WIP : parsing pep XML files

src/input/pepxmlsaxhandler.cpp

+/**
+ * \file input/pepxmlsaxhandler.cpp
+ * \date 18/6/2018
+ * \author Olivier Langella
+ * \brief parse pepxml result file
+ */
+
+
+/*******************************************************************************
+ * 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/>.
+ *
+ ******************************************************************************/
+
+#include "pepxmlsaxhandler.h"
+
+
+#include <pappsomspp/exception/exceptionnotfound.h>
+#include <cmath>
+#include "../core/peptideevidence.h"
+#include "../utils/peptidestore.h"
+#include "../utils/proteinstore.h"
+
+PepXmlSaxHandler::PepXmlSaxHandler(WorkMonitorInterface *p_monitor,
+                                   Project *p_project)
+  : _p_project(p_project)
+{
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  _p_monitor = p_monitor;
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}
+
+PepXmlSaxHandler::~PepXmlSaxHandler()
+{
+}
+
+
+bool
+PepXmlSaxHandler::startElement(const QString &namespaceURI,
+                               const QString &localName, const QString &qName,
+                               const QXmlAttributes &attributes)
+{
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  _tag_stack.push_back(qName);
+  bool is_ok = true;
+
+  try
+    {
+      // startElement_group
+      if(_tag_stack.size() == 1)
+        {
+          _is_xtpcpp_xpip = true;
+          if(qName != "xpip")
+            {
+              _is_xtpcpp_xpip = false;
+              throw pappso::ExceptionNotFound(
+                QObject::tr("ERROR this file is not a pep xml file %1")
+                  .arg(qName));
+            }
+        }
+      else if(qName == "protein_match")
+        {
+          if(_count_total % 100 == 0)
+            {
+              _p_monitor->message(QString("reading protein matches %1 on %2")
+                                    .arg(_count_protein_matches)
+                                    .arg(_total_protein_matches),
+                                  _count_total);
+            }
+          is_ok = startElement_protein_match(attributes);
+        }
+      else if(qName == "peptide_match")
+        {
+          is_ok = startElement_peptide_match(attributes);
+        }
+      else if(qName == "protein")
+        {
+          if(_count_total % 100 == 0)
+            {
+              _p_monitor->message(QString("reading proteins %1 on %2")
+                                    .arg(_count_proteins)
+                                    .arg(_total_proteins),
+                                  _count_total);
+            }
+          is_ok = startElement_protein(attributes);
+        }
+      else if(qName == "identification_source")
+        {
+          is_ok = startElement_identification_source(attributes);
+        }
+      else if(qName == "param")
+        {
+          is_ok = startElement_param(attributes);
+        }
+      else if(qName == "stat")
+        {
+          is_ok = startElement_stat(attributes);
+        }
+      else if(qName == "identification_group")
+        {
+          is_ok = startElement_identification_group(attributes);
+        }
+      else if(qName == "peptide_evidence_list")
+        {
+          is_ok = startElement_peptide_evidence_list(attributes);
+        }
+      else if(qName == "counts")
+        {
+          is_ok = startElement_counts(attributes);
+        }
+      else if(qName == "label_method")
+        {
+          is_ok = startElement_label_method(attributes);
+        }
+      //<sample value="P6_08_10"/>
+      else if(qName == "msrun")
+        {
+          is_ok = startElement_msrun(attributes);
+        }
+      else if(qName == "peptide")
+        {
+          if(_count_total % 100 == 0)
+            {
+              _p_monitor->message(QObject::tr("reading peptide %1 on %2")
+                                    .arg(_count_peptides)
+                                    .arg(_total_peptides),
+                                  _count_total);
+            }
+          is_ok = startElement_peptide(attributes);
+        }
+      else if(qName == "peptide_evidence")
+        {
+          if(_count_total % 100 == 0)
+            {
+              _p_monitor->message(
+                QObject::tr("reading peptide evidence %1 on %2")
+                  .arg(_count_peptide_evidences)
+                  .arg(_total_peptide_evidences),
+                _count_total);
