new protein xtp object and sequence database

src/CMakeLists.txt

@@ -58,6 +58,8 @@ SET(CPP_FILES
   core/peptidematch.cpp
   ./core/project.cpp
   core/proteinmatch.cpp
+  core/proteinxtp.cpp
+  core/sequencedatabase.cpp
   core/identification_sources/identificationdatasource.cpp
   core/identification_sources/identificationxtandemfile.cpp
   files/xpipfile.cpp

src/core/automaticfilterparameters.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 "automaticfilterparameters.h"
+
+AutomaticFilterParameters::AutomaticFilterParameters()
+{
+
+}
+
+AutomaticFilterParameters::AutomaticFilterParameters(const AutomaticFilterParameters& other)
+{
+
+}
+
+AutomaticFilterParameters::~AutomaticFilterParameters()
+{
+
+}
+
+void AutomaticFilterParameters::setFilterPeptideEvalue( pappso::pappso_double evalue) {
+    _filter_minimum_peptide_evalue = evalue;
+}
+
+void AutomaticFilterParameters::setFilterProteinEvalue( pappso::pappso_double evalue) {
+    _filter_minimum_protein_evalue = evalue;
+}
+void AutomaticFilterParameters::setFilterMinimumPeptidePerMatch(unsigned int number) {
+    _filter_minimum_peptide_per_match = number;
+}
+void AutomaticFilterParameters::setFilterCrossSamplePeptideNumber(bool cross) {
+    _filter_is_cross_sample_peptide_number = cross;
+}
+pappso::pappso_double AutomaticFilterParameters::getFilterPeptideEvalue() const {
+    return (_filter_minimum_peptide_evalue );
+}
+pappso::pappso_double AutomaticFilterParameters::getFilterProteinEvalue() const {
+    return ( _filter_minimum_protein_evalue );
+}
+unsigned int AutomaticFilterParameters::getFilterMinimumPeptidePerMatch()const {
+    return (_filter_minimum_peptide_per_match );
+}
+bool AutomaticFilterParameters::getFilterCrossSamplePeptideNumber()const {
+    return _filter_is_cross_sample_peptide_number ;
+}

src/core/automaticfilterparameters.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 AUTOMATICFILTERPARAMETERS_H
+#define AUTOMATICFILTERPARAMETERS_H
+#include <pappsomspp/types.h>
+
+class AutomaticFilterParameters
+{
+public:
+    AutomaticFilterParameters();
+    AutomaticFilterParameters(const AutomaticFilterParameters& other);
+    ~AutomaticFilterParameters();
+
+
+    void setFilterPeptideEvalue( pappso::pappso_double evalue);
+    void setFilterProteinEvalue( pappso::pappso_double evalue);
+    void setFilterMinimumPeptidePerMatch(unsigned int number);
+    void setFilterCrossSamplePeptideNumber(bool cross);
+
+    pappso::pappso_double getFilterPeptideEvalue() const;
+    pappso::pappso_double getFilterProteinEvalue()const;
+    unsigned int getFilterMinimumPeptidePerMatch()const;
+    bool getFilterCrossSamplePeptideNumber()const;
+
+
+private :
+
+    pappso::pappso_double _filter_minimum_peptide_evalue=1;
+    pappso::pappso_double _filter_minimum_protein_evalue=1;
+    unsigned int _filter_minimum_peptide_per_match=1;
+    bool _filter_is_cross_sample_peptide_number=false;
+};
+
+#endif // AUTOMATICFILTERPARAMETERS_H

src/core/identificationgroup.cpp

@@ -24,6 +24,7 @@
 #include "identificationgroup.h"
 #include "project.h"
 
+
 IdentificationGroup::IdentificationGroup(Project * project)
 {
     _p_project = project;
@@ -43,6 +44,7 @@ void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters
         p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
     }
 
