From 027247715b7c162fb76ecac3fab06158b62a1bd9 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 12 Jul 2018 22:21:49 +0200
Subject: [PATCH] write TIC in ODS file
---
src/core/msrun.cpp | 6 +-
src/output/ods/samplesheet.cpp | 387 ++++++++++++++++++---------
src/utils/msrunstatisticshandler.cpp | 6 +-
3 files changed, 261 insertions(+), 138 deletions(-)
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 17723ee25..15f10376d 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -157,11 +157,11 @@ MsRun::checkMsRunStatistics()
setMsRunStatistics(MsRunStatistics::total_spectra_ms3,
(unsigned int)stats.getMsLevelCount(3));
setMsRunStatistics(MsRunStatistics::tic_spectra_ms1,
- (unsigned int)stats.getMsLevelTic(1));
+ stats.getMsLevelTic(1));
setMsRunStatistics(MsRunStatistics::tic_spectra_ms2,
- (unsigned int)stats.getMsLevelTic(2));
+ stats.getMsLevelTic(2));
setMsRunStatistics(MsRunStatistics::tic_spectra_ms3,
- (unsigned int)stats.getMsLevelTic(3));
+ stats.getMsLevelTic(3));
}
catch(pappso::ExceptionNotFound &error)
{
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index a9f2665a6..c90b0bd68 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -6,183 +6,304 @@
*/
/*******************************************************************************
-* 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 "samplesheet.h"
-SampleSheet::SampleSheet (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("samples");
-
- OdsTableSettings table_settings;
- table_settings.setVerticalSplit(1);
- _p_writer->setCurrentOdsTableSettings(table_settings);
+SampleSheet::SampleSheet(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("samples");
- writeHeaders();
+ OdsTableSettings table_settings;
+ table_settings.setVerticalSplit(1);
+ _p_writer->setCurrentOdsTableSettings(table_settings);
- std::vector<IdentificationDataSourceSp> idrun_list = _p_project->getIdentificationDataSourceStore().getIdentificationDataSourceList();
+ writeHeaders();
- for (IdentificationDataSourceSp idrun_sp: idrun_list) {
- writeIdentificationDataSource(idrun_sp.get());
+ 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
+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");
+ _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");
- // total_spectra_assigned=1, ///< total_spectra_assigned in one identification file (one sample)
- _p_writer->setCellAnnotation("total spectra assigned in one identification file (one mzdata sample) given by the identification engine");
- _p_writer->writeCell("Total spectra assigned");
- //
- //total_spectra_used=2,///< total_spectra_used in one identification file (one sample)
- _p_writer->setCellAnnotation("total spectra used in one identification file (one mzdata sample) given by the identification engine");
- _p_writer->writeCell("Total spectra used");
+ // total_spectra_assigned=1, ///< total_spectra_assigned in one
+ // identification file (one sample)
+ _p_writer->setCellAnnotation(
+ "total spectra assigned in one identification file (one mzdata sample) "
+ "given by the identification engine");
+ _p_writer->writeCell("Total spectra assigned");
+ //
+ // total_spectra_used=2,///< total_spectra_used in one identification file
+ // (one sample)
+ _p_writer->setCellAnnotation(
+ "total spectra used in one identification file (one mzdata sample) given "
+ "by the identification engine");
+ _p_writer->writeCell("Total spectra used");
- _p_writer->setCellAnnotation("Percentage of spectra assignment (spectra assigned / spectra used");
- _p_writer->writeCell("Assignment percentage");
+ _p_writer->setCellAnnotation(
+ "Percentage of spectra assignment (spectra assigned / spectra used");
+ _p_writer->writeCell("Assignment percentage");
- //total_unique_assigned=5,///< total number unique peptide sequence assigned
- _p_writer->setCellAnnotation("total unique peptide sequence assigned in one identification file (one mzdata sample) given by the identification engine");
- _p_writer->writeCell("Total unique assigned");
+ // total_unique_assigned=5,///< total number unique peptide sequence assigned
+ _p_writer->setCellAnnotation(
