peptide sheet

src/output/ods/peptidesheet.cpp

+/**
+ * \file output/ods/peptidesheet.cpp
+ * \date 27/4/2017
+ * \author Olivier Langella
+ * \brief ODS peptide sheet
+ */
+
+/*******************************************************************************
+* 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 "peptidesheet.h"
+
+
+PeptideSheet::PeptideSheet (CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+    _p_writer = p_writer;
+    p_writer->writeSheet("peptides");
+
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    for (IdentificationGroup * p_ident:identification_list) {
+
+        //writeHeaders(p_ident);
+        writeIdentificationGroup(p_ident);
+    }
+}
+
+PeptideSheet::~PeptideSheet()
+{
+
+}
+
+void PeptideSheet::writeHeaders(IdentificationGroup * p_ident)  {
+    // Group ID	Peptide ID	SequenceLI	Modifs	Charge	MH+ theo	Number of subgroups	Subgroup ids	Number of spectra
+  //MS Sample :	20120906_balliau_extract_1_A01_urnb-1
+
+
+    _p_writer->writeLine();
+    _p_writer->writeCell("Group ID");
+    _p_writer->writeCell("Peptide ID");
+    _p_writer->writeCell("SequenceLI");
+    _p_writer->writeCell("Modifs");
+    _p_writer->writeCell("Charge");
+    _p_writer->writeCell("MH+ theo");
+    _p_writer->writeCell("Number of subgroups");
+    _p_writer->writeCell("Number of spectra");
+
+
+}
+
+void PeptideSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+
+    writeHeaders(p_ident);
+    for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
+
+        std::vector<const ProteinMatch *> protein_match_list = group_pair.second.get()->getProteinMatchList();
+
+        std::sort(protein_match_list.begin(), protein_match_list.end(),
+                  [](const ProteinMatch * a, const ProteinMatch * b)
+        {
+            return a->getGrpProteinSp().get()->getSubGroupNumber() < b->getGrpProteinSp().get()->getSubGroupNumber();
+        });
+
+        for (auto & protein_match:protein_match_list) {
+            writeOneProtein(group_pair.second.get(), protein_match);
+        }
+    }
+    _p_writer->writeLine();
+    _p_writer->writeLine();
+}

src/output/ods/peptidesheet.h

+/**
+ * \file output/ods/peptidesheet.h
+ * \date 27/4/2017
+ * \author Olivier Langella
+ * \brief ODS peptide sheet
+ */
+
+/*******************************************************************************
+* 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 PEPTIDESHEET_H
+#define PEPTIDESHEET_H
+
+#include "../../core/project.h"
+#include <odsstream/calcwriterinterface.h>
+#include "../../core/proteinmatch.h"
+
+class PeptideSheet
+{
+public :
+    PeptideSheet (CalcWriterInterface * p_writer, const Project * p_project);
+private :
+    void writeIdentificationGroup(IdentificationGroup * p_ident);
+    void writeHeaders(IdentificationGroup * p_ident);
+    void writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match);
+
+private :
+    const Project * _p_project;
+    CalcWriterInterface * _p_writer;
+};
+
+
+#endif // PEPTIDESHEET_H

src/output/ods/proteinsheet.h

@@ -36,13 +36,13 @@
 
 class ProteinSheet
 {
-    public :
-        ProteinSheet (CalcWriterInterface * p_writer, const Project * p_project);
+public :
+    ProteinSheet (CalcWriterInterface * p_writer, const Project * p_project);
 private :
     void writeIdentificationGroup(IdentificationGroup * p_ident);
     void writeHeaders(IdentificationGroup * p_ident);
     void writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match);
-    
+
 private :
     const Project * _p_project;
     CalcWriterInterface * _p_writer;