+   
 }
 void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
     _protein_match_list.push_back(protein_match);

src/core/proteinmatch.cpp

@@ -63,6 +63,9 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
     }
 
 
+    //update protein evalue ?
+
+
     if (_number_of_valid_peptides >= automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
         if (_evalue <= automatic_filter_parameters.getFilterProteinEvalue()) {
             _proxy_valid = true;
@@ -70,7 +73,7 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
     }
 }
 
-const pappso::ProteinSp & ProteinMatch::getProteinSp() const {
+const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
     return _protein_sp;
 }
 void ProteinMatch::setEvalue(pappso::pappso_double evalue) {
@@ -80,7 +83,7 @@ void ProteinMatch::setEvalue(pappso::pappso_double evalue) {
 pappso::pappso_double ProteinMatch::getEvalue() const {
     return _evalue;
 }
-void ProteinMatch::setProteinSp(pappso::ProteinSp protein_sp) {
+void ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp) {
     _protein_sp = protein_sp;
 }
 
@@ -92,7 +95,7 @@ bool ProteinMatch::isChecked() const {
     return _checked;
 }
 
-bool ProteinMatch::isValidAndChecked() const{
+bool ProteinMatch::isValidAndChecked() const {
     return _proxy_valid && _checked;
 }
 

src/core/proteinmatch.h

@@ -21,25 +21,25 @@
 *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
 ******************************************************************************/
 
-#ifndef PROTEINMATCH_H
-#define PROTEINMATCH_H
-
 #include <vector>
 #include <pappsomspp/types.h>
-#include <pappsomspp/protein/protein.h>
+#include "proteinxtp.h"
 #include "peptidematch.h"
 #include "automaticfilterparameters.h"
 
+#ifndef PROTEINMATCH_H
+#define PROTEINMATCH_H
+
 class ProteinMatch
 {
 public:
     ProteinMatch();
     ~ProteinMatch();
     
-    const pappso::ProteinSp & getProteinSp() const;
+    const ProteinXtpSp & getProteinXtpSp() const;
     void setEvalue(pappso::pappso_double evalue);
     pappso::pappso_double getEvalue() const;
-    void setProteinSp(pappso::ProteinSp protein_sp);
+    void setProteinXtpSp(ProteinXtpSp protein_sp);
     void addPeptideMatch(PeptideMatch * peptide_match);
     std::vector<PeptideMatch *> & getPeptideMatchList();
     void setChecked(bool arg1);
@@ -54,7 +54,7 @@ public:
 
 private:
     std::vector<PeptideMatch *> _peptide_match_list;
-    pappso::ProteinSp _protein_sp = nullptr;
+    ProteinXtpSp _protein_sp = nullptr;
     pappso::pappso_double _evalue=0;
     /** @brief manually checked by user (true by default)
      */

src/core/proteinxtp.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 "proteinxtp.h"
+
+ProteinXtp::ProteinXtp():pappso::Protein()
+{
+
+}
+
+ProteinXtp::ProteinXtp(const ProteinXtp& other):pappso::Protein(other)
+{
+    _is_decoy=other._is_decoy;
+    _is_contaminant=other._is_contaminant;
+}
+
+ProteinXtp::~ProteinXtp()
+{
+
+}
+
+bool ProteinXtp::operator==(const ProteinXtp& other) const
+{
+    return pappso::Protein::operator==(other);
+}
+
+ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
+    return std::make_shared<ProteinXtp>(*this);
+}
+

src/core/proteinxtp.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
+******************************************************************************/
+
+#include <pappsomspp/protein/protein.h>
+#include "sequencedatabase.h"
+
+#ifndef PROTEIN_XTP_H
+#define PROTEIN_XTP_H
+
+
+class ProteinXtp;
+
+/** \brief shared pointer on a Protein object
+ */
+typedef std::shared_ptr<const ProteinXtp> ProteinXtpSp;
+
+class ProteinXtp : public pappso::Protein {
+public:
+    ProteinXtp();
+    ProteinXtp(const ProteinXtp& other);
+    virtual ~ProteinXtp();
+    bool operator==(const ProteinXtp& other) const;
+
+
+    ProteinXtpSp makeProteinXtpSp() const;
+
+private:
+    SequenceDatabase * _p_sequence_database;
+    bool _is_decoy=false;
+    bool _is_contaminant=false;
+};
+
+#endif // PROTEIN_XTP_H