+ "total unique peptide sequence assigned in one identification file (one "
+ "mzdata sample) given by the identification engine");
+ _p_writer->writeCell("Total unique assigned");
- if (_msrun_statistics) {
- _p_writer->setCellAnnotation("total number of scans during the MS run (from mz file)");
- _p_writer->writeCell("Total scans");
+ if(_msrun_statistics)
+ {
+ _p_writer->setCellAnnotation(
+ "total number of scans during the MS run (from mz file)");
+ _p_writer->writeCell("Total scans");
- _p_writer->setCellAnnotation("total number of MS level 1 during the MS run (from mz file)");
- _p_writer->writeCell("Total MS1");
+ _p_writer->setCellAnnotation(
+ "total number of MS level 1 during the MS run (from mz file)");
+ _p_writer->writeCell("Total MS1");
- _p_writer->setCellAnnotation("total number of MS level 2 during the MS run (from mz file)");
- _p_writer->writeCell("Total MS2");
+ _p_writer->setCellAnnotation(
+ "total number of MS level 2 during the MS run (from mz file)");
+ _p_writer->writeCell("Total MS2");
- _p_writer->setCellAnnotation("total number of MS level 3 during the MS run (from mz file)");
- _p_writer->writeCell("Total MS3");
+ _p_writer->setCellAnnotation(
+ "total number of MS level 3 during the MS run (from mz file)");
+ _p_writer->writeCell("Total MS3");
- }
+ _p_writer->setCellAnnotation("total ion current in MS level 1 spectra "
+ "during the MS run (from mz file)");
+ _p_writer->writeCell("TIC MS1");
- /*
- total_peptide_used=3,///< total number of peptides generated and used in identification
- total_proteins_used=4,///< total number of proteins generated and used in identification
+ _p_writer->setCellAnnotation("total ion current in MS level 2 spectra "
+ "during the MS run (from mz file)");
+ _p_writer->writeCell("TIC MS2");
- */
+ _p_writer->setCellAnnotation("total ion current in MS level 3 spectra "
+ "during the MS run (from mz file)");
+ _p_writer->writeCell("TIC MS3");
+ }
+ /*
+ total_peptide_used=3,///< total number of peptides generated and used in
+ identification total_proteins_used=4,///< total number of proteins generated
+ and used in identification
+
+ */
}
-void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ident_data_source) {
- _p_writer->writeLine();
- MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
- if (_msrun_statistics) {
- if (msrun_sp->findMsRunFile()) msrun_sp->checkMsRunStatistics();
+void
+SampleSheet::writeIdentificationDataSource(
+ IdentificationDataSource *p_ident_data_source)
+{
+ _p_writer->writeLine();
+ MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
+ if(_msrun_statistics)
+ {
+ if(msrun_sp->findMsRunFile())
+ msrun_sp->checkMsRunStatistics();
}
- _p_writer->writeCell(msrun_sp.get()->getXmlId());
- _p_writer->writeCell(msrun_sp.get()->getSampleName());
- _p_writer->writeCell(msrun_sp.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());
+ _p_writer->writeCell(msrun_sp.get()->getXmlId());
+ _p_writer->writeCell(msrun_sp.get()->getSampleName());
+ _p_writer->writeCell(msrun_sp.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();
+ 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(fasta_files.join(" "));
- QVariant var_sample = p_ident_data_source->getIdentificationEngineParam(IdentificationEngineParam::tandem_param);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toString());
+ QVariant var_sample = p_ident_data_source->getIdentificationEngineParam(
+ IdentificationEngineParam::tandem_param);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toString());
}
- var_sample = p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toInt());
+ var_sample = p_ident_data_source->getIdentificationEngineStatistics(
+ IdentificationEngineStatistics::total_spectra_assigned);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
}
- var_sample = p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toInt());
+ else
+ {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+ var_sample = p_ident_data_source->getIdentificationEngineStatistics(
+ IdentificationEngineStatistics::total_spectra_used);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toInt());
