan "
+ // << file_search_string << " " << scan_num;
+ for(const PeptideMatch &p_peptide_match :
+ protein_match->getPeptideMatchList())
+ {
+ for(pappso::AaModificationP mod : mod_list)
+ {
+ if(p_peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNumberOfModification(mod) > 0)
+ {
+ return true;
}
}
}
- return false;
+ return false;
}
}
- catch (pappso::PappsoException exception_pappso) {
- //QMessageBox::warning(this,
- // tr("Error in ProteinTableModel::acceptRow :"), exception_pappso.qwhat());
- qDebug() << "Error in ProteinTableModel::acceptRow :" << exception_pappso.qwhat();
+ catch(pappso::PappsoException exception_pappso)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error in ProteinTableModel::acceptRow :"),
+ // exception_pappso.qwhat());
+ qDebug() << "Error in ProteinTableModel::acceptRow :"
+ << exception_pappso.qwhat();
}
- catch (std::exception exception_std) {
- //QMessageBox::warning(this,
- // tr("Error in ProteinTableModel::acceptRow :"), exception_std.what());
- qDebug() << "Error in ProteinTableModel::acceptRow :" << exception_std.what();
+ catch(std::exception exception_std)
+ {
+ // QMessageBox::warning(this,
+ // tr("Error in ProteinTableModel::acceptRow :"),
+ // exception_std.what());
+ qDebug() << "Error in ProteinTableModel::acceptRow :"
+ << exception_std.what();
}
- return true;
+ return true;
- //return true;
+ // return true;
}
-
-void ProteinTableProxyModel::onTableClicked(const QModelIndex &index)
+void
+ProteinTableProxyModel::onTableClicked(const QModelIndex &index)
{
- qDebug() << "ProteinTableProxyModel::onTableClicked begin " << index.row();
- qDebug() << "ProteinTableProxyModel::onTableClicked begin " << this->mapToSource(index).row();
-
- //_protein_table_model_p->onTableClicked(this->mapToSource(index));
- QModelIndex source_index(this->mapToSource(index));
- int row = source_index.row();
- ProteinListColumn col = (ProteinListColumn) source_index.column();
- ProteinMatch* p_protein_match = _protein_table_model_p->getIdentificationGroup()->getProteinMatchList().at(row);
- if (col == ProteinListColumn::checked) //add a checkbox to cell(1,0)
+ qDebug() << "ProteinTableProxyModel::onTableClicked begin " << index.row();
+ qDebug() << "ProteinTableProxyModel::onTableClicked begin "
+ << this->mapToSource(index).row();
+
+ //_protein_table_model_p->onTableClicked(this->mapToSource(index));
+ QModelIndex source_index(this->mapToSource(index));
+ int row = source_index.row();
+ ProteinListColumn col = (ProteinListColumn)source_index.column();
+ ProteinMatch *p_protein_match =
+ _protein_table_model_p->getIdentificationGroup()->getProteinMatchList().at(
+ row);
+ if(col == ProteinListColumn::checked) // add a checkbox to cell(1,0)
{
- if ( p_protein_match->isChecked()) {
- p_protein_match->setChecked(false);
+ if(p_protein_match->isChecked())
+ {
+ p_protein_match->setChecked(false);
}
- else {
- p_protein_match->setChecked(true);
+ else
+ {
+ p_protein_match->setChecked(true);
}
- _p_protein_list_window->edited();
+ _p_protein_list_window->edited();
}
- else {
- if ((col == ProteinListColumn::accession)||(col == ProteinListColumn::description)||(col == ProteinListColumn::coverage)) {
- _p_protein_list_window->askProteinDetailView(p_protein_match);
+ else
+ {
+ if((col == ProteinListColumn::accession) ||
+ (col == ProteinListColumn::description) ||
+ (col == ProteinListColumn::coverage))
+ {
+ _p_protein_list_window->askProteinDetailView(p_protein_match);
}
- else {
- _p_protein_list_window->askPeptideListView(p_protein_match);
+ else
+ {
+ _p_protein_list_window->askPeptideListView(p_protein_match);
