From ffe4369166c84682f344a63e1a7171680befb7d6 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 6 Nov 2017 21:53:01 +0100
Subject: [PATCH] fastafile object has an xml id
---
src/core/project.cpp | 4 ++++
src/core/project.h | 1 +
src/files/fastafile.cpp | 12 ++++++++----
src/files/fastafile.h | 5 +++++
src/output/ods/infosheet.cpp | 17 +++++++++--------
src/output/xpip.cpp | 2 +-
src/utils/fastafilestore.cpp | 11 +++++++----
src/utils/proteinstore.cpp | 20 ++++++++++----------
src/utils/proteinstore.h | 12 ++++++------
9 files changed, 51 insertions(+), 33 deletions(-)
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 834e30e3..4a370017 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -70,6 +70,10 @@ const GroupingType Project::getGroupingType() const {
FastaFileStore & Project::getFastaFileStore() {
return _fasta_file_store;
}
+
+const FastaFileStore & Project::getFastaFileStore() const {
+ return _fasta_file_store;
+}
MsRunStore & Project::getMsRunStore() {
return _msrun_store;
}
diff --git a/src/core/project.h b/src/core/project.h
index 78c0067a..b7cbebe5 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -53,6 +53,7 @@ public:
MsRunStore & getMsRunStore();
const MsRunStore & getMsRunStore() const;
FastaFileStore & getFastaFileStore();
+ const FastaFileStore & getFastaFileStore() const;
IdentificationDataSourceStore & getIdentificationDataSourceStore();
const IdentificationDataSourceStore & getIdentificationDataSourceStore() const;
void readXpipFile(WorkMonitorInterface * p_monitor, QFileInfo xpip_source);
diff --git a/src/files/fastafile.cpp b/src/files/fastafile.cpp
index e075c7ab..a4bbdef0 100644
--- a/src/files/fastafile.cpp
+++ b/src/files/fastafile.cpp
@@ -76,6 +76,12 @@ FastaFile::~FastaFile()
}
+void FastaFile::setXmlId(const QString xmlid) {
+ _xml_id = xmlid;
+}
+const QString & FastaFile::getXmlId() const {
+ return _xml_id;
+}
const QString FastaFile::getFilename() const {
return _fasta_source.fileName();
}
@@ -84,7 +90,7 @@ const QString FastaFile::getAbsoluteFilePath() const {
return _fasta_source.absoluteFilePath();
}
void FastaFile::setContaminants(ProteinStore & protein_store) const {
-
+ protein_store.addContaminantFastaFile(this);
if (_fasta_source.exists()) {
AccessionContaminantReader accession_reader(protein_store);
pappso::FastaReader reader(accession_reader);
@@ -92,7 +98,6 @@ 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";
@@ -106,7 +111,7 @@ void FastaFile::setContaminants(ProteinStore & protein_store) const {
}
void FastaFile::setDecoys(ProteinStore & protein_store) const {
-
+ protein_store.addDecoyFastaFile(this);
if (_fasta_source.exists()) {
AccessionDecoyReader accession_reader(protein_store);
pappso::FastaReader reader(accession_reader);
@@ -114,7 +119,6 @@ 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/files/fastafile.h b/src/files/fastafile.h
index 243f9dcb..59213a2f 100644
--- a/src/files/fastafile.h
+++ b/src/files/fastafile.h
@@ -50,9 +50,14 @@ public:
/** @brief read fasta file and set accessions as decoys
* */
void setDecoys(ProteinStore & protein_store) const;
+
+
+ void setXmlId(const QString xmlid);
+ const QString & getXmlId() const;
private :
const QFileInfo _fasta_source;
+ QString _xml_id;
};
diff --git a/src/output/ods/infosheet.cpp b/src/output/ods/infosheet.cpp
index ce22bd2c..ff5761fa 100644
--- a/src/output/ods/infosheet.cpp
+++ b/src/output/ods/infosheet.cpp
@@ -72,30 +72,31 @@ InfoSheet::InfoSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer,
p_writer->writeLine();
p_writer->writeLine();
- std::vector<FastaFile> conta_file_list = p_project->getProteinStore().getContaminantFastaFileList();
+ std::vector<const 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());
+ for (const FastaFile * fasta_file : conta_file_list) {
+ p_writer->writeCell(fasta_file->getAbsoluteFilePath());
}
-
}
- std::vector<FastaFile> decoy_file_list = p_project->getProteinStore().getDecoyFastaFileList();
+ p_writer->writeLine();
+
+ std::vector<const 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());
+ for (const FastaFile * fasta_file : decoy_file_list) {
+ p_writer->writeCell(fasta_file->getAbsoluteFilePath());
}
-
}
+ p_writer->writeLine();
}
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 733b6556..16a9e64d 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -189,7 +189,7 @@ void Xpip::writeMsrunList(const MsRunStore & msrun_store) {
_output_stream->writeStartElement("fasta_file_list");
