prepare spectra sheet for PTM

src/output/ods/ptm/ptmspectrasheet.cpp

+/**
+ * \file /output/ods/ptm/ptmspectrasheet.cpp
+ * \date 16/2/2018
+ * \author Olivier Langella
+ * \brief ODS PTM spectra sheet
+ */
+
+/*******************************************************************************
+* Copyright (c) 2018 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 "ptmspectrasheet.h"
+
+
+PtmSpectraSheet::PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): SpectraSheet(p_ods_export, p_writer, p_project, QString("PTM spectra")) {
+    qDebug() << "PtmSpectraSheet::PtmSpectraSheet begin" ;
+    qDebug() << "PtmSpectraSheet::PtmSpectraSheet end" ;
+}
+
+void PtmSpectraSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+    _p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
+    
+    
+    qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList" ;
+    std::vector<PtmIslandSp> ptm_island_list;
+    for (auto ptm_island_sp : _p_ptm_grouping_experiment->getPtmIslandList() ) {
+        qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList copy" ;
+        ptm_island_list.push_back(ptm_island_sp);
+    }
+    qDebug() << "PtmIslandSheet::writeIdentificationGroup sort" ;
+    std::sort(ptm_island_list.begin(), ptm_island_list.end(),
+              [](PtmIslandSp & a, PtmIslandSp & b)
+    {
+        return a.get()->getGroupingId() < b.get()->getGroupingId();
+    });
+
+    qDebug() << "PtmIslandSheet::writeIdentificationGroup 2" ;
+    for (auto & ptm_island:ptm_island_list) {
+        writeOnePtmIsland(ptm_island);
+    }
+}

src/output/ods/ptm/ptmspectrasheet.h

+/**
+ * \file /output/ods/ptm/ptmspectrasheet.h
+ * \date 16/2/2018
+ * \author Olivier Langella
+ * \brief ODS PTM spectra sheet
+ */
+
+/*******************************************************************************
+* Copyright (c) 2018 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 PTMSPECTRASHEET_H
+#define PTMSPECTRASHEET_H
+
+#include "../../../core/project.h"
+#include <odsstream/calcwriterinterface.h>
+#include "../../../grouping/ptm/ptmisland.h"
+#include "../odsexport.h"
+#include "../spectrasheet.h"
+
+class PtmSpectraSheet:public SpectraSheet
+{
+public :
+    PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+protected :
+    void writeIdentificationGroup(IdentificationGroup * p_ident);
+
+protected:
+    const PtmGroupingExperiment * _p_ptm_grouping_experiment;
+
+};
+
+#endif // PTMSPECTRASHEET_H

src/output/ods/spectrasheet.cpp

@@ -31,11 +31,10 @@
 #include <tuple>
 #include <pappsomspp/utils.h>
 
-
-SpectraSheet::SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+SpectraSheet::SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name): _p_project(p_project) {
     _p_ods_export = p_ods_export;
     _p_writer = p_writer;
-    p_writer->writeSheet("spectra");
+    p_writer->writeSheet(sheet_name);
 
     std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
     for (IdentificationGroup * p_ident:identification_list) {
@@ -44,6 +43,9 @@ SpectraSheet::SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_wr
     }
 }
 
+SpectraSheet::SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): SpectraSheet(p_ods_export, p_writer, p_project, QString("spectra")) {
+}
+
 
 void SpectraSheet::writeCellHeader(PeptideListColumn column) {
     qDebug() << "SpectraSheet::writeCellHeader begin " << (std::int8_t) column;

src/output/ods/spectrasheet.h

@@ -40,13 +40,14 @@ class SpectraSheet
 {
 public :
     SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
-private :
-    void writeIdentificationGroup(IdentificationGroup * p_ident);
+protected :
+    SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name);
+    virtual void writeIdentificationGroup(IdentificationGroup * p_ident);
     void writeHeaders(IdentificationGroup * p_ident);
     void writeBestPeptideEvidence(const GroupingGroup * p_group, const PeptideEvidence * p_peptide_evidence);
     void writeCellHeader(PeptideListColumn column);
 
-private :
+protected :
     OdsExport * _p_ods_export;
     const Project * _p_project;
     CalcWriterInterface * _p_writer;