+            }
+          is_ok = startElement_peptide_evidence(attributes);
+        }
+      else if(qName == "modification")
+        {
+          is_ok = startElement_modification(attributes);
+        }
+      else if(qName == "mod")
+        {
+          is_ok = startElement_mod(attributes);
+        }
+      else if(qName == "filter_params")
+        {
+          is_ok = startElement_filter_params(attributes);
+        }
+      else if(qName == "description")
+        {
+          is_ok = startElement_description(attributes);
+        }
+      else if(qName == "fasta_file")
+        {
+          is_ok = startElement_fasta_file(attributes);
+        }
+      else if(qName == "contaminants")
+        {
+          is_ok = startElement_contaminants(attributes);
+        }
+      else if(qName == "decoys")
+        {
+          is_ok = startElement_decoys(attributes);
+        }
+
+      _current_text.clear();
+    }
+  catch(pappso::PappsoException exception_pappso)
+    {
+      _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::startElement tag "
+                              "%1, PAPPSO exception:\n%2")
+                    .arg(qName)
+                    .arg(exception_pappso.qwhat());
+      return false;
+    }
+  catch(std::exception exception_std)
+    {
+      _errorStr =
+        QObject::tr(
+          "ERROR in PepXmlSaxHandler::startElement tag %1, std exception:\n%2")
+          .arg(qName)
+          .arg(exception_std.what());
+      return false;
+    }
+  return is_ok;
+}
+
+bool
+PepXmlSaxHandler::endElement(const QString &namespaceURI,
+                             const QString &localName, const QString &qName)
+{
+
+  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+  bool is_ok = true;
+  // endElement_peptide_list
+  try
+    {
+      if(qName == "protein")
+        {
+          is_ok = endElement_protein();
+        }
+      else if(qName == "peptide")
+        {
+          is_ok = endElement_peptide();
+        }
+      else if(qName == "msrun")
+        {
+          is_ok = endElement_msrun();
+        }
+      else if(qName == "sequence")
+        {
+          is_ok = endElement_sequence();
+        }
+      else if(qName == "protein_match")
+        {
+          is_ok = endElement_protein_match();
+        }
+      else if(qName == "peptide_evidence")
+        {
+          is_ok = endElement_peptide_evidence();
+        }
+      else if(qName == "peptide_evidence_list")
+        {
+          is_ok = endElement_peptide_evidence_list();
+        }
+      else if(qName == "identification_group")
+        {
+          is_ok = endElement_identification_group();
+        }
+      else if(qName == "identification_source")
+        {
+          is_ok = endElement_identification_source();
+        }
+
+      // end of detection_moulon
+      // else if ((_tag_stack.size() > 1) &&
+      //         (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
+    }
+  catch(pappso::PappsoException exception_pappso)
+    {
+      _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::endElement tag %1, "
+                              "PAPPSO exception:\n%2")
+                    .arg(qName)
+                    .arg(exception_pappso.qwhat());
+      return false;
+    }
+  catch(std::exception exception_std)
+    {
+      _errorStr =
+        QObject::tr(
+          "ERROR in PepXmlSaxHandler::endElement tag %1, std exception:\n%2")
+          .arg(qName)
+          .arg(exception_std.what());
+      return false;
+    }
+
+  _current_text.clear();
+  _tag_stack.pop_back();
+
+  return is_ok;
+}
+
+// <msms_pipeline_analysis date="2015-01-19T13:28:41"
+// xmlns="http://regis-web.systemsbiology.net/pepXML"
+// xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+// xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"
+// summary_xml="/gorgone/pappso/abrf_2015/mzXML/JD_06232014_sample1-A.pep.xml">
+
+bool
+PepXmlSaxHandler::startElement_msms_pipeline_analysis(QXmlAttributes attributes)
+{
+  QString original_filename = attributes.value("summary_xml");
+}
+
+// <msms_run_summary
+// base_name="/gorgone/pappso/abrf_2015/mzXML/JD_06232014_sample1-A"
+// msManufacturer="Thermo Scientific" msModel="Q Exactive"
+// raw_data_type="raw" raw_data=".mzXML">
+bool
+PepXmlSaxHandler::startElement_msms_run_summary(QXmlAttributes attributes)
+{
+  QString mz_datafile = QString("%1%2")
+                          .arg(attributes.value("base_name"))
