diff --git a/xtandempipeline/.classpath b/xtandempipeline/.classpath
index d012119feb98ac1c8d364379090b519379be9314..76d3be6e834bd9ddcfd8f4931cb926510977cc74 100644
--- a/xtandempipeline/.classpath
+++ b/xtandempipeline/.classpath
@@ -32,5 +32,7 @@
<classpathentry kind="lib" path="lib/swt/swt-gtk-linux-x86_64.jar"/>
<classpathentry kind="lib" path="lib/cxf-common-utilities-2.2.4.jar"/>
<classpathentry kind="lib" path="lib/mascotdatfile-3.3.jar"/>
+ <classpathentry kind="lib" path="lib/ods2csv.jar"/>
+ <classpathentry kind="lib" path="lib/javacsv.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
diff --git a/xtandempipeline/CMakeLists.txt b/xtandempipeline/CMakeLists.txt
index fe77b981120771fb1cdd09309d425d6723be8803..a8d7bbe4d5e83ba9e1f333d887cb3f4e4af24d55 100644
--- a/xtandempipeline/CMakeLists.txt
+++ b/xtandempipeline/CMakeLists.txt
@@ -175,6 +175,8 @@ INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/XtandemPipeline.jar DEST
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/libproteomicsvg.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/libodsstream.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/${MASCOT_DAT_FILE_JAR} DESTINATION share/xtandempipeline)
+INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/ods2csv.jar DESTINATION share/xtandempipeline)
+INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/javacsv.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/cxf-common-utilities-2.2.4.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/PPClient.jar DESTINATION share/xtandempipeline)
diff --git a/xtandempipeline/build_ubuntu.xml.cmake b/xtandempipeline/build_ubuntu.xml.cmake
index e01bae61a96fd6012f0ca52e26d35ae1bd2675a0..857e4dd7993566b20f29add069ba9356ddd511c8 100644
--- a/xtandempipeline/build_ubuntu.xml.cmake
+++ b/xtandempipeline/build_ubuntu.xml.cmake
@@ -19,6 +19,19 @@
<property name="confDir" location="src/conf/release" />
<property name="docDir" location="doc" />
+ <target name="updateSharedLibraries">
+
+ <copy file="@CMAKE_SOURCE_DIR@/lib/javacsv.jar" tofile="${share}/xtandempipeline/javacsv.jar" overwrite="true" />
+ <copy file="@CMAKE_SOURCE_DIR@/lib/ods2csv.jar" tofile="${share}/xtandempipeline/ods2csv.jar" overwrite="true" />
+ <copy file="@CMAKE_SOURCE_DIR@/lib/libproteomicsvg.jar" tofile="${share}/xtandempipeline/libproteomicsvg.jar" overwrite="true" />
+ <copy file="@CMAKE_SOURCE_DIR@/lib/libodsstream.jar" tofile="${share}/xtandempipeline/libodsstream.jar" overwrite="true" />
+ <copy file="@CMAKE_SOURCE_DIR@/lib/PPClient.jar" tofile="${share}/xtandempipeline/PPClient.jar" overwrite="true" />
+ <copy file="@CMAKE_SOURCE_DIR@/lib/mascotdatfile-3.3.jar" tofile="${share}/xtandempipeline/mascotdatfile-3.3.jar" overwrite="true" />
+ <copy file="@CMAKE_SOURCE_DIR@/lib/cxf-common-utilities-2.2.4.jar" tofile="${share}/xtandempipeline/cxf-common-utilities-2.2.4.jar" overwrite="true" />
+
+ </target>
+
+
<target name="reset">
<!-- reset the build and dist directory -->
<delete dir="${build}" />
@@ -26,13 +39,6 @@
<mkdir dir="${build}" />
<mkdir dir="${dist}" />
<mkdir dir="${confDest}" />
-
-
- <copy file="@CMAKE_SOURCE_DIR@/lib/libproteomicsvg.jar" tofile="${share}/xtandempipeline/libproteomicsvg.jar" overwrite="true" />
- <copy file="@CMAKE_SOURCE_DIR@/lib/libodsstream.jar" tofile="${share}/xtandempipeline/libodsstream.jar" overwrite="true" />
- <copy file="@CMAKE_SOURCE_DIR@/lib/PPClient.jar" tofile="${share}/xtandempipeline/PPClient.jar" overwrite="true" />
- <copy file="@CMAKE_SOURCE_DIR@/lib/mascotdatfile-3.3.jar" tofile="${share}/xtandempipeline/mascotdatfile-3.3.jar" overwrite="true" />
- <copy file="@CMAKE_SOURCE_DIR@/lib/cxf-common-utilities-2.2.4.jar" tofile="${share}/xtandempipeline/cxf-common-utilities-2.2.4.jar" overwrite="true" />
</target>
@@ -45,6 +51,8 @@
<path id="classpath">
<!--xml-apis-ext.jar xml-apis.jar xercesImpl.jar xalan2.jar swt.jar batik.jar liblog4j1.2-java -->
<fileset dir="${sys.dir}" includes="commons-httpclient.jar commons-codec.jar commons-logging.jar log4j-1.2.jar xml-apis-ext.jar xml-apis.jar xercesImpl.jar xalan2.jar swt.jar batik.jar" />
+ <fileset dir="${share.dest}/xtandempipeline" includes="javacsv.jar" />
+ <fileset dir="${share.dest}/xtandempipeline" includes="ods2csv.jar" />
<fileset dir="${share.dest}/xtandempipeline" includes="libproteomicsvg.jar" />
<fileset dir="${share.dest}/xtandempipeline" includes="libodsstream.jar" />
