new fasta file object and identification engine parameters

src/CMakeLists.txt

@@ -61,6 +61,7 @@ SET(CPP_FILES
   core/proteinmatch.cpp
   core/proteinxtp.cpp
   core/sequencedatabase.cpp
+  files/fastafile.cpp
   files/xpipfile.cpp
   grouping/groupingexperiment.cpp
   grouping/groupinggroup.cpp

src/core/identification_sources/identificationdatasource.cpp

@@ -72,8 +72,15 @@ const QString& IdentificationDataSource::getIdentificationEngineVersion() const
 void IdentificationDataSource::setIdentificationEngineVersion(const QString& version) {
     _version = version;
 }
+void IdentificationDataSource::setIdentificationEngineParam(IdentificationEngineParam param, const QString& value) {
+    _params.insert(std::pair<IdentificationEngineParam, QString>(param, value));
+}
 
 pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
     pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp, scan_number);
     return spectrum_sp;
 }
+
+void IdentificationDataSource::addFastaFile (FastaFile file) {
+    _fastafile_list.push_back(file);
+}

src/core/identification_sources/identificationdatasource.h

@@ -27,6 +27,7 @@
 #include <pappsomspp/spectrum/spectrum.h>
 #include <memory>
 #include "../msrun.h"
+#include "../../files/fastafile.h"
 
 class Project;
 
@@ -65,6 +66,14 @@ public:
     /** \brief set identification engine version
      */
     virtual void setIdentificationEngineVersion(const QString& version);
+    
+    /** \brief set identification engine parameter value
+     */
+    virtual void setIdentificationEngineParam(IdentificationEngineParam param, const QString& value);
+    
+    /** \brief add Fastafile used by the identification engine
+     */
+    void addFastaFile (FastaFile file);
 
 protected :
     QString _resource_name;
@@ -73,6 +82,8 @@ private :
     //static std::map<QString, pappso::MsRunIdSp> _map_msrunidsp;
     QString _version;
     MsRunSp _ms_run_sp = nullptr;
+    std::map<IdentificationEngineParam, QString> _params;
+    std::vector<FastaFile> _fastafile_list;
 };
 
 #endif // IDENTIFICATIONDATASOURCE_H

src/files/fastafile.cpp

+
+/*******************************************************************************
+* 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 "fastafile.h"
+
+FastaFile::FastaFile(const QString & fasta_source) : _fasta_source(fasta_source)
+{
+
+}
+
+FastaFile::FastaFile(const QUrl & fasta_source) : _fasta_source(fasta_source)
+{
+
+}
+FastaFile::FastaFile(const QFileInfo & fasta_source): _fasta_source(fasta_source.absoluteFilePath())
+{
+}
+FastaFile::FastaFile(const FastaFile & other) : _fasta_source(other._fasta_source)
+{
+
+}
+FastaFile::~FastaFile()
+{
+
+}

src/files/fastafile.h

+
+/*******************************************************************************
+* 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 FASTAFILE_H
+#define FASTAFILE_H
+
+#include <QUrl>
+#include <QFileInfo>
+class FastaFile
+{
+public:
+    FastaFile(const QString & fasta_source);
+    FastaFile(const QUrl & fasta_source);
+    FastaFile(const QFileInfo & fasta_source);
+    FastaFile(const FastaFile & other);
+    ~FastaFile();
+
+private :
+    const QUrl _fasta_source;
+
+};
+
+#endif // FASTAFILE_H

src/input/xtandemsaxhandler.cpp

@@ -34,6 +34,7 @@
 #include <cmath>
 #include "../utils/peptidestore.h"
 #include "../utils/proteinstore.h"
+#include "../files/fastafile.h"
 
 XtandemSaxHandler::XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group,
                                      IdentificationDataSource * p_identification_data_source):_p_project(p_project)
@@ -334,8 +335,11 @@ bool XtandemSaxHandler::endElement_note() {
     else {
 
 //<group label="input parameters" type="parameters">
+        //<note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/QExactive_analysis_FDR_nosemi.xml</note>
+        if (_current_note_label == "list path, default parameters") {
+            _p_identification_data_source->setIdentificationEngineParam(IdentificationEngineParam::tandem_param,_current_text);
+        }
         /*
-         * 	<note type="input" label="list path, default parameters">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/QExactive_analysis_FDR_nosemi.xml</note>
         <note type="input" label="list path, taxonomy information">/gorgone/pappso/tmp/temp_condor_job8533994640337729751189420695540169/database.xml</note>
         <note type="input" label="output, histogram column width">30</note>
         <note type="input" label="output, histograms">yes</note>
@@ -441,23 +445,28 @@ bool XtandemSaxHandler::endElement_note() {
         */
 
 //<group label="performance parameters" type="parameters">
+
+        //<note label="list path, sequence source #1">/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta</note>
+        //<note label="list path, sequence source #2">/gorgone/pappso/formation/TD/Database/contaminants_standarts.fasta</note>
+        if (_current_note_label.startsWith("list path, sequence source")) {
+            _p_identification_data_source->addFastaFile(FastaFile(_current_text));
+        }
+
         /*
-        	<note label="list path, sequence source #1">/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta</note>
-        	<note label="list path, sequence source #2">/gorgone/pappso/formation/TD/Database/contaminants_standarts.fasta</note>
-        	<note label="list path, sequence source description #1">no description</note>
-        	<note label="list path, sequence source description #2">no description</note>
-        	<note label="modelling, duplicate peptide ids">6019</note>
-        	<note label="modelling, duplicate proteins">19735</note>
-        	<note label="modelling, estimated false positives">18</note>
-        	<note label="modelling, reversed sequence false positives">20</note>
-        	<note label="modelling, spectrum noise suppression ratio">0.00</note>
-        	<note label="modelling, total peptides used">96618641</note>
-        	<note label="modelling, total proteins used">273656</note>
-        	<note label="modelling, total spectra assigned">7464</note>
-        	<note label="modelling, total spectra used">12199</note>
-        	<note label="modelling, total unique assigned">6260</note>
-        	<note label="process, start time">2013:12:20:16:47:19</note>
-        	*/
+        <note label="list path, sequence source description #1">no description</note>
+        <note label="list path, sequence source description #2">no description</note>
+        <note label="modelling, duplicate peptide ids">6019</note>
+        <note label="modelling, duplicate proteins">19735</note>
+        <note label="modelling, estimated false positives">18</note>
+        <note label="modelling, reversed sequence false positives">20</note>
+        <note label="modelling, spectrum noise suppression ratio">0.00</note>
+        <note label="modelling, total peptides used">96618641</note>
+        <note label="modelling, total proteins used">273656</note>
+        <note label="modelling, total spectra assigned">7464</note>
+        <note label="modelling, total spectra used">12199</note>
+        <note label="modelling, total unique assigned">6260</note>
+        <note label="process, start time">2013:12:20:16:47:19</note>
+        */
         //<note label="process, version">X! Tandem Sledgehammer (2013.09.01.1)</note>
         if (_current_note_label == "process, version") {
             QRegExp rx("\\((.*)\\)");

src/utils/types.h

@@ -37,6 +37,13 @@ enum class IdentificationEngine {
     peptider ///< peptider
 };
 
+/** \def IdentificationEngineParam identification engine parameters
+ *
+ */
+enum class IdentificationEngineParam {
+    tandem_param ///< X!Tandem xml parameters file
+};
+
 /** \def GroupingType list of available grouping algoritms
  *
  */