}
}
- qDebug() << "ProteinTableProxyModel::onTableClicked end " << index.row();
-
+ qDebug() << "ProteinTableProxyModel::onTableClicked end " << index.row();
}
-bool ProteinTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
- QVariant leftData = sourceModel()->data(left);
- QVariant rightData = sourceModel()->data(right);
- if (leftData.type() == QVariant::UInt) {
- return leftData.toUInt() < rightData.toUInt();
+bool
+ProteinTableProxyModel::lessThan(const QModelIndex &left,
+ const QModelIndex &right) const
+{
+ QVariant leftData = sourceModel()->data(left);
+ QVariant rightData = sourceModel()->data(right);
+ if(leftData.type() == QVariant::UInt)
+ {
+ return leftData.toUInt() < rightData.toUInt();
}
- if (leftData.type() == QVariant::UInt) {
- return leftData.toUInt() < rightData.toUInt();
+ if(leftData.type() == QVariant::UInt)
+ {
+ return leftData.toUInt() < rightData.toUInt();
}
- if (leftData.type() == QVariant::Double) {
- return leftData.toDouble() < rightData.toDouble();
+ if(leftData.type() == QVariant::Double)
+ {
+ return leftData.toDouble() < rightData.toDouble();
}
- return leftData.toString() < rightData.toString();
+ return leftData.toString() < rightData.toString();
}
-QVariant ProteinTableProxyModel::headerData(int section, Qt::Orientation orientation,
- int role) const {
- int col = mapToSource(index(0,section)).column();
+QVariant
+ProteinTableProxyModel::data(const QModelIndex &index, int role) const
+{
- return sourceModel()->headerData(col, orientation,
- role);
+ return sourceModel()->data(mapToSource(index), role);
+}
+
+QVariant
+ProteinTableProxyModel::headerData(int section, Qt::Orientation orientation,
+ int role) const
+{
+ int col = mapToSource(index(0, section)).column();
+ return sourceModel()->headerData(col, orientation, role);
}
-void ProteinTableProxyModel::hideNotValid(bool hide) {
- _hide_not_valid = hide;
+void
+ProteinTableProxyModel::hideNotValid(bool hide)
+{
+ _hide_not_valid = hide;
}
-void ProteinTableProxyModel::hideNotChecked(bool hide) {
- qDebug() << "ProteinTableProxyModel::hideNotChecked begin ";
- _hide_not_checked = hide;
- qDebug() << "ProteinTableProxyModel::hideNotChecked end ";
+void
+ProteinTableProxyModel::hideNotChecked(bool hide)
+{
+ qDebug() << "ProteinTableProxyModel::hideNotChecked begin ";
+ _hide_not_checked = hide;
+ qDebug() << "ProteinTableProxyModel::hideNotChecked end ";
}
-void ProteinTableProxyModel::hideNotGrouped(bool hide) {
- _hide_not_grouped = hide;
+void
+ProteinTableProxyModel::hideNotGrouped(bool hide)
+{
+ _hide_not_grouped = hide;
}
-void ProteinTableProxyModel::setSearchOn(QString search_on) {
- _search_on = search_on;
+void
+ProteinTableProxyModel::setSearchOn(QString search_on)
+{
+ _search_on = search_on;
}
-void ProteinTableProxyModel::setMsrunFileSearch(QString msrun_file_search) {
+void
+ProteinTableProxyModel::setMsrunFileSearch(QString msrun_file_search)
+{
}
-void ProteinTableProxyModel::setProteinSearchString(QString protein_search_string) {
- _protein_search_string = protein_search_string;
+void
+ProteinTableProxyModel::setProteinSearchString(QString protein_search_string)
+{
+ _protein_search_string = protein_search_string;
}
-void ProteinTableProxyModel::setProteinListColumnDisplay(ProteinListColumn column, bool toggled) {
- qDebug() << "ProteinTableProxyModel::setProteinListColumnDisplay begin " << toggled;
- beginResetModel();
- QSettings settings;
- settings.setValue(QString("protein_list_columns/%1").arg(_protein_table_model_p->getTitle(column)),toggled);
-
- _column_display[(std::int8_t) column] = toggled;