+                          .arg(attributes.value("raw_data"));
+}
+
+// <search_database
+// local_path="/gorgone/pappso/abrf_2015/fasta/iPRG2015.fasta" type="AA"/>
+bool
+PepXmlSaxHandler::startElement_search_database(QXmlAttributes attributes)
+{
+  QString fastafile = attributes.value("local_path");
+}
+
+// <search_summary
+// base_name="/gorgone/pappso/moulon/users/Olivier/Delphine_Pecqueur/mzXML/330_01_01_C3G3_150122_01"
+// search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic"
+// fragment_mass_type="monoisotopic" search_id="1">
+bool
+PepXmlSaxHandler::startElement_search_summary(QXmlAttributes attributes)
+{
+  _current_search_engine = attributes.value("search_engine");
+}
+
+// <spectrum_query spectrum="JD_06232014_sample1-A.00005.00005.2"
+// start_scan="5" end_scan="5" precursor_neutral_mass="819.347822"
+// assumed_charge="2" index="1" retention_time_sec="1.4">
+// <spectrum_query spectrum="JD_06232014_sample1-A.00006.00006.2"
+// start_scan="6" end_scan="6" precursor_neutral_mass="870.405029296875"
+// assumed_charge="2" index="1">
+bool
+PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
+{
+  unsigned int start_scan = attributes.value("start_scan").toUInt();
+  unsigned int end_scan   = attributes.value("end_scan").toUInt();
+  if(start_scan != end_scan)
+    {
+      String message = "ERROR reading pepxml file :\n" +
+                       "unable to read search results from '" +
+                       this.currentSearchEngine + "' as start " +
+                       currentStartScan + " and end " + currentEndScan +
+                       " scans are different";
+      logger.error(message);
+      throw new MSMSException(message);
+    }
+  currentZ = new Integer(attrs.getValue("assumed_charge"));
+  if(attrs.getValue("retention_time_sec") == null)
+    {
+      String message =
+        "ERROR reading pepxml file :\n" +
+        "unable to read search results from '" + this.currentSearchEngine +
+        "' as retention time is not given in spectrum_query elements";
+      logger.warn(message);
+      // throw new MSMSException(message);
+
+      currentRt = (double)0;
+    }
+  else
+    {
+      currentRt = new Double(attrs.getValue("retention_time_sec"));
+    }
+  currentPrecursorNeutralMass =
+    new Double(attrs.getValue("precursor_neutral_mass")) + Utils.mhplus;
+}
+
+// <search_hit hit_rank="5" peptide="MKDFSTK" peptide_prev_aa="K"
+// peptide_next_aa="R" protein="sp|P34218|SAS3_YEAST" num_tot_proteins="1"
+// num_matched_ions="2" tot_num_ions="12" calc_neutral_pep_mass="871.410939"
+// massdiff="-1.006264" num_tol_term="2" num_missed_cleavages="1"
+// num_matched_peptides="190">
+bool
+PepXmlSaxHandler::startElement_search_hit(QXmlAttributes attributes)
+{
+  QString proteinName = attributes.value("protein");
+
+  Protein protein = new Protein();
+  protein.set_description(proteinName);
+  if(identification.contain_protein(protein))
+    {
+      // new protein, new match
+      currentMatch = new Match();
+      currentMatch.set_protein_match(protein);
+      identification.add_protein(protein, currentMatch);
+    }
+
+  else
+    {
+      // get existing match for this protein
+      currentMatch = (Match)identification.get_match(protein);
+    }
+  protein = currentMatch.get_protein_match();
+  protein.setDatabase(
+    identification.getDatabaseSet().getInstance(this.fastaFile.getName()));
+
+  this.currentPeptide = new PeptideProphet();
+  currentPeptide.set_sample_id(
+    identification.getMsRunSet().getInstance(identificationDataSource),
+    identificationDataSource);
+
+  _current_peptide_sp =
+    PeptideXtp(attributes.value("peptide").simplified()).makePeptideXtpSp();
+
+  currentPeptide.set_pre(attrs.getValue("peptide_prev_aa"));
+  currentPeptide.set_post(attrs.getValue("peptide_next_aa"));
+
+  currentPeptide.set_scan(this.currentEndScan.intValue());
+  Double calc_neutral_pep_mass =
+    new Double(attrs.getValue("calc_neutral_pep_mass")) + Utils.mhplus;
+  Double massdiff = new Double(attrs.getValue("massdiff"));
+
+  currentPeptide.set_mhplus_theo(calc_neutral_pep_mass);
+  currentPeptide.set_deltamass(massdiff);
+  currentPeptide.set_mhplus_obser(currentPrecursorNeutralMass);
+  currentPeptide.set_charge(this.currentZ);
+  currentPeptide.setRt(this.currentRt.floatValue());
+
+  /*
+   * if (Math.abs(massdiff) > 1) { String message =
+   * "massdiff is too high"; logger.error(message); throw new
+   * MSMSException(message); }
+   */