}
- if (!p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned).isNull() && !p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used).isNull()) {
- _p_writer->writeCellPercentage(p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_assigned).toDouble() / p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_spectra_used).toDouble());
+ if(!p_ident_data_source
+ ->getIdentificationEngineStatistics(
+ IdentificationEngineStatistics::total_spectra_assigned)
+ .isNull() &&
+ !p_ident_data_source
+ ->getIdentificationEngineStatistics(
+ IdentificationEngineStatistics::total_spectra_used)
+ .isNull())
+ {
+ _p_writer->writeCellPercentage(
+ p_ident_data_source
+ ->getIdentificationEngineStatistics(
+ IdentificationEngineStatistics::total_spectra_assigned)
+ .toDouble() /
+ p_ident_data_source
+ ->getIdentificationEngineStatistics(
+ IdentificationEngineStatistics::total_spectra_used)
+ .toDouble());
}
- else {
- _p_writer->writeEmptyCell();
+ else
+ {
+ _p_writer->writeEmptyCell();
}
- var_sample = p_ident_data_source->getIdentificationEngineStatistics(IdentificationEngineStatistics::total_unique_assigned);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toInt());
+ var_sample = p_ident_data_source->getIdentificationEngineStatistics(
+ IdentificationEngineStatistics::total_unique_assigned);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toInt());
}
- if (_msrun_statistics) {
- var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toInt());
+ if(_msrun_statistics)
+ {
+ var_sample =
+ msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+ var_sample =
+ msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms1);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
}
- var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms1);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toInt());
+ else
+ {
+ _p_writer->writeCell(var_sample.toInt());
}
- var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms2);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toInt());
+ var_sample =
+ msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms2);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
}
- var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms3);
- if (var_sample.isNull()) {
- _p_writer->writeEmptyCell();
- } else {
- _p_writer->writeCell(var_sample.toInt());
+ else
+ {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+ var_sample =
+ msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms3);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+
+ var_sample =
+ msrun_sp.get()->getMsRunStatistics(MsRunStatistics::tic_spectra_ms1);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toDouble());
+ }
+ var_sample =
+ msrun_sp.get()->getMsRunStatistics(MsRunStatistics::tic_spectra_ms2);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toDouble());
+ }
+ var_sample =
+ msrun_sp.get()->getMsRunStatistics(MsRunStatistics::tic_spectra_ms3);
+ if(var_sample.isNull())
+ {
+ _p_writer->writeEmptyCell();
+ }
+ else
+ {
+ _p_writer->writeCell(var_sample.toDouble());
}
}
-
}
diff --git a/src/utils/msrunstatisticshandler.cpp b/src/utils/msrunstatisticshandler.cpp
index d61bed553..a73714ccf 100644
--- a/src/utils/msrunstatisticshandler.cpp
+++ b/src/utils/msrunstatisticshandler.cpp
@@ -28,6 +28,7 @@
#include "msrunstatisticshandler.h"
#include <pappsomspp/msrun/msrunreader.h>
+#include <QDebug>
bool
@@ -44,8 +45,8 @@ MsRunStatisticsHandler::setQualifiedSpectrum(
return;
if(ms_level > _count_ms_level_spectrum.size())
{
- _count_ms_level_spectrum.resize(ms_level);
- _tic_ms_level_spectrum.resize(ms_level);
+ _count_ms_level_spectrum.resize(ms_level, 0);
+ _tic_ms_level_spectrum.resize(ms_level, 0);
}
_count_ms_level_spectrum[ms_level - 1]++;
@@ -77,6 +78,7 @@ MsRunStatisticsHandler::getMsLevelTic(unsigned int ms_level) const
return 0;
if(ms_level > _tic_ms_level_spectrum.size())
return 0;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << _tic_ms_level_spectrum[ms_level - 1];
return (_tic_ms_level_spectrum[ms_level - 1]);
}
--
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