- endResetModel();
-
- resteItemDelegates();
+void
+ProteinTableProxyModel::setProteinListColumnDisplay(ProteinListColumn column,
+ bool toggled)
+{
+ qDebug() << "ProteinTableProxyModel::setProteinListColumnDisplay begin "
+ << toggled;
+ beginResetModel();
+ QSettings settings;
+ settings.setValue(QString("protein_list_columns/%1")
+ .arg(_protein_table_model_p->getTitle(column)),
+ toggled);
+
+ _column_display[(std::int8_t)column] = toggled;
+ endResetModel();
+
+ resteItemDelegates();
}
-bool ProteinTableProxyModel::getProteinListColumnDisplay(ProteinListColumn column) const {
- return _column_display[(std::int8_t) column];
+bool
+ProteinTableProxyModel::getProteinListColumnDisplay(
+ ProteinListColumn column) const
+{
+ return _column_display[(std::int8_t)column];
}
+void
+ProteinTableProxyModel::resteItemDelegates() const
+{
-void ProteinTableProxyModel::resteItemDelegates() const {
-
- for (int i = 0; i < columnCount(); ++i) {
- _p_protein_list_window->ui->tableView->setItemDelegateForColumn(i, _p_protein_list_window->ui->tableView->itemDelegate());
- if (mapToSource(index(0, i)).column() == (std::int8_t) ProteinListColumn::coverage) {
- _p_protein_list_window->ui->tableView->setItemDelegateForColumn(i, _percent_delegate);
+ for(int i = 0; i < columnCount(); ++i)
+ {
+ _p_protein_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _p_protein_list_window->ui->tableView->itemDelegate());
+ if(mapToSource(index(0, i)).column() ==
+ (std::int8_t)ProteinListColumn::coverage)
+ {
+ _p_protein_list_window->ui->tableView->setItemDelegateForColumn(
+ i, _percent_delegate);
}
}
}
diff --git a/src/gui/protein_list_view/proteintableproxymodel.h b/src/gui/protein_list_view/proteintableproxymodel.h
index 13fe073b9..adefbcb08 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.h
+++ b/src/gui/protein_list_view/proteintableproxymodel.h
@@ -1,25 +1,26 @@
/*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 PROTEINTABLEPROXYMODEL_H
#define PROTEINTABLEPROXYMODEL_H
@@ -36,43 +37,48 @@ class ProteinTableModel;
class ProteinTableProxyModel : public QSortFilterProxyModel
{
- Q_OBJECT
-public:
- ProteinTableProxyModel(ProteinListWindow * p_protein_list_window, ProteinTableModel* protein_table_model_p);
- virtual ~ProteinTableProxyModel();
-
- bool filterAcceptsRow(int source_row,
- const QModelIndex &source_parent) const override;
- bool filterAcceptsColumn(int source_column, const QModelIndex & source_parent) const override;
-
- QVariant headerData(int section, Qt::Orientation orientation,
- int role) const override;
- bool lessThan(const QModelIndex & left, const QModelIndex & right) const override;
-
- void hideNotValid(bool hide);
- void hideNotChecked(bool hide);
- void hideNotGrouped(bool hide);
- void setProteinSearchString(QString protein_search_string);
- void setMsrunFileSearch(QString msrun_file_search);
- void setSearchOn(QString search_on);
- void setProteinListColumnDisplay(ProteinListColumn column, bool toggled);
- bool getProteinListColumnDisplay(ProteinListColumn column) const;
- void resteItemDelegates() const;
+ Q_OBJECT
+ public:
+ ProteinTableProxyModel(ProteinListWindow *p_protein_list_window,
+ ProteinTableModel *protein_table_model_p);
+ virtual ~ProteinTableProxyModel();
-public slots:
- void onTableClicked(const QModelIndex &index);
-
+ bool filterAcceptsRow(int source_row,
+ const QModelIndex &source_parent) const override;
+ bool filterAcceptsColumn(int source_column,
+ const QModelIndex &source_parent) const override;
-private:
- ProteinTableModel* _protein_table_model_p;