+  // valeur specifique de la séquence matche
+  // peptide.set_start(Integer.parseInt(attrs.getValue("start")));
+  // peptide.set_stop(Integer.parseInt(attrs.getValue("end")));
+  // peptide.set_evalue(Float.valueOf(attrs.getValue("expect")));
+  // peptide.set_hypercorr(Float.valueOf(attrs.getValue("hyperscore")));
+}
+
+bool
+XtpXpipSaxHandler::endElement_search_hit()
+{
+  if(currentPeptideProphetProbability != null)
+    {
+      currentPeptide.setProphetProbability(currentPeptideProphetProbability);
+    }
+  if(currentPeptideInterProphetProbability != null)
+    {
+      currentPeptide.setInterProphetProbability(
+        currentPeptideInterProphetProbability);
+    }
+  currentPeptide.setSearchEngine(this.currentSearchEngine);
+
+  identification.add_peptide(this.currentPeptide);
+  currentMatch.add_peptide_match(currentPeptide);
+
+  currentPeptideProphetProbability      = null;
+  currentPeptideInterProphetProbability = null;
+  currentExpectedValue                  = null;
+}
+
+// <peptideprophet_result probability="0.0245"
+// all_ntt_prob="(0.0000,0.0093,0.0245)">
+bool
+PepXmlSaxHandler::startElement_peptideprophet_result(QXmlAttributes attributes)
+{
+  this.currentPeptideProphetProbability =
+    Double.parseDouble(attrs.getValue("probability"));
+}
+
+// <interprophet_result probability="0.00886064"
+// all_ntt_prob="(0,0.0033303,0.00886064)">
+bool
+PepXmlSaxHandler::startElement_interprophet_result(QXmlAttributes attributes)
+{
+  this.currentPeptideInterProphetProbability =
+    Double.parseDouble(attrs.getValue("probability"));
+}
+
+/*
+ * <search_score name="xcorr" value="0.528"/> <search_score name="deltacn"
+ * value="0.059"/> <search_score name="deltacnstar" value="0.000"/>
+ * <search_score name="spscore" value="29.4"/> <search_score name="sprank"
+ * value="2"/> <search_score name="expect" value="1.00E+00"/>
+ */
+bool
+PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes)
+{
+  String name     = attrs.getValue("name");
+  String valueStr = attrs.getValue("value");
+  if(!valueStr.isEmpty())
+    {
+      if(name.equals("expect"))
+        {
+          currentExpectedValue = new Double(valueStr);
+          currentPeptide.set_evalue(currentExpectedValue.floatValue());
+        }
+      // <search_score name="hyperscore" value="232"/>
+      if(name.equals("hyperscore"))
+        {
+          currentPeptide.set_hypercorr(Float.parseFloat(valueStr));
+        }
+    }
+}
+
+// <modification_info modified_peptide="SQRDCR"> <mod_aminoacid_mass
+// position="5" mass="160.030649"/> </modification_info>
+bool
+PepXmlSaxHandler::startElement_mod_aminoacid_mass(QXmlAttributes attributes)
+{
+  double massFloat = attributes.value("mass").toDouble();
+  int position    = attributes.value("position").toUInt();
+  String aa = _current_peptide_sp.get()->getSequence().substring(position - 1, position);
+  Float massDiff = massFloat - Utils.getAaMass(aa.charAt(0));
+
+  this.currentPeptide.set_Modifs(aa, position - 1, massDiff);
+  // modifs liste for isotopic analysis
+  identification.add_modifs_to_liste(new Modifs(massFloat));
+
+    pappso::AaModificationP modif = Utils::guessAaModificationPbyMonoisotopicMassDelta(attributes.value("modified").simplified().toDouble());
+    
+pappso::AaModificationP modif = pappso::AaModification::getInstance(attributes.value("mass").simplified());
+  unsigned int position = attributes.value("position").simplified().toUInt();
+  _current_peptide_sp.get()->addAaModification(modif, position-1);
+}
+
+
+bool
+PepXmlSaxHandler::endElement_modification_info()
+{
+}
+
+
+bool PepXmlSaxHandler::error(const QXmlParseException &exception) {
+    _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                            "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
+                    exception.message());
+
+    return false;
+}
+
+
+bool PepXmlSaxHandler::fatalError(const QXmlParseException &exception) {
+    _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                            "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
+                    exception.message());
+    return false;
+}
+
+QString PepXmlSaxHandler::errorString() const {
+    return _errorStr;
+}
+
+
+bool PepXmlSaxHandler::endDocument() {
+    return true;
+}
+
+bool PepXmlSaxHandler::startDocument() {
+    return true;
+}
+
+bool PepXmlSaxHandler::characters(const QString &str) {
+    _current_text += str;
+    return true;
+}

