Commit 484f35dc authored by Filippo Rusconi's avatar Filippo Rusconi
Browse files

New upstream version 0.4.9

parent a7905b39
......@@ -30,6 +30,16 @@ AutomaticFilterParameters::AutomaticFilterParameters()
AutomaticFilterParameters::AutomaticFilterParameters(
const AutomaticFilterParameters &other)
{
this->operator=(other);
}
AutomaticFilterParameters::~AutomaticFilterParameters()
{
}
AutomaticFilterParameters &
AutomaticFilterParameters::operator=(const AutomaticFilterParameters &other)
{
_filter_minimum_peptide_evalue = other._filter_minimum_peptide_evalue;
_filter_minimum_protein_evalue = other._filter_minimum_protein_evalue;
......@@ -39,12 +49,11 @@ AutomaticFilterParameters::AutomaticFilterParameters(
m_filter_peptide_observed_in_less_samples_than =
other.m_filter_peptide_observed_in_less_samples_than;
m_filterFDR = other.m_filterFDR;
}
AutomaticFilterParameters::~AutomaticFilterParameters()
{
return *this;
}
void
AutomaticFilterParameters::setFilterPeptideFDR(double fdr)
{
......
......@@ -32,6 +32,8 @@ class AutomaticFilterParameters
AutomaticFilterParameters(const AutomaticFilterParameters &other);
~AutomaticFilterParameters();
AutomaticFilterParameters &operator=(const AutomaticFilterParameters &);
void setFilterPeptideEvalue(pappso::pappso_double evalue);
void setFilterPeptideFDR(double fdr);
......
......@@ -385,6 +385,36 @@ IdentificationGroup::collectMhDelta(
}
}
}
void
IdentificationGroup::collectTargetDecoyMhDelta(
std::vector<pappso::pappso_double> &delta_list,
pappso::PrecisionUnit unit,
ValidationState state) const
{
std::set<const PeptideEvidence *> peptide_evidence_list;
for(auto &p_protein_match : _protein_match_list)
{
if(p_protein_match->getValidationState() == state)
{
p_protein_match->collectPeptideEvidences(peptide_evidence_list,
state);
}
}
for(const PeptideEvidence *p_peptide_evidence : peptide_evidence_list)
{
if(unit == pappso::PrecisionUnit::ppm)
{
delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
}
else
{
delta_list.push_back(p_peptide_evidence->getDeltaMass());
}
}
}
void
IdentificationGroup::startGrouping(
ContaminantRemovalMode contaminantRemovalMode,
......
......@@ -157,14 +157,33 @@ class IdentificationGroup
bool containSample(const QString &sample) const;
/** @brief collect mass delta between theoretical mass and observed mass
* each peptide evidence is only counted once
/** @brief collect mass delta between theoretical mass and observed mass for
* target sequences
*
* each peptide evidence is only counted once it counts only
* peptide evidence for target Sequences
* @param delta_list list of mass delta
* @param unit precision unit, ppm or dalton
* @param state validation state of the peptides to collect
*/
void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
pappso::PrecisionUnit unit,
ValidationState state) const;
/** @brief collect mass delta between theoretical mass and observed mass
*
* each peptide evidence is only counted once it counts target or decoy
* peptide evidence
* @param delta_list list of mass delta
* @param unit precision unit, ppm or dalton
* @param state validation state of the peptides to collect
*/
void collectTargetDecoyMhDelta(std::vector<pappso::pappso_double> &delta_list,
pappso::PrecisionUnit unit,
ValidationState state) const;
/** @brief look for a peptide in the same XIC
* @param peptide_evidence_list the peptide evidence list to build
* @param p_msrun MSrun to look for
......
......@@ -32,8 +32,7 @@ PeptideMatch::PeptideMatch()
PeptideMatch::PeptideMatch(const PeptideMatch &other)
{
_start = other._start;
_p_peptide_evidence = other._p_peptide_evidence;
this->operator=(other);
}
bool
PeptideMatch::operator==(const PeptideMatch &other) const
......@@ -45,6 +44,17 @@ PeptideMatch::operator==(const PeptideMatch &other) const
}
return false;
}
PeptideMatch &
PeptideMatch::operator=(const PeptideMatch &other)
{
_start = other._start;
_p_peptide_evidence = other._p_peptide_evidence;
return *this;
}
void
PeptideMatch::setPeptideEvidenceSp(PeptideEvidenceSp sp_peptide_evidence)
{
......
......@@ -22,8 +22,7 @@
*implementation
******************************************************************************/
#ifndef PEPTIDEMATCH_H
#define PEPTIDEMATCH_H
#pragma once
#include "peptideevidence.h"
......@@ -35,6 +34,8 @@ class PeptideMatch
bool operator==(const PeptideMatch &other) const;
PeptideMatch &operator=(const PeptideMatch &);
/** @brief set start position of this peptide inside the protein sequence
* @param start position in the protein amino acid sequence (starts at 0)
......@@ -66,5 +67,3 @@ class PeptideMatch
unsigned int _start = 0;
PeptideEvidence *_p_peptide_evidence = nullptr;
};
#endif // PEPTIDEMATCH_H
......@@ -2,7 +2,7 @@
* \file /core/tandem_run/tandemcondorprocess.cpp
* \date 5/9/2017
* \author Olivier Langella
* \brief handles execution of a bunch of X!Tandem process throught condor job
* \brief handles execution of a bunch of X!Tandem process through condor job
*/
/*******************************************************************************
......
