diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index e5538e8d193198cd35eeb98b7c1daf054c72b450..69230341ca31b0da67725ccc7866de6ec6c02558 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -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}")
diff --git a/src/gui/about_dialog/about_dialog.ui b/src/gui/about_dialog/about_dialog.ui
index c843d538c998ac16b6efb1344caf468821d29c85..5e05f8b2fc1de817c559f9357e45014eea961790 100644
--- a/src/gui/about_dialog/about_dialog.ui
+++ b/src/gui/about_dialog/about_dialog.ui
@@ -14,7 +14,7 @@
</rect>
</property>
<property name="windowTitle">
- <string>Dialog</string>
+ <string>About</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
diff --git a/src/output/MassChroqPrmWriter.java b/src/output/MassChroqPrmWriter.java
deleted file mode 100644
index 50b3815b06be1e0f12a84e3938c706885bf4412e..0000000000000000000000000000000000000000
--- a/src/output/MassChroqPrmWriter.java
+++ /dev/null
@@ -1,182 +0,0 @@
-/*******************************************************************************
- * 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");
- }
-
-}