src/input/pepxmlsaxhandler.h

+/**
+ * \file input/pepxmlsaxhandler.h
+ * \date 18/6/2018
+ * \author Olivier Langella
+ * \brief parse pepxml result file
+ */
+
+
+/*******************************************************************************
+* 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/>.
+*
+******************************************************************************/
+
+
+#ifndef PEPXMLSAXHANDLER_H
+#define PEPXMLSAXHANDLER_H
+
+#include <QXmlDefaultHandler>
+#include <pappsomspp/pappsoexception.h>
+#include "../core/proteinxtp.h"
+#include "../core/peptidextp.h"
+#include <pappsomspp/amino_acid/aamodification.h>
+#include "../core/project.h"
+#include "../core/proteinmatch.h"
+
+class PepXmlSaxHandler : public QXmlDefaultHandler
+{
+  public:
+  PepXmlSaxHandler(Project *p_project,
+                    IdentificationGroup *p_identification_group,
+                    IdentificationDataSource *p_identification_data_source);
+  ~PepXmlSaxHandler();
+
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
+
+  bool endElement(const QString &namespaceURI, const QString &localName,
+                  const QString &qName);
+
+  bool startDocument();
+
+  bool endDocument();
+
+  bool characters(const QString &str);
+
+  bool fatalError(const QXmlParseException &exception);
+  bool error(const QXmlParseException &exception);
+
+  QString errorString() const;
+
+
+  private:
+  bool startElement_msms_pipeline_analysis(QXmlAttributes attrs);
+  bool startElement_protein(QXmlAttributes attributes);
+  bool startElement_note(QXmlAttributes attributes);
+  bool startElement_file(QXmlAttributes attributes);
+  bool startElement_aa(QXmlAttributes attributes);
+  bool startElement_domain(QXmlAttributes attributes);
+  bool endElement_domain();
+  bool endElement_note();
+
+  private:
+  std::vector<QString> _tag_stack;
+  QString _errorStr;
+  QString _current_text;
+
+  Project *_p_project;
+  IdentificationGroup *_p_identification_group;
+  IdentificationDataSource *_p_identification_data_source;
+  MsRunSp _sp_msrun;
+
+  ProteinMatch *_p_protein_match;
+  PeptideEvidence *_p_peptide_evidence;
+  PeptideMatch _current_peptide_match;
+  ProteinXtp _current_protein;
+  PeptideXtpSp _current_peptide_sp;
+
+  QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
+
+  QString _current_group_label;
+  QString _current_group_type;
+  QString _current_note_label;
+  QString _current_note_type;
+  unsigned int _scan;
+  pappso::pappso_double _mhplus_obser;
+  unsigned int _charge;
+  pappso::pappso_double _retention_time;
+  bool _is_protein_description = false;
+};
+
+#endif // PEPXMLSAXHANDLER_H

src/input/xtandemsaxhandler.h

@@ -7,26 +7,27 @@
 
 
 /*******************************************************************************
-* 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
+ ******************************************************************************/
 
