groupingsheet.cpp

/**
 * \file /output/groupingsheet.cpp
 * \date 9/5/2017
 * \author Olivier Langella
 * \brief ODS grouping 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 "groupingsheet.h"


GroupingSheet::GroupingSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
    _p_writer = p_writer;
    _p_ods_export = p_ods_export;
    p_writer->writeSheet("groups");

    
    OdsTableSettings table_settings;
    table_settings.setVerticalSplit(1);
    _p_writer->setCurrentOdsTableSettings(table_settings);

    writeHeaders();

    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
    for (IdentificationGroup * p_ident:identification_list) {
        //writeHeaders(p_ident);
        writeIdentificationGroup(p_ident);
    }
}

void GroupingSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
    _p_writer->writeLine();
    if (_p_project->getProjectMode() == ProjectMode::individual) {
        _p_writer->writeCell(p_ident->getMsRunSpList().at(0).get()->getSampleName());
    }
    _p_writer->writeCell((unsigned int) p_ident->countGroup());
    _p_writer->writeCell((unsigned int) p_ident->countSubGroup());
    _p_writer->writeCell(p_ident->countProteinMatch(ValidationState::grouped));
    _p_writer->writeCell(p_ident->countPeptideMass(ValidationState::grouped));
    _p_writer->writeCell(p_ident->countPeptideMatch(ValidationState::grouped));
    //_p_writer->writeCell(p_ident->countSequence(ValidationState::grouped));
    _p_writer->writeCell(p_ident->countPeptideMassSample(ValidationState::grouped));
    _p_writer->writeCell(p_ident->getProteinFdr(ValidationState::valid));
    _p_writer->writeCell(p_ident->getPeptideMassFdr(ValidationState::valid));
}


void GroupingSheet::writeHeaders()  {
    // groups, subgroups, proteins, psm, sequence, peptide/mass, pep FDR, prot FDR

    _p_writer->writeLine();
    if (_p_project->getProjectMode() == ProjectMode::individual) {
        _p_writer->writeCell("sample");
    }
    _p_writer->setCellAnnotation("number of groups");
    _p_writer->writeCell("groups");
    _p_writer->setCellAnnotation("number of subgroups");
    _p_writer->writeCell("subgroups");
    _p_writer->setCellAnnotation("number of grouped proteins");
    _p_writer->writeCell("proteins");
    _p_writer->setCellAnnotation("number of distinct grouped peptides in the whole experiment");
    _p_writer->writeCell("peptides");
    _p_writer->setCellAnnotation("number of peptide hits : each grouped peptide spectrum match given by the identification engine");
    _p_writer->writeCell("psm");
    //_p_writer->writeCell("sequences");
    _p_writer->setCellAnnotation("number of unique combinations : grouped peptide sequence+modifications+sample name");
    _p_writer->writeCell("peptide/mass/sample");
    _p_writer->setCellAnnotation("FDR at the protein level (number of decoy valid proteins / totale number of valid proteins)");
    _p_writer->writeCell("prot FDR");
    _p_writer->setCellAnnotation("FDR at the peptide level (number of decoy valid peptides / totale number of valid peptides)");
    _p_writer->writeCell("pep FDR");


}