From bc14bede99750d6955a417aa1104fd9f31226dec Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 9 May 2017 11:35:18 +0200
Subject: [PATCH] xtpcpp (0.1.9-1) jessie
---
CMakeLists.txt | 2 +-
debian/changelog | 6 ++
.../identificationdatasource.cpp | 23 ++++-
.../identificationdatasource.h | 14 +++
src/core/project.cpp | 3 +
src/core/project.h | 1 +
src/output/ods/groupingsheet.cpp | 88 +++++++++++++++++++
src/output/ods/groupingsheet.h | 52 +++++++++++
src/output/ods/samplesheet.cpp | 50 ++++++++++-
src/output/ods/samplesheet.h | 3 +
src/utils/identificationdatasourcestore.cpp | 9 ++
src/utils/identificationdatasourcestore.h | 2 +
12 files changed, 246 insertions(+), 7 deletions(-)
create mode 100644 src/output/ods/groupingsheet.cpp
create mode 100644 src/output/ods/groupingsheet.h
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 04a60ba1c..520e3cb0d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -42,7 +42,7 @@ SET(SOFTWARE_NAME "XTPcpp")
SET(XTPCPP_VERSION_MAJOR "0")
SET(XTPCPP_VERSION_MINOR "1")
-SET(XTPCPP_VERSION_PATCH "8")
+SET(XTPCPP_VERSION_PATCH "9")
SET(XTPCPP_VERSION "${XTPCPP_VERSION_MAJOR}.${XTPCPP_VERSION_MINOR}.${XTPCPP_VERSION_PATCH}")
# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
diff --git a/debian/changelog b/debian/changelog
index 3c27aace1..0706dd34f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+xtpcpp (0.1.9-1) jessie; urgency=medium
+
+ * MGF peak sorting, waiting dialog, new ODS sheets (samples, groups)
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr> Tue, 09 May 2017 11:30:23 +0200
+
xtpcpp (0.1.8-1) jessie; urgency=medium
* better peptide viewer
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index 0b57d6454..dcb377db8 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -54,8 +54,7 @@ const QString & IdentificationDataSource::getResourceName () const {
}
const QString IdentificationDataSource::getSampleName () const {
- QFileInfo file(_ms_run_sp.get()->getFilename());
- return file.baseName();
+ return _ms_run_sp.get()->getSampleName();
}
void IdentificationDataSource::setMsRunSp (MsRunSp ms_run_sp) {
@@ -68,6 +67,18 @@ MsRunSp IdentificationDataSource::getMsRunSp () const {
IdentificationEngine IdentificationDataSource::getIdentificationEngine() const {
return _engine;
}
+const QString IdentificationDataSource::getIdentificationEngineName() const {
+ QString name = "unknown";
+ switch (_engine) {
+ case IdentificationEngine::XTandem :
+ name = "X!Tandem";
+ break;
+ case IdentificationEngine::peptider :
+ name = "peptider";
+ break;
+ }
+ return name;
+}
const QString& IdentificationDataSource::getIdentificationEngineVersion() const {
return _version;
}
@@ -78,6 +89,14 @@ void IdentificationDataSource::setIdentificationEngineParam(IdentificationEngine
_params.insert(std::pair<IdentificationEngineParam, QVariant>(param, value));
}
+const QVariant IdentificationDataSource::getIdentificationEngineParam(IdentificationEngineParam param) const {
+ try {
+ return _params.at(param);
+ }
+ catch (std::out_of_range) {
+ return QVariant();
+ }
+}
pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp, scan_number);
return spectrum_sp;
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 5f311eea6..daf0ab5c1 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -44,7 +44,12 @@ public:
~IdentificationDataSource();
bool operator==(const IdentificationDataSource& other) const;
+ /** @brief URL or filename containing identification data
+ * */
const QString & getResourceName () const;
+
+ /** @brief get biological sample name
+ * */
const QString getSampleName () const;
void setMsRunSp (MsRunSp ms_run_sp);
MsRunSp getMsRunSp () const;
@@ -60,6 +65,10 @@ public:
/** \brief identification engine
*/
virtual IdentificationEngine getIdentificationEngine() const;
+
+ /** \brief identification engine name
+ */
+ const QString getIdentificationEngineName() const;
/** \brief identification engine version
*/
@@ -72,6 +81,11 @@ public:
*/
virtual void setIdentificationEngineParam(IdentificationEngineParam param, const QVariant& value);
+
+ /** \brief get specific identification engine parameter value
+ */
+ virtual const QVariant getIdentificationEngineParam(IdentificationEngineParam param) const;
+
/** \brief add Fastafile used by the identification engine
*/
void addFastaFile (FastaFileSp file);
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 0e36c7d10..b1390103d 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -85,6 +85,9 @@ ProteinStore & Project::getProteinStore() {
IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() {
return _identification_data_source_store;
}
+const IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() const{
+ return _identification_data_source_store;
+}
const AutomaticFilterParameters & Project::getAutomaticFilterParameters() const {
return _automatic_filter_parameters;
}
diff --git a/src/core/project.h b/src/core/project.h
index c27f9cf39..32f964490 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -51,6 +51,7 @@ public:
const MsRunStore & getMsRunStore() const;
FastaFileStore & getFastaFileStore();
IdentificationDataSourceStore & getIdentificationDataSourceStore();
+ const IdentificationDataSourceStore & getIdentificationDataSourceStore() const;
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
diff --git a/src/output/ods/groupingsheet.cpp b/src/output/ods/groupingsheet.cpp
new file mode 100644
index 000000000..40cf6078c
--- /dev/null
+++ b/src/output/ods/groupingsheet.cpp
@@ -0,0 +1,88 @@
+/**
+ * \file /output/groupingsheet.cpp
+ * \date 9/5/2017
+ * \author Olivier Langella
+ * \brief ODS grouping sheet
+ */
+
+/*******************************************************************************
+* 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 "groupingsheet.h"
+
+
+GroupingSheet::GroupingSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+ _p_writer = p_writer;
+ _p_ods_export = p_ods_export;
+ p_writer->writeSheet("groups");
+
+
+ writeHeaders();
+
+ std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+ for (IdentificationGroup * p_ident:identification_list) {
+ //writeHeaders(p_ident);
+ writeIdentificationGroup(p_ident);
+ }
+}
+
+void GroupingSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+ _p_writer->writeLine();
+ if (!_p_project->isCombineMode()) {
+ _p_writer->writeCell(p_ident->getMsRunSpList().at(0).get()->getSampleName());
+ }
+ _p_writer->writeCell((unsigned int) p_ident->countGroup());
+ _p_writer->writeCell((unsigned int) p_ident->countSubGroup());
+ _p_writer->writeCell(p_ident->countProteinMatch(ValidationState::grouped));
+ _p_writer->writeCell(p_ident->countPeptideMatch(ValidationState::grouped));
+ //_p_writer->writeCell(p_ident->countSequence(ValidationState::grouped));
+ _p_writer->writeCell(p_ident->countPeptideMassSample(ValidationState::grouped));
+ _p_writer->writeCell(p_ident->getProteinFdr(ValidationState::valid));
+ _p_writer->writeCell(p_ident->getPeptideMassFdr(ValidationState::valid));
+}
+
+
+void GroupingSheet::writeHeaders() {
+ // groups, subgroups, proteins, psm, sequence, peptide/mass, pep FDR, prot FDR
+
+ _p_writer->writeLine();
+ if (!_p_project->isCombineMode()) {
+ _p_writer->writeCell("sample");
+ }
+ _p_writer->setCellAnnotation("number of groups");
+ _p_writer->writeCell("groups");
+ _p_writer->setCellAnnotation("number of subgroups");
+ _p_writer->writeCell("subgroups");
+ _p_writer->setCellAnnotation("number of grouped proteins");
+ _p_writer->writeCell("proteins");
+ _p_writer->setCellAnnotation("number of peptide hits : each grouped peptide spectrum match given by the identification engine");
+ _p_writer->writeCell("psm");
+ //_p_writer->writeCell("sequences");
+ _p_writer->setCellAnnotation("number of unique combinations : grouped peptide sequence+modifications+sample name");
+ _p_writer->writeCell("peptide/mass/sample");
+ _p_writer->setCellAnnotation("FDR at the protein level (number of decoy valid proteins / totale number of valid proteins)");
+ _p_writer->writeCell("prot FDR");
+ _p_writer->setCellAnnotation("FDR at the peptide level (number of decoy valid peptides / totale number of valid peptides)");
+ _p_writer->writeCell("pep FDR");
+
+
+}
diff --git a/src/output/ods/groupingsheet.h b/src/output/ods/groupingsheet.h
new file mode 100644
index 000000000..d73bbc86b
--- /dev/null
+++ b/src/output/ods/groupingsheet.h
@@ -0,0 +1,52 @@
+/**
+ * \file /output/groupingsheet.h
+ * \date 9/5/2017
+ * \author Olivier Langella
+ * \brief ODS grouping sheet
+ */
+
+/*******************************************************************************
+* 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 GROUPINGSHEET_H
+#define GROUPINGSHEET_H
+
+#include "../../core/project.h"
+#include <odsstream/calcwriterinterface.h>
+#include "odsexport.h"
+
+class GroupingSheet
+{
+public :
+ GroupingSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+private:
+
+ void writeIdentificationGroup(IdentificationGroup * p_ident);
+ void writeHeaders();
+
+private :
+ OdsExport * _p_ods_export;
+ const Project * _p_project;
+ CalcWriterInterface * _p_writer;
+};
+
+#endif // GROUPINGSHEET_H
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index f4e36b620..b2a4617db 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -33,9 +33,51 @@ SampleSheet::SampleSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writ
_p_writer = p_writer;
_p_ods_export = p_ods_export;
p_writer->writeSheet("samples");
-
- std::vector<MsRunSp> msrun_list = _p_project->getMsRunStore().getMsRunList();
-
- for (MsRunSp msrun_sp: msrun_list) {
+
+ writeHeaders();
+
+ std::vector<IdentificationDataSourceSp> idrun_list = _p_project->getIdentificationDataSourceStore().getIdentificationDataSourceList();
+
+ for (IdentificationDataSourceSp idrun_sp: idrun_list) {
+ writeIdentificationDataSource(idrun_sp.get());
}
}
+
+void SampleSheet::writeHeaders() {
+ // MS sample name X!tandem xml result file name X!Tandem version
+ //X!tandem xml model file name total spectra used total spectra assigned assigned/used percent
+ //total unique assigned database file names MS/MS data source file name MS/MS data source file path
+ //MS level 1 MS level 2 TIC mean in MS 1 TIC mean in MS 2 rt min rt max
+
+
+ _p_writer->writeLine();
+ _p_writer->writeCell("sample ID");
+ _p_writer->writeCell("sample");
+ _p_writer->writeCell("MS run file");
+ _p_writer->writeCell("Identification engine");
+ _p_writer->writeCell("Identification engine version");
+ _p_writer->writeCell("Identification result file");
+ _p_writer->writeCell("Identification fasta files");
+ _p_writer->writeCell("X!Tandem parameters");
+
+
+}
+
+void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ident_data_source) {
+ _p_writer->writeLine();
+ _p_writer->writeCell(p_ident_data_source->getMsRunSp().get()->getXmlId());
+ _p_writer->writeCell(p_ident_data_source->getMsRunSp().get()->getSampleName());
+ _p_writer->writeCell(p_ident_data_source->getMsRunSp().get()->getFilename());
+ _p_writer->writeCell(p_ident_data_source->getIdentificationEngineName());
+ _p_writer->writeCell(p_ident_data_source->getIdentificationEngineVersion());
+ _p_writer->writeCell(p_ident_data_source->getResourceName());
+
+ QStringList fasta_files;
+ for (FastaFileSp fasta_file:p_ident_data_source->getFastaFileList()) {
+ fasta_files << fasta_file.get()->getAbsoluteFilePath();
+ }
+ _p_writer->writeCell(fasta_files.join(" "));
+
+ _p_writer->writeCell(p_ident_data_source->getIdentificationEngineParam(IdentificationEngineParam::tandem_param).toString());
+
+}
diff --git a/src/output/ods/samplesheet.h b/src/output/ods/samplesheet.h
index 6ed33b3b5..620fab433 100644
--- a/src/output/ods/samplesheet.h
+++ b/src/output/ods/samplesheet.h
@@ -39,6 +39,9 @@ class SampleSheet
public :
SampleSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+private:
+ void writeHeaders();
+ void writeIdentificationDataSource(IdentificationDataSource * p_ident_data_source);
private :
OdsExport * _p_ods_export;
const Project * _p_project;
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
index 012e65c8c..9c424e95d 100644
--- a/src/utils/identificationdatasourcestore.cpp
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -63,3 +63,12 @@ qDebug() << " " << _map_identification_data_sources.size();
}
throw pappso::PappsoException(QObject::tr("Identification resource %1 not recognized").arg(location));
}
+
+
+std::vector<IdentificationDataSourceSp> IdentificationDataSourceStore::getIdentificationDataSourceList() const {
+ std::vector<IdentificationDataSourceSp> idsource_list;
+ for (auto & msrun_pair :_map_identification_data_sources) {
+ idsource_list.push_back(msrun_pair.second);
+ }
+ return idsource_list;
+}
diff --git a/src/utils/identificationdatasourcestore.h b/src/utils/identificationdatasourcestore.h
index e634800fb..a2e204f34 100644
--- a/src/utils/identificationdatasourcestore.h
+++ b/src/utils/identificationdatasourcestore.h
@@ -42,6 +42,8 @@ public:
IdentificationDataSourceStore();
~IdentificationDataSourceStore();
IdentificationDataSourceSp getInstance(const QString & location);
+
+ std::vector<IdentificationDataSourceSp> getIdentificationDataSourceList() const;
private :
std::map<QString, IdentificationDataSourceSp> _map_identification_data_sources;
};
--
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