 #ifndef XTANDEMSAXHANDLER_H
 #define XTANDEMSAXHANDLER_H
@@ -40,68 +41,69 @@
 #include "../core/project.h"
 #include "../core/proteinmatch.h"
 
-class XtandemSaxHandler: public QXmlDefaultHandler
+class XtandemSaxHandler : public QXmlDefaultHandler
 {
-public:
-    XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group, 
-    IdentificationDataSource * p_identification_data_source);
-    ~XtandemSaxHandler();
-
-    bool startElement(const QString & namespaceURI, const QString & localName,
-                      const QString & qName, const QXmlAttributes & attributes);
-
-    bool endElement(const QString & namespaceURI, const QString & localName,
-                    const QString & qName);
-
-    bool startDocument();
-
-    bool endDocument();
-
-    bool characters(const QString &str);
-
-    bool fatalError(const QXmlParseException &exception);
-    bool error(const QXmlParseException &exception);
-
-    QString errorString() const;
-
-
-private:
-    bool startElement_group(QXmlAttributes attrs);
-    bool startElement_protein(QXmlAttributes attributes);
-    bool startElement_note(QXmlAttributes attributes);
-    bool startElement_file(QXmlAttributes attributes);
-    bool startElement_aa(QXmlAttributes attributes);
-    bool startElement_domain(QXmlAttributes attributes);
-    bool endElement_domain();
-    bool endElement_note();
-
-private:
-    std::vector<QString> _tag_stack;
-    QString _errorStr;
-    QString _current_text;
-
-    Project * _p_project;
-    IdentificationGroup * _p_identification_group;
-    IdentificationDataSource * _p_identification_data_source;
-    MsRunSp _sp_msrun;
-
-    ProteinMatch * _p_protein_match;
-    PeptideEvidence * _p_peptide_evidence;
-    PeptideMatch _current_peptide_match;
-    ProteinXtp _current_protein;
-    PeptideXtpSp _current_peptide_sp;
-
-    QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
-
-    QString _current_group_label;
-    QString _current_group_type;
-    QString _current_note_label;
-    QString _current_note_type;
-    unsigned int _scan;
-    pappso::pappso_double _mhplus_obser;
-    unsigned int _charge;
-    pappso::pappso_double _retention_time;
-    bool _is_protein_description = false;
+  public:
+  XtandemSaxHandler(Project *p_project,
+                    IdentificationGroup *p_identification_group,
+                    IdentificationDataSource *p_identification_data_source);
+  ~XtandemSaxHandler();
+
+  bool startElement(const QString &namespaceURI, const QString &localName,
+                    const QString &qName, const QXmlAttributes &attributes);
+
+  bool endElement(const QString &namespaceURI, const QString &localName,
+                  const QString &qName);
+
+  bool startDocument();
+
+  bool endDocument();
+
+  bool characters(const QString &str);
+
+  bool fatalError(const QXmlParseException &exception);
+  bool error(const QXmlParseException &exception);
+
+  QString errorString() const;
+
+
+  private:
+  bool startElement_group(QXmlAttributes attrs);
+  bool startElement_protein(QXmlAttributes attributes);
+  bool startElement_note(QXmlAttributes attributes);
+  bool startElement_file(QXmlAttributes attributes);
+  bool startElement_aa(QXmlAttributes attributes);
+  bool startElement_domain(QXmlAttributes attributes);
+  bool endElement_domain();
+  bool endElement_note();
+
+  private:
+  std::vector<QString> _tag_stack;
+  QString _errorStr;
+  QString _current_text;
+
+  Project *_p_project;
+  IdentificationGroup *_p_identification_group;
+  IdentificationDataSource *_p_identification_data_source;
+  MsRunSp _sp_msrun;
+
+  ProteinMatch *_p_protein_match;
+  PeptideEvidence *_p_peptide_evidence;
+  PeptideMatch _current_peptide_match;
+  ProteinXtp _current_protein;
+  PeptideXtpSp _current_peptide_sp;
+
+  QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
+
+  QString _current_group_label;
+  QString _current_group_type;
+  QString _current_note_label;
+  QString _current_note_type;
+  unsigned int _scan;
+  pappso::pappso_double _mhplus_obser;
+  unsigned int _charge;
+  pappso::pappso_double _retention_time;
+  bool _is_protein_description = false;
 };
 