- ProteinListWindow * _p_protein_list_window;
- QString _search_on = "accession";
- QString _protein_search_string;
- bool _hide_not_valid = true;
- bool _hide_not_checked = true;
- bool _hide_not_grouped = true;
- std::vector<bool> _column_display;
- PercentItemDelegate * _percent_delegate;
+ QVariant headerData(int section, Qt::Orientation orientation,
+ int role) const override;
+ QVariant data(const QModelIndex &index,
+ int role = Qt::DisplayRole) const override;
+ bool lessThan(const QModelIndex &left,
+ const QModelIndex &right) const override;
+
+ void hideNotValid(bool hide);
+ void hideNotChecked(bool hide);
+ void hideNotGrouped(bool hide);
+ void setProteinSearchString(QString protein_search_string);
+ void setMsrunFileSearch(QString msrun_file_search);
+ void setSearchOn(QString search_on);
+ void setProteinListColumnDisplay(ProteinListColumn column, bool toggled);
+ bool getProteinListColumnDisplay(ProteinListColumn column) const;
+ void resteItemDelegates() const;
+
+ public slots:
+ void onTableClicked(const QModelIndex &index);
+
+
+ private:
+ ProteinTableModel *_protein_table_model_p;
+ ProteinListWindow *_p_protein_list_window;
+ QString _search_on = "accession";
+ QString _protein_search_string;
+ bool _hide_not_valid = true;
+ bool _hide_not_checked = true;
+ bool _hide_not_grouped = true;
+ std::vector<bool> _column_display;
+ PercentItemDelegate *_percent_delegate;
};
#endif // PROTEINTABLEPROXYMODEL_H
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index 809b68575..87f24235f 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -308,7 +308,8 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
"unable to read search results from '%1' as retention time "
"is not given in spectrum_query elements")
.arg(_current_search_engine);
- qDebug() << message;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << message;
// throw new MSMSException(message);
_current_retention_time = 0;
@@ -325,7 +326,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
@@ -590,8 +591,9 @@ PepXmlSaxHandler::startElement_mod_aminoacid_mass(QXmlAttributes attributes)
bool is_ok = true;
double mass = attributes.value("mass").toDouble();
unsigned int position = attributes.value("position").toUInt() - 1;
- const pappso::Aa aa(_current_peptide_sp.get()->getSequence()[position].toLatin1());
- double mass_modif = mass - aa.getMass();
+ const pappso::Aa aa(
+ _current_peptide_sp.get()->getSequence()[position].toLatin1());
+ double mass_modif = mass - aa.getMass();
pappso::AaModificationP modif =
Utils::guessAaModificationPbyMonoisotopicMassDelta(mass_modif);
diff --git a/src/utils/utils.cpp b/src/utils/utils.cpp
index 227c40d54..6ead07187 100644
--- a/src/utils/utils.cpp
+++ b/src/utils/utils.cpp
@@ -3,120 +3,203 @@
#include <pappsomspp/mass_range.h>
#include <cmath>
-const QUrl Utils::getOlsUrl(QString psimod_accession) {
+const QUrl
+Utils::getOlsUrl(QString psimod_accession)
+{
- QString iri(QString("http://purl.obolibrary.org/obo/%1").arg(psimod_accession.replace(":","_")));
- QUrl url(QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1").arg(iri));
- return url;
+ QString iri(QString("http://purl.obolibrary.org/obo/%1")
+ .arg(psimod_accession.replace(":", "_")));
+ QUrl url(
+ QString("http://www.ebi.ac.uk/ols/ontologies/mod/terms?iri=%1").arg(iri));
+ return url;
}
-const QString Utils::getXmlDouble(pappso::pappso_double number) {
- return QString::number(number,'g',6);
+const QString
+Utils::getXmlDouble(pappso::pappso_double number)
+{
+ return QString::number(number, 'g', 6);
}
-const QString Utils::getDatabaseName(ExternalDatabase database) {