src/core/sequencedatabase.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 "sequencedatabase.h"
+
+SequenceDatabase::SequenceDatabase()
+{
+
+}
+
+SequenceDatabase::~SequenceDatabase()
+{
+
+}

src/core/sequencedatabase.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 SEQUENCEDATABASE_H
+#define SEQUENCEDATABASE_H
+#include <memory>
+
+
+class SequenceDatabase;
+
+/** \brief shared pointer on a SequenceDatabase object
+ */
+typedef std::shared_ptr<SequenceDatabase> SequenceDatabaseSp;
+
+class SequenceDatabase
+{
+public:
+    SequenceDatabase();
+    virtual ~SequenceDatabase();
+};
+
+#endif // SEQUENCEDATABASE_H

src/gui/peptide_list_view/peptidelistwindow.cpp

@@ -73,7 +73,7 @@ PeptideListWindow::~PeptideListWindow()
 void PeptideListWindow::setProteinMatch(Project * p_project, ProteinMatch * p_protein_match) {
     _peptide_table_model_p->setProteinMatch(p_project, p_protein_match);
     _p_proxy_model->setSourceModel(_peptide_table_model_p);
-    ui->proteinLabel->setText(p_protein_match->getProteinSp().get()->getDescription());
+    ui->proteinLabel->setText(p_protein_match->getProteinXtpSp().get()->getDescription());
 
 }
 

src/gui/protein_list_view/proteintablemodel.cpp

@@ -167,12 +167,12 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
         }
         if (col == 1) {
             if (_p_identification_group != nullptr) {
-                return _p_identification_group->getProteinMatchList().at(row)->getProteinSp().get()->getAccession();
+                return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getAccession();
             }
         }
         if (col == 2) {
             if (_p_identification_group != nullptr) {
-                return _p_identification_group->getProteinMatchList().at(row)->getProteinSp().get()->getDescription();
+                return _p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getDescription();
             }
         }
         if (col == 3) {
@@ -219,7 +219,7 @@ void ProteinTableModel::onTableClicked(const QModelIndex &index)
 bool ProteinTableModel::acceptRow(int source_row) {
     ProteinMatch * protein_match = _p_identification_group->getProteinMatchList().at(source_row);
     if (!_protein_search_string.isEmpty()) {
-        if (!protein_match->getProteinSp().get()->getDescription().contains(_protein_search_string)) {
+        if (!protein_match->getProteinXtpSp().get()->getDescription().contains(_protein_search_string)) {
             return false;
         }
     }

src/input/xpipsaxhandler.cpp

@@ -292,7 +292,7 @@ bool XpipSaxHandler::endElement_sequence() {
     return true;
 }
 bool XpipSaxHandler::endElement_protein() {
-    _p_protein_match->setProteinSp(_current_protein.makeProteinSp());
+    _p_protein_match->setProteinXtpSp(_current_protein.makeProteinXtpSp());
 
     return true;
 }

src/input/xpipsaxhandler.h

@@ -25,7 +25,7 @@
 
 #include <QXmlDefaultHandler>
 #include <pappsomspp/pappsoexception.h>
-#include <pappsomspp/protein/protein.h>
+#include "../core/proteinxtp.h"
 #include <pappsomspp/peptide/peptide.h>
 #include <pappsomspp/amino_acid/aamodification.h>
 #include "../core/project.h"
@@ -83,7 +83,7 @@ private:
     Project * _p_project;
     ProteinMatch * _p_protein_match;
     PeptideMatch * _p_peptide_match;
-    pappso::Protein _current_protein;
+    ProteinXtp _current_protein;
     pappso::NoConstPeptideSp _current_peptide_sp;
     IdentificationGroup * _current_identification_group_p;