......@@ -2,7 +2,7 @@
* \file /core/tandem_run/tandemcondorprocess.h
* \date 5/9/2017
* \author Olivier Langella
* \brief handles execution of a bunch of X!Tandem process throught condor job
* \brief handles execution of a bunch of X!Tandem process through condor job
*/
/*******************************************************************************
......
......@@ -68,7 +68,14 @@ TandemParameters::~TandemParameters()
TandemParameters::TandemParameters(const TandemParameters &other)
{
qDebug() << "TandemParameters::TandemParameters copy begin";
this->operator=(other);
}
TandemParameters &
TandemParameters::operator=(const TandemParameters &other)
{
qDebug() << "copy begin";
//_map_label_value = other._map_label_value;
_method_name = other._method_name;
......@@ -76,15 +83,14 @@ TandemParameters::TandemParameters(const TandemParameters &other)
other._map_label_value.constBegin();
while(i != other._map_label_value.constEnd())
{
qDebug() << "TandemParameters::TandemParameters copy " << i.key() << " "
<< i.value();
qDebug() << "copy " << i.key() << " " << i.value();
_map_label_value.insert(i.key(), i.value());
i++; // added
}
qDebug() << "TandemParameters::TandemParameters copy end";
qDebug() << "copy end";
return *this;
}
bool
TandemParameters::equals(const TandemParameters &other) const
{
......
......@@ -38,6 +38,7 @@ class TandemParameters
public:
TandemParameters();
TandemParameters(const TandemParameters &other);
TandemParameters &operator=(const TandemParameters &);
virtual ~TandemParameters();
const QString &getValue(const QString &label) const;
......
......@@ -75,7 +75,7 @@
&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
p, li { white-space: pre-wrap; }
&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Cantarell'; font-size:11pt; font-weight:400; font-style:normal;&quot;&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;X!TandemPipeline C++ is developped by PAPPSO team (&lt;a href=&quot;http://pappso.inra.fr&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://pappso.inra.fr&lt;/span&gt;&lt;/a&gt;).&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;X!TandemPipeline C++ is developed by PAPPSO team (&lt;a href=&quot;http://pappso.inra.fr&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://pappso.inra.fr&lt;/span&gt;&lt;/a&gt;).&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;This software is distributed under the terms of the GNU General Public License.&lt;/p&gt;
&lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
......
......@@ -3479,7 +3479,7 @@
<item row="7" column="0">
<widget class="QLabel" name="label_71">
<property name="text">
<string>Write spectrum informations</string>
<string>Write spectrum information</string>
</property>
</widget>
</item>
......
......@@ -2,7 +2,7 @@
* \file gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
* \date 25/01/2019
* \author Olivier Langella
* \brief all needed informations to write a MassChroqML file
* \brief all needed information to write a MassChroqML file
*/
/*******************************************************************************
......
......@@ -2,7 +2,7 @@
* \file gui/export/export_masschroq_dialog/masschroqfileparameters.h
* \date 25/01/2019
* \author Olivier Langella
* \brief all needed informations to write a MassChroqML file
* \brief all needed information to write a MassChroqML file
*/
/*******************************************************************************
......
......@@ -103,7 +103,7 @@
<item>
<widget class="QGroupBox" name="use_htcondor_groupbox">
<property name="title">
<string>&amp;run X!Tandem throught HTCondor</string>
<string>&amp;run X!Tandem through HTCondor</string>
</property>
<property name="checkable">
<bool>true</bool>
......
......@@ -438,7 +438,7 @@ TandemRunDialog::selectTdfFolder()
{
throw pappso::PappsoException(
tr(
"The directory %1/ dosent contain the mandatory analysis.tdf "
"The directory %1/ does not contain the mandatory analysis.tdf "
"file")
.arg(directory_name));
}
......
......@@ -3338,7 +3338,7 @@
<item row="7" column="0">
<widget class="QLabel" name="writeSpectrumInformationsLabel">
<property name="text">
<string>Write spectrum informations</string>
<string>Write spectrum information</string>
</property>
</widget>
</item>
......
......@@ -392,7 +392,7 @@ XtandemSaxHandler::startElement_domain(QXmlAttributes attributes)
_p_peptide_evidence->setChecked(true);
// missing informations
// missing information
// peptide.set_hypercorr(Float.valueOf(attrs.getValue("hyperscore")));
// peptide.set_pre(attrs.getValue("pre"));
// peptide.set_post(attrs.getValue("post"));
......
/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
* Copyright (c) 2015 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of PAPPSOms-tools.
* This file is part of XTPcpp.
*
* PAPPSOms-tools is free software: you can redistribute it and/or modify
* 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.
*
* PAPPSOms-tools is distributed in the hope that it will be useful,
* 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 PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
#include "config.h"
......
......@@ -41,7 +41,7 @@ InfoSheet::InfoSheet(OdsExport *p_ods_export,
{
_p_ods_export = p_ods_export;
_p_writer = p_writer;
p_writer->writeSheet("X!TandemPipeline informations");
p_writer->writeSheet("X!TandemPipeline information");
p_writer->writeCell("X!TandemPipeline version :");
p_writer->writeLine();
......
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