<fileset dir="${share.dest}/xtandempipeline" includes="PPClient.jar" />
@@ -55,6 +63,8 @@
<target name="compile" depends="init" description="compile the source and put in build directory">
<!-- Compile the java code from ${src} into ${build} -->
+ <copy file="${share}/xtandempipeline/javacsv.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
+ <copy file="${share}/xtandempipeline/ods2csv.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
<copy file="${share}/xtandempipeline/libproteomicsvg.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
<copy file="${share}/xtandempipeline/libodsstream.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
<copy file="${share}/xtandempipeline/PPClient.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
@@ -89,7 +99,7 @@
<!--<fileset file=".classpath" />-->
<manifest>
<attribute name="Main-Class" value="fr.inra.pappso.xtandempipeline.XtandemPipelineMain" />
- <attribute name="Class-Path" value="${sys.dir}/commons-httpclient.jar ${sys.dir}/commons-codec.jar ${sys.dir}/commons-logging.jar ${sys.dir}/log4j-1.2.jar ${sys.dir}/xml-apis-ext.jar ${sys.dir}/xml-apis.jar ${sys.dir}/xercesImpl.jar ${sys.dir}/xalan2.jar ${sys.dir}/swt.jar ${sys.dir}/batik.jar ${usr.dir}/share/xtandempipeline/libproteomicsvg.jar ${usr.dir}/share/xtandempipeline/libodsstream.jar ${usr.dir}/share/xtandempipeline/PPClient.jar ${usr.dir}/share/xtandempipeline/@MASCOT_DAT_FILE_JAR@ ${usr.dir}/share/xtandempipeline/cxf-common-utilities-2.2.4.jar" />
+ <attribute name="Class-Path" value="${usr.dir}/share/xtandempipeline/ods2csv.jar ${usr.dir}/share/xtandempipeline/javacsv.jar ${sys.dir}/commons-httpclient.jar ${sys.dir}/commons-codec.jar ${sys.dir}/commons-logging.jar ${sys.dir}/log4j-1.2.jar ${sys.dir}/xml-apis-ext.jar ${sys.dir}/xml-apis.jar ${sys.dir}/xercesImpl.jar ${sys.dir}/xalan2.jar ${sys.dir}/swt.jar ${sys.dir}/batik.jar ${usr.dir}/share/xtandempipeline/libproteomicsvg.jar ${usr.dir}/share/xtandempipeline/libodsstream.jar ${usr.dir}/share/xtandempipeline/PPClient.jar ${usr.dir}/share/xtandempipeline/@MASCOT_DAT_FILE_JAR@ ${usr.dir}/share/xtandempipeline/cxf-common-utilities-2.2.4.jar" />
</manifest>
</jar>
@@ -104,6 +114,8 @@
</target>
<target name="copyInShare" description="copies jar needed by the ubuntu package into the share directory">
+ <copy file="@xtandempipeline_SOURCE_DIR@/lib/javacsv.jar" todir="${share}/xtandempipeline" overwrite="true" />
+ <copy file="@xtandempipeline_SOURCE_DIR@/lib/ods2csv.jar" todir="${share}/xtandempipeline" overwrite="true" />
<copy file="@xtandempipeline_SOURCE_DIR@/lib/libproteomicsvg.jar" todir="${share}/xtandempipeline" overwrite="true" />
<copy file="@xtandempipeline_SOURCE_DIR@/lib/libodsstream.jar" todir="${share}/xtandempipeline" overwrite="true" />
<copy file="@xtandempipeline_SOURCE_DIR@/lib/PPClient.jar" todir="${share}/xtandempipeline" overwrite="true" />
diff --git a/xtandempipeline/lib/javacsv.jar b/xtandempipeline/lib/javacsv.jar
new file mode 100644
index 0000000000000000000000000000000000000000..ceb59eb464c3b059ae28007e79994b4fbbb960b5
Binary files /dev/null and b/xtandempipeline/lib/javacsv.jar differ
diff --git a/xtandempipeline/lib/ods2csv.jar b/xtandempipeline/lib/ods2csv.jar
new file mode 100644
index 0000000000000000000000000000000000000000..9fb0da05b12e721e72d0cf5ce9485fd14a06597a
Binary files /dev/null and b/xtandempipeline/lib/ods2csv.jar differ
diff --git a/xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp.cmake b/xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp.cmake
index a8171ccacebc3cfab7126135b95511d539de718b..fac932e25391a1f70e3e8221acfa7da224cbf4a5 100644
--- a/xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp.cmake
+++ b/xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp.cmake
@@ -61,6 +61,8 @@
<jar href="lib/libproteomicsvg.jar" main="false" download="eager" />
<jar href="lib/libodsstream.jar" main="false" download="eager" />
+ <jar href="lib/javacsv.jar" main="false" download="eager" />
+ <jar href="lib/ods2csv.jar" main="false" download="eager" />
</resources>
<resources os="Windows" arch="x86">
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java
index c23fe188ecaa50b0d2fc55967912572415faeb22..da2433280bd1b1d6697ee3bcebbfeba597a18b90 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java
@@ -5,7 +5,6 @@ import java.util.Collection;
