description of the meaning of sheets in ODS output

src/output/ods/infosheet.cpp

@@ -6,97 +6,164 @@
  */
 
 /*******************************************************************************
-* 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
-******************************************************************************/
+ * 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 "infosheet.h"
 #include "../../config.h"
 #include <QDebug>
+#include <QSettings>
 
 
-InfoSheet::InfoSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
-    _p_ods_export = p_ods_export;
-    _p_writer = p_writer;
-    p_writer->writeSheet("X!TandemPipeline informations");
+InfoSheet::InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+                     const Project *p_project)
+  : _p_project(p_project)
+{
+  _p_ods_export = p_ods_export;
+  _p_writer     = p_writer;
+  p_writer->writeSheet("X!TandemPipeline informations");
 
-    p_writer->writeCell("X!TandemPipeline version :");
-    p_writer->writeLine();
-    p_writer->writeCell(QString("%1").arg(XTPCPP_VERSION));
+  p_writer->writeCell("X!TandemPipeline version :");
+  p_writer->writeLine();
+  p_writer->writeCell(QString("%1").arg(XTPCPP_VERSION));
 
-    p_writer->writeLine();
-    p_writer->writeLine();
-    p_writer->writeCell("X!TandemPipeline filters :");
-    p_writer->writeLine();
-    AutomaticFilterParameters filter_param = p_project->getAutomaticFilterParameters();
+  p_writer->writeLine();
+  p_writer->writeLine();
+  p_writer->writeCell("X!TandemPipeline filters :");
+  p_writer->writeLine();
+  AutomaticFilterParameters filter_param =
+    p_project->getAutomaticFilterParameters();
 
-    p_writer->writeCell("Mode");
-    if (p_project->getProjectMode() == ProjectMode::combined) {
-        p_writer->writeCell("combine");
+  p_writer->writeCell("Mode");
+  if(p_project->getProjectMode() == ProjectMode::combined)
+    {
+      p_writer->writeCell("combine");
     }
-    else {
-        p_writer->writeCell("individual");
+  else
+    {
+      p_writer->writeCell("individual");
     }
-    p_writer->writeLine();
-    p_writer->writeCell("Maximum peptide Evalue");
-    p_writer->writeCell(filter_param.getFilterPeptideEvalue());
-    p_writer->writeLine();
-    p_writer->writeCell("Minimum number of peptides per protein");
-    p_writer->writeCell(filter_param.getFilterMinimumPeptidePerMatch());
-    p_writer->writeLine();
-    p_writer->writeCell("Overall samples");
-    p_writer->writeCell(filter_param.getFilterCrossSamplePeptideNumber());
-    p_writer->writeLine();
-    p_writer->writeCell("Maximum protein Evalue");
-    p_writer->writeCell(filter_param.getFilterProteinEvalue());
-    p_writer->writeLine();
+  p_writer->writeLine();
+  p_writer->writeCell("Maximum peptide Evalue");
+  p_writer->writeCell(filter_param.getFilterPeptideEvalue());
+  p_writer->writeLine();
+  p_writer->writeCell("Minimum number of peptides per protein");
+  p_writer->writeCell(filter_param.getFilterMinimumPeptidePerMatch());
+  p_writer->writeLine();
+  p_writer->writeCell("Overall samples");
+  p_writer->writeCell(filter_param.getFilterCrossSamplePeptideNumber());
+  p_writer->writeLine();
+  p_writer->writeCell("Maximum protein Evalue");
+  p_writer->writeCell(filter_param.getFilterProteinEvalue());
+  p_writer->writeLine();
 
 
-    p_writer->writeLine();
-    p_writer->writeLine();
+  p_writer->writeLine();
+  p_writer->writeLine();
 