- QString database_name;
- switch (database) {
- case ExternalDatabase::AGI_LocusCode :
+const QString
+Utils::getIdentificationEngineName(IdentificationEngine engine)
+{
+ QString engine_name;
+ switch(engine)
+ {
+ case IdentificationEngine::XTandem:
+ engine_name = "X!Tandem";
+ break;
+ case IdentificationEngine::mascot:
+ engine_name = "Mascot";
+ break;
+
+ case IdentificationEngine::peptider:
+ engine_name = "Peptider";
+ break;
+ case IdentificationEngine::OMSSA:
+ engine_name = "OMSSA";
+ break;
+ case IdentificationEngine::SEQUEST:
+ engine_name = "Sequest";
+ break;
+ case IdentificationEngine::Comet:
+ engine_name = "Comet";
+ break;
+ case IdentificationEngine::Morpheus:
+ engine_name = "Morpheus";
+ break;
+ case IdentificationEngine::MSGFplus:
+ engine_name = "MS-GF+";
+ break;
+ }
+ return engine_name;
+}
+
+const QString
+Utils::getDatabaseName(ExternalDatabase database)
+{
+ QString database_name;
+ switch(database)
+ {
+ case ExternalDatabase::AGI_LocusCode:
database_name = "AGI_LocusCode";
break;
- case ExternalDatabase::NCBI_gi :
+ case ExternalDatabase::NCBI_gi:
database_name = "NCBI_gi";
break;
- case ExternalDatabase::SwissProt :
+ case ExternalDatabase::SwissProt:
database_name = "Swiss-Prot";
break;
- case ExternalDatabase::TrEMBL :
+ case ExternalDatabase::TrEMBL:
database_name = "TrEMBL";
break;
- case ExternalDatabase::ref :
+ case ExternalDatabase::ref:
database_name = "ref";
break;
}
- return database_name;
+ return database_name;
}
-std::vector<std::pair<pappso::pappso_double, size_t>> Utils::getHistogram(std::vector<pappso::pappso_double> data_values, unsigned int number_of_class) {
- std::vector<std::pair<pappso::pappso_double, size_t>> histogram(number_of_class+1);
- try {
- qDebug() << "Utils::getHistogram begin";
-
- std::sort(data_values.begin(), data_values.end());
- pappso::pappso_double min = *data_values.begin();
- pappso::pappso_double max = *(data_values.end()-1);
- pappso::pappso_double total = std::abs(max-min);
- pappso::pappso_double offset = (total/ (pappso::pappso_double) number_of_class);
- //qDebug() << "Utils::getHistogram number_of_class offset=" << offset;
- for (unsigned int i= 0; i < histogram.size(); i++) {
- histogram[i] = std::pair<pappso::pappso_double, size_t> {(min + (offset * i) + (offset/2)), 0};
- //qDebug() << "Utils::getHistogram x=" << histogram[i].first;
+std::vector<std::pair<pappso::pappso_double, size_t>>
+Utils::getHistogram(std::vector<pappso::pappso_double> data_values,
+ unsigned int number_of_class)
+{
+ std::vector<std::pair<pappso::pappso_double, size_t>> histogram(
+ number_of_class + 1);
+ try
+ {
+ qDebug() << "Utils::getHistogram begin";
+
+ std::sort(data_values.begin(), data_values.end());
+ pappso::pappso_double min = *data_values.begin();
+ pappso::pappso_double max = *(data_values.end() - 1);
+ pappso::pappso_double total = std::abs(max - min);
+ pappso::pappso_double offset =
+ (total / (pappso::pappso_double)number_of_class);
+ // qDebug() << "Utils::getHistogram number_of_class offset=" << offset;
+ for(unsigned int i = 0; i < histogram.size(); i++)
+ {
+ histogram[i] = std::pair<pappso::pappso_double, size_t>{
+ (min + (offset * i) + (offset / 2)), 0};
+ // qDebug() << "Utils::getHistogram x=" << histogram[i].first;
}
- //qDebug() << "Utils::getHistogram data_values";
- for (pappso::pappso_double value :data_values) {
- //qDebug() << "Utils::getHistogram value=" << value;
- unsigned int i = std::abs((value-min)/offset );
- //qDebug() << "Utils::getHistogram i=" << i << " size=" << histogram.size();
