From 1dd2746f2037a2db1f8f3a573cbfc28bd2b1398f Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 6 Nov 2017 16:29:30 +0100
Subject: [PATCH] handle decoy and contaminant filter status, more information
in ODS output
---
src/core/project.cpp | 4 ++++
src/core/project.h | 1 +
src/files/fastafile.cpp | 2 ++
src/output/ods/infosheet.cpp | 30 ++++++++++++++++++++++++++++++
src/utils/proteinstore.cpp | 18 ++++++++++++++++++
src/utils/proteinstore.h | 16 ++++++++++++++++
6 files changed, 71 insertions(+)
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 743a3ceb5..834e30e30 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -84,6 +84,10 @@ ProteinStore & Project::getProteinStore() {
return _protein_store;
}
+const ProteinStore & Project::getProteinStore() const {
+ return _protein_store;
+}
+
IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() {
return _identification_data_source_store;
}
diff --git a/src/core/project.h b/src/core/project.h
index 52c8077be..78c0067a5 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -49,6 +49,7 @@ public:
ProjectSp makeProjectSp() const;
ProteinStore & getProteinStore();
PeptideStore & getPeptideStore();
+ const ProteinStore & getProteinStore() const;
MsRunStore & getMsRunStore();
const MsRunStore & getMsRunStore() const;
FastaFileStore & getFastaFileStore();
diff --git a/src/files/fastafile.cpp b/src/files/fastafile.cpp
index f4eb6876d..e075c7ab0 100644
--- a/src/files/fastafile.cpp
+++ b/src/files/fastafile.cpp
@@ -92,6 +92,7 @@ void FastaFile::setContaminants(ProteinStore & protein_store) const {
if (fasta_file.open(QIODevice::ReadOnly)) {
reader.parse(&fasta_file);
fasta_file.close();
+ protein_store.addContaminantFastaFile(*this);
}
else {
qDebug() << "FastaFile::setContaminants "<< _fasta_source.absoluteFilePath() << " not open";
@@ -113,6 +114,7 @@ void FastaFile::setDecoys(ProteinStore & protein_store) const {
if (fasta_file.open(QIODevice::ReadOnly)) {
reader.parse(&fasta_file);
fasta_file.close();
+ protein_store.addDecoyFastaFile(*this);
}
else {
qDebug() << "FastaFile::setDecoys "<< _fasta_source.absoluteFilePath() << " not open";
diff --git a/src/output/ods/infosheet.cpp b/src/output/ods/infosheet.cpp
index 038e9b62a..ce22bd2c2 100644
--- a/src/output/ods/infosheet.cpp
+++ b/src/output/ods/infosheet.cpp
@@ -67,5 +67,35 @@ InfoSheet::InfoSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer,
p_writer->writeCell("Maximum protein Evalue");
p_writer->writeCell(filter_param.getFilterProteinEvalue());
p_writer->writeLine();
+
+
+ p_writer->writeLine();
+ p_writer->writeLine();
+
+ std::vector<FastaFile> conta_file_list = p_project->getProteinStore().getContaminantFastaFileList();
+ if (conta_file_list.size() == 0) {
+ p_writer->writeCell("contaminant pattern");
+ p_writer->writeCell(p_project->getProteinStore().getRegexpContaminant().pattern());
+ }
+ else {
+ p_writer->writeCell("contaminant fasta files");
+ for (FastaFile & fasta_file : conta_file_list) {
+ p_writer->writeCell(fasta_file.getAbsoluteFilePath());
+ }
+
+ }
+ std::vector<FastaFile> decoy_file_list = p_project->getProteinStore().getDecoyFastaFileList();
+ if (conta_file_list.size() == 0) {
+ p_writer->writeCell("decoy pattern");
+ p_writer->writeCell(p_project->getProteinStore().getRegexpDecoy().pattern());
+ }
+ else {
+ p_writer->writeCell("decoy fasta files");
+ for (FastaFile & fasta_file : decoy_file_list) {
+ p_writer->writeCell(fasta_file.getAbsoluteFilePath());
+ }
+
+ }
+
}
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index 6a6a9666c..733835e0c 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -28,6 +28,7 @@
******************************************************************************/
#include "proteinstore.h"
+#include "../files/fastafile.h"
#include <QDebug>
#include <QSettings>
@@ -46,6 +47,13 @@ ProteinStore::~ProteinStore()
{
}
+
+ const std::vector<FastaFile> & ProteinStore::getContaminantFastaFileList() const {
+ return _fasta_contaminant_list;
+ }
+ const std::vector<FastaFile> & ProteinStore::getDecoyFastaFileList() const {
+ return _fasta_decoy_list;
+ }
QRegExp ProteinStore::getRegexpContaminant() const {
return (_regexp_contaminant);
}
@@ -73,16 +81,26 @@ void ProteinStore::setRegexpDecoyPattern(const QString & pattern) {
}
void ProteinStore::clearDecoys() {
+ _fasta_decoy_list.clear();
for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
acc_protein.second.get()->setIsDecoy(false);
}
}
void ProteinStore::clearContaminants() {
+ _fasta_contaminant_list.clear();
for (std::pair<const QString, ProteinXtpSp> & acc_protein :_map_accession_protein_list) {
acc_protein.second.get()->setIsContaminant(false);
}
}
+void ProteinStore::addContaminantFastaFile(const FastaFile & fasta_file) {
+ _fasta_contaminant_list.push_back(fasta_file);
+}
+void ProteinStore::addDecoyFastaFile(const FastaFile & fasta_file) {
+ _fasta_decoy_list.push_back(fasta_file);
+}
+
+
void ProteinStore::setDecoyAccession(QString accession) {
std::map<QString, ProteinXtpSp>::iterator it = _map_accession_protein_list.find(accession);
if (it != _map_accession_protein_list.end()) {
diff --git a/src/utils/proteinstore.h b/src/utils/proteinstore.h
index f0c50fb82..454904b4e 100644
--- a/src/utils/proteinstore.h
+++ b/src/utils/proteinstore.h
@@ -37,6 +37,9 @@
#include <QString>
#include <QRegExp>
#include <map>
+#include <vector>
+
+class FastaFile;
class ProteinStore
{
@@ -54,6 +57,13 @@ public:
QRegExp getRegexpContaminant() const;
+ void addContaminantFastaFile(const FastaFile & fasta_file);
+ void addDecoyFastaFile(const FastaFile & fasta_file);
+
+ const std::vector<FastaFile> & getContaminantFastaFileList() const;
+ const std::vector<FastaFile> & getDecoyFastaFileList() const;
+
+
void clearContaminants();
void clearDecoys();
@@ -65,6 +75,12 @@ private :
private :
std::map<QString, ProteinXtpSp> _map_accession_protein_list;
+
+ /** \brief decoy Fasta file liste */
+ std::vector<FastaFile> _fasta_decoy_list;
+ /** \brief contaminant Fasta file liste */
+ std::vector<FastaFile> _fasta_contaminant_list;
+
/** \brief recognize decoy accession */
QRegExp _regexp_decoy;
/** \brief recognize contaminant accession */
--
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