-    std::vector<const FastaFile *> conta_file_list = p_project->getProteinStore().getContaminantFastaFileList();
-    if (conta_file_list.size() == 0) {
-        p_writer->writeCell("contaminant pattern");
-        p_writer->writeCell(p_project->getProteinStore().getRegexpContaminant().pattern());
+  std::vector<const FastaFile *> conta_file_list =
+    p_project->getProteinStore().getContaminantFastaFileList();
+  if(conta_file_list.size() == 0)
+    {
+      p_writer->writeCell("contaminant pattern");
+      p_writer->writeCell(
+        p_project->getProteinStore().getRegexpContaminant().pattern());
     }
-    else {
-        p_writer->writeCell("contaminant fasta files");
-        for (const FastaFile * fasta_file : conta_file_list) {
-            p_writer->writeCell(fasta_file->getAbsoluteFilePath());
+  else
+    {
+      p_writer->writeCell("contaminant fasta files");
+      for(const FastaFile *fasta_file : conta_file_list)
+        {
+          p_writer->writeCell(fasta_file->getAbsoluteFilePath());
         }
     }
-    p_writer->writeLine();
-    
-    std::vector<const FastaFile *> decoy_file_list = p_project->getProteinStore().getDecoyFastaFileList();
-    if (conta_file_list.size() == 0) {
-        p_writer->writeCell("decoy pattern");
-        p_writer->writeCell(p_project->getProteinStore().getRegexpDecoy().pattern());
+  p_writer->writeLine();
+
+  std::vector<const FastaFile *> decoy_file_list =
+    p_project->getProteinStore().getDecoyFastaFileList();
+  if(conta_file_list.size() == 0)
+    {
+      p_writer->writeCell("decoy pattern");
+      p_writer->writeCell(
+        p_project->getProteinStore().getRegexpDecoy().pattern());
     }
-    else {
-        p_writer->writeCell("decoy fasta files");
-        for (const FastaFile * fasta_file : decoy_file_list) {
-            p_writer->writeCell(fasta_file->getAbsoluteFilePath());
+  else
+    {
+      p_writer->writeCell("decoy fasta files");
+      for(const FastaFile *fasta_file : decoy_file_list)
+        {
+          p_writer->writeCell(fasta_file->getAbsoluteFilePath());
         }
     }
-    p_writer->writeLine();
+  p_writer->writeLine();
 
-}
 
+  p_writer->writeLine();
+  p_writer->writeLine();
+  p_writer->writeCell("sheet definitions");
+  p_writer->writeLine();
+  p_writer->writeCell(QUrl("https://doi.org/10.1021/acs.jproteome.6b00632"),
+                      "X!TandemPipeline DOI link");
+  p_writer->writeLine();
+  QSettings settings;
+
+  if(settings.value("export_ods/groups", "true").toBool())
+    {
+      p_writer->writeCell("groups");
+      p_writer->writeCell("simple statistics on the current grouping "
+                          "experiment (numbers of groups, subgroups...)");
+      p_writer->writeLine();
+    }
+
+  if(settings.value("export_ods/proteins", "true").toBool())
+    {
+      p_writer->writeCell("proteins");
+      p_writer->writeCell(
+        "list of proteins after the protein inference computation");
+      p_writer->writeLine();
+    }
+  if(settings.value("export_ods/peptides", "true").toBool())
+    {
+      p_writer->writeCell("peptides");
+      p_writer->writeCell("list of peptides used by the grouping algorithm. "
+                          "Beware : peptides are intended as unique pairs of "
+                          "sequence+mass, given that Leucine and Isoleucine as "
+                          "the same mass, all Leucines are considered as "
+                          "Isoleucines");
+      p_writer->writeLine();
+    }
+  if(settings.value("export_ods/spectra", "true").toBool())
+    {
+      p_writer->writeCell("spectra");
+      p_writer->writeCell("list of all validated and checked spectrum match. "
+                          "Only the best assigned peptide (best Evalue) is "
+                          "reported ");
+      p_writer->writeLine();
+    }
+  if(settings.value("export_ods/peptidepos", "true").toBool())
+    {
+      p_writer->writeCell("peptide pos");
+      p_writer->writeCell("list of all *real* peptides identified on their "
+                          "proteins, with their position on the sequence.");
+      p_writer->writeLine();
+    }
+}