- histogram.at(i).second++;
+ // qDebug() << "Utils::getHistogram data_values";
+ for(pappso::pappso_double value : data_values)
+ {
+ // qDebug() << "Utils::getHistogram value=" << value;
+ unsigned int i = std::abs((value - min) / offset);
+ // qDebug() << "Utils::getHistogram i=" << i << " size=" <<
+ // histogram.size();
+ histogram.at(i).second++;
}
}
- catch (std::exception exception_std) {
- throw pappso::PappsoException(QObject::tr("Utils::getHistogram error %1").arg(exception_std.what()));
+ catch(std::exception exception_std)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Utils::getHistogram error %1").arg(exception_std.what()));
}
- qDebug() << "Utils::getHistogram end";
- return histogram;
+ qDebug() << "Utils::getHistogram end";
+ return histogram;
}
-pappso::AaModificationP Utils::guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass) {
- pappso::PrecisionP precision = pappso::Precision::getDaltonInstance(0.01);
+pappso::AaModificationP
+Utils::guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass)
+{
+ pappso::PrecisionP precision = pappso::Precision::getDaltonInstance(0.01);
- pappso::AaModificationP oxidation = pappso::AaModification::getInstance("MOD:00719");
- if (pappso::MassRange(oxidation->getMass(),precision).contains(mass)) {
- return oxidation;
+ pappso::AaModificationP oxidation =
+ pappso::AaModification::getInstance("MOD:00719");
+ if(pappso::MassRange(oxidation->getMass(), precision).contains(mass))
+ {
+ return oxidation;
}
- pappso::AaModificationP iodoacetamide = pappso::AaModification::getInstance("MOD:00397");
- if (pappso::MassRange(iodoacetamide->getMass(),precision).contains(mass)) {
- return iodoacetamide;
+ pappso::AaModificationP iodoacetamide =
+ pappso::AaModification::getInstance("MOD:00397");
+ if(pappso::MassRange(iodoacetamide->getMass(), precision).contains(mass))
+ {
+ return iodoacetamide;
}
- pappso::AaModificationP acetylated = pappso::AaModification::getInstance("MOD:00408");
- if (pappso::MassRange(acetylated->getMass(),precision).contains(mass)) {
- return acetylated;
+ pappso::AaModificationP acetylated =
+ pappso::AaModification::getInstance("MOD:00408");
+ if(pappso::MassRange(acetylated->getMass(), precision).contains(mass))
+ {
+ return acetylated;
}
- pappso::AaModificationP phosphorylated = pappso::AaModification::getInstance("MOD:00696");
- if (pappso::MassRange(phosphorylated->getMass(),precision).contains(mass)) {
- return phosphorylated;
+ pappso::AaModificationP phosphorylated =
+ pappso::AaModification::getInstance("MOD:00696");
+ if(pappso::MassRange(phosphorylated->getMass(), precision).contains(mass))
+ {
+ return phosphorylated;
}
- pappso::AaModificationP ammonia = pappso::AaModification::getInstance("MOD:01160");
- if (pappso::MassRange(ammonia->getMass(),precision).contains(mass)) {
- return ammonia;
+ pappso::AaModificationP ammonia =
+ pappso::AaModification::getInstance("MOD:01160");
+ if(pappso::MassRange(ammonia->getMass(), precision).contains(mass))
+ {
+ return ammonia;
}
- pappso::AaModificationP dehydrated = pappso::AaModification::getInstance("MOD:00704");
- if (pappso::MassRange(dehydrated->getMass(),precision).contains(mass)) {
- return dehydrated;
+ pappso::AaModificationP dehydrated =
+ pappso::AaModification::getInstance("MOD:00704");
+ if(pappso::MassRange(dehydrated->getMass(), precision).contains(mass))
+ {
+ return dehydrated;
}
- pappso::AaModificationP dimethylated = pappso::AaModification::getInstance("MOD:00429");
- if (pappso::MassRange(dimethylated->getMass(),precision).contains(mass)) {
- return dimethylated;
