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Commit ecebd14d authored by Langella Olivier's avatar Langella Olivier
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about dialog

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src/CMakeLists.txt
+ 4
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View file @ ecebd14d
......@@ -17,10 +17,10 @@ FIND_PACKAGE( Qt5 COMPONENTS Core Gui Svg Xml PrintSupport REQUIRED )
QT5_ADD_RESOURCES(xtpcpp_RCC_SRCS ${xtpcpp_RCCS})
FIND_PACKAGE( QCustomPlot REQUIRED )
#FIND_PACKAGE( Odsstream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
SET (ODSSTREAM_DIR "/home/olivier/eclipse/git/libodsstream")
SET (ODSSTREAM_INCLUDE_DIR "${ODSSTREAM_DIR}/src")
SET (ODSSTREAM_QT5_LIBRARY "${ODSSTREAM_DIR}/build/src/libodsstream-qt5.so")
FIND_PACKAGE( Odsstream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
#SET (ODSSTREAM_DIR "/home/olivier/eclipse/git/libodsstream")
#SET (ODSSTREAM_INCLUDE_DIR "${ODSSTREAM_DIR}/src")
#SET (ODSSTREAM_QT5_LIBRARY "${ODSSTREAM_DIR}/build/src/libodsstream-qt5.so")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5Gui_EXECUTABLE_COMPILE_FLAGS} ${Qt5Svg_EXECUTABLE_COMPILE_FLAGS}")
......
src/gui/about_dialog/about_dialog.ui
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View file @ ecebd14d
......@@ -14,7 +14,7 @@
</rect>
</property>
<property name="windowTitle">
<string>Dialog</string>
<string>About</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
......
src/output/MassChroqPrmWriter.java deleted 100644 → 0
+ 0
− 182
View file @ 3316c943
/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
*
* This file is part of XTandemPipeline.
*
* XTandemPipeline 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.
*
* XTandemPipeline 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 XTandemPipeline. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr>
******************************************************************************/
package fr.inra.pappso.xtandempipeline.output;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
import org.apache.log4j.Logger;
import fr.inra.moulon.proticport.model.exceptions.ProticPortException;
import fr.inra.pappso.xtandempipeline.Utils;
import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
import fr.inra.pappso.xtandempipeline.class_msms.ModifsList;
import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
import fr.inra.pappso.xtandempipeline.class_msms.Protein;
import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMass;
import fr.inra.pappso.xtandempipeline.class_msms.GroupingProtein.PeptideMassSet;
import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
import fr.inra.pappso.xtandempipeline.grouping.Group;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSet;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
import fr.inra.pappso.xtandempipeline.grouping.SubGroupSet;
import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpPeptide;
public class MassChroqPrmWriter {
private static final Logger logger = Logger
.getLogger(MassChroqPrmWriter.class);
static String namespaceURI = "http://sashimi.sourceforge.net/schema_revision/mzXML_2.0";
static String xmlnsxsi = "http://www.w3.org/2001/XMLSchema-instance";
static String xsischemaLocation = "http://sashimi.sourceforge.net/schema_revision/mzXML_2.0 http://sashimi.sourceforge.net/schema_revision/mzXML_2.0/mzXML_idx_2.0.xsd";
protected XMLStreamWriter writer;
private Hashtable<MsRun, String> sample2xmlId;
private String groupe_id;
private String xtpExperimentType;
private Hashtable<String, String> accession2xmlid;
MassChroqPrmWriter(XMLStreamWriter writer) throws ProticPortException {
this.sample2xmlId = new Hashtable<MsRun, String>();
this.groupe_id = "G1";
this.writer = writer;
}
public void write(ModifsList isotopic_mods, Identification ident)
throws XMLStreamException, ProticPortException {
logger.debug("write begin");
long duracel = System.currentTimeMillis();
xtpExperimentType = XtandemPipelineSession.getInstance()
.getDataTypeBase().getType();
if (this.xtpExperimentType.equals("phospho")) {
accession2xmlid = new Hashtable<String, String>();
}
// writer.setPrefix("xsi", xmlnsxsi);
// writer.setDefaultNamespace(namespaceURI);
writer.writeStartElement("masschroqprm");
// writer.writeNamespace("xsi", xmlnsxsi);
// writer.writeDefaultNamespace(namespaceURI);
// writer.writeAttribute(xmlnsxsi, "schemaLocation", xsischemaLocation);
this.writePeptides(ident);
logger.info("Duration creating MassChroQml xml document: "
+ (System.currentTimeMillis() - duracel) + " ms");
// masschroq
writer.writeEndElement();
}
private void writePeptides(Identification ident) {
logger.debug("write begin");
/*
*
*
* <peptide seq="TCVADESHAGCEK" id="p1"> <psimod at="2"
* acc="MOD:00397"/> <psimod at="11" acc="MOD:00397"/> </peptide>
*/
try {
/*
*
<parameters>
<parentIonMassTolerance>
<daltonPrecision value="1.5"/>
</parentIonMassTolerance>
<fragmentIonMassTolerance>
<daltonPrecision value="0.02"/>
</fragmentIonMassTolerance>
</parameters>
*/
writer.writeStartElement("parameters");
writer.writeStartElement("parentIonMassTolerance");
writer.writeComment("choose dalton or ppm mass precision to select parent ions based on the precursor mass of each MS/MS spectrum");
writer.writeStartElement("ppmPrecision");
writer.writeAttribute("value", "10");
writer.writeEndElement();
writer.writeEndElement();
writer.writeStartElement("fragmentIonMassTolerance");
writer.writeComment("choose dalton or ppm mass precision to MS/MS fragment ion observed mass with theoretical mass");
writer.writeStartElement("daltonPrecision");
writer.writeAttribute("value", "0.02");
writer.writeEndElement();
writer.writeEndElement();
writer.writeEndElement();
writer.writeStartElement("peptideList");
for (Group group : ident.getGrouping().getGroupList()) {
PeptideMassSet pepMassSet = new PeptideMassSet();
logger.debug("pepMassSet size : " + pepMassSet.size());
logger.debug("pepMassSet numbering");
pepMassSet.numberingGetPepMass2PeptideList(group);
// iterated current pepid to write buffer peptide element
for (PeptideMass pepMass : pepMassSet) {
writer.writeStartElement("peptide");
writer.writeAttribute("id",
Utils.getPappsoPeptideMassId(group, pepMass));
Peptide bestPeptide = pepMass.getBestEvaluePeptide();
writer.writeAttribute("seq", bestPeptide.getSequence());
ArrayList<Modifs> arrModif = bestPeptide.get_Modifs();
for (Modifs modif : arrModif) {
writer.writeStartElement("psimod");
writer.writeAttribute("at", "" + modif.get_posi());
writer.writeAttribute("acc", ""
+ modif.getPsiMod().getAccession());
writer.writeEndElement();
}
writer.writeEndElement();
}
}
writer.writeEndElement();
} catch (Exception e) {
logger.error(e.getMessage());
}
logger.debug("write end");
}
}
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