 #endif // XTANDEMSAXHANDLER_H

src/main.cpp

 
 /*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-*     PAPPSOms-tools 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.
-*
-*     PAPPSOms-tools 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 PAPPSOms-tools.  If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-*     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of PAPPSOms-tools.
+ *
+ *     PAPPSOms-tools 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.
+ *
+ *     PAPPSOms-tools 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 PAPPSOms-tools.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
 
+#include "config.h"
+#include "gui/mainwindow.h"
+#include "utils/types.h"
 #include <QApplication>
 #include <QTimer>
 #include <iostream>
 #include <pappsomspp/pappsoexception.h>
-#include "config.h"
-#include "gui/mainwindow.h"
-#include "utils/types.h"
 
 using namespace std;
 
-int main(int argc, char *argv[])
+int
+main(int argc, char *argv[])
 {
-    QTextStream errorStream(stderr, QIODevice::WriteOnly);
-    QApplication app(argc, argv);
+  QTextStream errorStream(stderr, QIODevice::WriteOnly);
+  QApplication app(argc, argv);
 
-    qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
-    qRegisterMetaType<std::vector<pappso::mz>>("std::vector<pappso::mz>");
-    qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
-    qRegisterMetaType<std::vector<pappso::XicSp>>("std::vector<pappso::XicSp>");
-    qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
-    qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
-    qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
-    qRegisterMetaType<MsRunSp>("MsRunSp");
-    qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>("std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
-    
+  qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
+  qRegisterMetaType<std::vector<pappso::mz>>("std::vector<pappso::mz>");
+  qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
+  qRegisterMetaType<std::vector<pappso::XicSp>>("std::vector<pappso::XicSp>");
+  qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
+  qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
+  qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
+  qRegisterMetaType<MsRunSp>("MsRunSp");
+  qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>(
+    "std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
 
-    try {
-        QCoreApplication::setOrganizationName("PAPPSO");
-        QCoreApplication::setOrganizationDomain("pappso.inra.fr");
-        QCoreApplication::setApplicationName("xtpcpp");
-        MainWindow window;
-        window.show();
+  try
+    {
+      QCoreApplication::setOrganizationName("PAPPSO");
+      QCoreApplication::setOrganizationDomain("pappso.inra.fr");
+      QCoreApplication::setApplicationName("xtpcpp");
+      MainWindow window;
+      window.show();
 
-        // This code will start the messaging engine in QT and in
-        // 10ms it will start the execution in the MainClass.run routine;
-        QTimer::singleShot(10, &window, SLOT(run()));
+      // This code will start the messaging engine in QT and in
+      // 10ms it will start the execution in the MainClass.run routine;
+      QTimer::singleShot(10, &window, SLOT(run()));
 
-        return app.exec();
+      return app.exec();
     }
-    catch (pappso::PappsoException& error)
+  catch(pappso::PappsoException &error)
     {
-        errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
-        errorStream << error.qwhat() << endl;
-        app.exit(1);
+      errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
+      errorStream << error.qwhat() << endl;
+      app.exit(1);
     }
 
-    catch (std::exception& error)
+  catch(std::exception &error)
     {
-        errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
-        errorStream << error.what() << endl;
-        app.exit(1);
+      errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
+      errorStream << error.what() << endl;
+      app.exit(1);
     }
 }