for (FastaFileSp fasta_file_sp : fasta_store.getFastaFileList()) {
_output_stream->writeStartElement("fasta_file");
- //_output_stream->writeAttribute("id",fasta_file_sp.get()->getXmlId());
+ _output_stream->writeAttribute("id",fasta_file_sp.get()->getXmlId());
_output_stream->writeAttribute("path",fasta_file_sp.get()->getAbsoluteFilePath());
_output_stream->writeEndElement();
diff --git a/src/utils/fastafilestore.cpp b/src/utils/fastafilestore.cpp
index ddafcd3c..617b2998 100644
--- a/src/utils/fastafilestore.cpp
+++ b/src/utils/fastafilestore.cpp
@@ -29,6 +29,7 @@
******************************************************************************/
#include "fastafilestore.h"
+#include <pappsomspp/utils.h>
#include <QDebug>
FastaFileStore::FastaFileStore()
{
@@ -41,19 +42,21 @@ FastaFileStore::~FastaFileStore()
}
FastaFileSp FastaFileStore::getInstance(const FastaFile & location) {
-qDebug() << "FastaFileStore::getInstance() begin ";
-qDebug() << "FastaFileStore::getInstance() begin "<< location.getAbsoluteFilePath();
+ qDebug() << "FastaFileStore::getInstance() begin ";
+ qDebug() << "FastaFileStore::getInstance() begin "<< location.getAbsoluteFilePath();
std::vector<FastaFileSp>::iterator it = _map_fastafile.begin();
std::vector<FastaFileSp>::iterator itend = _map_fastafile.end();
while (it != itend) {
if (it->get()->getFilename() == location.getFilename()) {
-
-qDebug() << "FastaFileStore::getInstance() end b "<< it->get()->getFilename();
+
+ qDebug() << "FastaFileStore::getInstance() end b "<< it->get()->getFilename();
return *it;
}
it++;
}
FastaFileSp fastafile_sp = std::make_shared<FastaFile>(location);
+
+ fastafile_sp.get()->setXmlId(QString("fasta%1").arg(pappso::Utils::getLexicalOrderedString(_map_fastafile.size())));
_map_fastafile.push_back(fastafile_sp);
qDebug() << "FastaFileStore::getFastaFileList() end a " << _map_fastafile.size();
return fastafile_sp;
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index 733835e0..7a864097 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -48,12 +48,12 @@ ProteinStore::~ProteinStore()
}
- const std::vector<FastaFile> & ProteinStore::getContaminantFastaFileList() const {
- return _fasta_contaminant_list;
- }
- const std::vector<FastaFile> & ProteinStore::getDecoyFastaFileList() const {
- return _fasta_decoy_list;
- }
+const std::vector<const FastaFile *> & ProteinStore::getContaminantFastaFileList() const {
+ return _fasta_contaminant_list;
+}
+const std::vector<const FastaFile *> & ProteinStore::getDecoyFastaFileList() const {
+ return _fasta_decoy_list;
+}
QRegExp ProteinStore::getRegexpContaminant() const {
return (_regexp_contaminant);
}
@@ -93,11 +93,11 @@ void ProteinStore::clearContaminants() {
}
}
-void ProteinStore::addContaminantFastaFile(const FastaFile & fasta_file) {
- _fasta_contaminant_list.push_back(fasta_file);
+void ProteinStore::addContaminantFastaFile(const FastaFile * p_fasta_file) {
+ _fasta_contaminant_list.push_back(p_fasta_file);
}
-void ProteinStore::addDecoyFastaFile(const FastaFile & fasta_file) {
- _fasta_decoy_list.push_back(fasta_file);
+void ProteinStore::addDecoyFastaFile(const FastaFile * p_fasta_file) {
+ _fasta_decoy_list.push_back(p_fasta_file);
}
diff --git a/src/utils/proteinstore.h b/src/utils/proteinstore.h
index 454904b4..fa06e130 100644
--- a/src/utils/proteinstore.h
+++ b/src/utils/proteinstore.h
@@ -57,11 +57,11 @@ public:
QRegExp getRegexpContaminant() const;
- void addContaminantFastaFile(const FastaFile & fasta_file);
- void addDecoyFastaFile(const FastaFile & fasta_file);
+ void addContaminantFastaFile(const FastaFile * p_fasta_file);
+ void addDecoyFastaFile(const FastaFile * p_fasta_file);
- const std::vector<FastaFile> & getContaminantFastaFileList() const;
- const std::vector<FastaFile> & getDecoyFastaFileList() const;
+ const std::vector<const FastaFile *> & getContaminantFastaFileList() const;
+ const std::vector<const FastaFile *> & getDecoyFastaFileList() const;
void clearContaminants();
@@ -77,9 +77,9 @@ private :
std::map<QString, ProteinXtpSp> _map_accession_protein_list;
/** \brief decoy Fasta file liste */
- std::vector<FastaFile> _fasta_decoy_list;
+ std::vector<const FastaFile *> _fasta_decoy_list;
/** \brief contaminant Fasta file liste */
- std::vector<FastaFile> _fasta_contaminant_list;
+ std::vector<const FastaFile *> _fasta_contaminant_list;
/** \brief recognize decoy accession */
QRegExp _regexp_decoy;
--
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