+ pappso::AaModificationP dimethylated =
+ pappso::AaModification::getInstance("MOD:00429");
+ if(pappso::MassRange(dimethylated->getMass(), precision).contains(mass))
+ {
+ return dimethylated;
}
- pappso::AaModificationP dimethylated_medium = pappso::AaModification::getInstance("MOD:00552");
- if (pappso::MassRange(dimethylated_medium->getMass(),precision).contains(mass)) {
- return dimethylated_medium;
+ pappso::AaModificationP dimethylated_medium =
+ pappso::AaModification::getInstance("MOD:00552");
+ if(pappso::MassRange(dimethylated_medium->getMass(), precision)
+ .contains(mass))
+ {
+ return dimethylated_medium;
}
- pappso::AaModificationP dimethylated_heavy = pappso::AaModification::getInstance("MOD:00638");
- if (pappso::MassRange(dimethylated_heavy->getMass(),precision).contains(mass)) {
- return dimethylated_heavy;
+ pappso::AaModificationP dimethylated_heavy =
+ pappso::AaModification::getInstance("MOD:00638");
+ if(pappso::MassRange(dimethylated_heavy->getMass(), precision).contains(mass))
+ {
+ return dimethylated_heavy;
}
- pappso::AaModificationP DimethylpyrroleAdduct = pappso::AaModification::getInstance("MOD:00628");
- if (pappso::MassRange(DimethylpyrroleAdduct->getMass(),precision).contains(mass)) {
- return DimethylpyrroleAdduct;
+ pappso::AaModificationP DimethylpyrroleAdduct =
+ pappso::AaModification::getInstance("MOD:00628");
+ if(pappso::MassRange(DimethylpyrroleAdduct->getMass(), precision)
+ .contains(mass))
+ {
+ return DimethylpyrroleAdduct;
}
- // modification not found, creating customized mod :
- return pappso::AaModification::getInstanceCustomizedMod(mass);
+ // modification not found, creating customized mod :
+ return pappso::AaModification::getInstanceCustomizedMod(mass);
- throw pappso::ExceptionNotFound(QObject::tr("Utils::guessAaModificationPbyMonoisotopicMassDelta => modification not found for mass %1").arg(mass));
+ throw pappso::ExceptionNotFound(
+ QObject::tr("Utils::guessAaModificationPbyMonoisotopicMassDelta => "
+ "modification not found for mass %1")
+ .arg(mass));
}
diff --git a/src/utils/utils.h b/src/utils/utils.h
index 09e851862..7fa5195ed 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -1,26 +1,27 @@
/*******************************************************************************
-* 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<QUrl>
+ * 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 <QUrl>
#include <QString>
#include "types.h"
#include <pappsomspp/types.h>
@@ -30,13 +31,16 @@
#define XTPUTILS_H
class Utils
{
-public:
- static const QUrl getOlsUrl(QString modification);
- static const QString getDatabaseName(ExternalDatabase database);
- static const QString getXmlDouble(pappso::pappso_double number);
- static pappso::AaModificationP guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass);
- static std::vector<std::pair<pappso::pappso_double, size_t>> getHistogram(std::vector<pappso::pappso_double> data_values, unsigned int number_of_class);
-
+ public:
+ static const QUrl getOlsUrl(QString modification);
+ static const QString getIdentificationEngineName(IdentificationEngine engine);
+ static const QString getDatabaseName(ExternalDatabase database);
+ static const QString getXmlDouble(pappso::pappso_double number);
+ static pappso::AaModificationP
+ guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass);
+ static std::vector<std::pair<pappso::pappso_double, size_t>>
+ getHistogram(std::vector<pappso::pappso_double> data_values,
+ unsigned int number_of_class);
};
#endif // XTPUTILS_H
--
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