import java.util.TreeSet;
import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
import fr.inra.pappso.xtandempipeline.grouping.Group;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java
index eb8ed4be1ae541bf953ec9a5c78e53e6d5875946..bb626d7ef8688dccdd1c39a4654be2d27bcffe2f 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java
@@ -5,7 +5,6 @@ import fr.inra.pappso.xtandempipeline.grouping.Group;
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.interfaces.GrpProtMatch;
import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
public class print_protein_to_phosphopeptide extends print_base {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java
new file mode 100644
index 0000000000000000000000000000000000000000..4114ea64dad729d14b3bc58dca28d84d4ed0caac
--- /dev/null
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java
@@ -0,0 +1,75 @@
+/*******************************************************************************
+ * Copyright (c) 2012 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:
+ * Benoit Valot <Benoit.Valot@moulon.inra.fr>
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr>
+ ******************************************************************************/
+
+package fr.inra.pappso.xtandempipeline.output;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.pappso.csv2ods.Ods2Csv;
+import fr.inra.pappso.libodsstream.OdsDocWriter;
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+
+public class CsvRedundantPeptideOutput extends OdsRedundantPeptideOutput {
+ private static final Logger logger = Logger
+ .getLogger(CsvRedundantPeptideOutput.class);
+ private Ods2Csv ods2csv;
+
+ public CsvRedundantPeptideOutput(OutputStream outputStream)
+ throws MSMSException {
+ try {
+
+ PipedOutputStream pos = new PipedOutputStream();
+ PipedInputStream pis = new PipedInputStream(pos);
+
+ odsTable = new OdsDocWriter(pos);
+
+ ods2csv = new Ods2Csv();
+ ods2csv.setSourceInputStream(pis);
+ ods2csv.setSinkOutputStream(outputStream);
+ //ods2csv.setSeparator('\t');
+ (new Thread(ods2csv)).start();
+ //ods2csv.run();
+ } catch (IOException e) {
+ String message = "IOException " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ } catch (XMLStreamException e) {
+ String message = "XMLStreamException " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ } catch (DatatypeConfigurationException e) {
+ String message = "DatatypeConfigurationException " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ }
+
+}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/IndentingXMLStreamWriter.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/IndentingXMLStreamWriter.java
new file mode 100644
index 0000000000000000000000000000000000000000..2daea8d784b635911852a3e6f8bdcbbc0f7588a4
--- /dev/null
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/IndentingXMLStreamWriter.java
@@ -0,0 +1,177 @@
+package fr.inra.pappso.xtandempipeline.output;
+
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamWriter;
+
+import org.apache.cxf.staxutils.DelegatingXMLStreamWriter;
+
+import java.util.Stack;
+
+/**
+ * @author Kohsuke Kawaguchi
+ */
+public class IndentingXMLStreamWriter extends DelegatingXMLStreamWriter {
+ private final static Object SEEN_NOTHING = new Object();
+ private final static Object SEEN_ELEMENT = new Object();
+ private final static Object SEEN_DATA = new Object();
+
+ private Object state = SEEN_NOTHING;
+ private Stack<Object> stateStack = new Stack<Object>();
+
+ private String indentStep = " ";
+ private int depth = 0;
+
+ public IndentingXMLStreamWriter(XMLStreamWriter writer) {
+ super(writer);
+ }
+
+ /**
+ * Return the current indent step.
+ *
+ * <p>
+ * Return the current indent step: each start tag will be indented by this
+ * number of spaces times the number of ancestors that the element has.
+ * </p>
+ *
+ * @return The number of spaces in each indentation step, or 0 or less for
+ * no indentation.
+ * @see #setIndentStep(int)
+ *
+ * @deprecated Only return the length of the indent string.
+ */
+ public int getIndentStep() {
+ return indentStep.length();
+ }
+
+ /**
+ * Set the current indent step.
+ *
+ * @param indentStep
+ * The new indent step (0 or less for no indentation).
+ * @see #getIndentStep()
+ *
+ * @deprecated Should use the version that takes string.
+ */
+ public void setIndentStep(int indentStep) {
+ StringBuilder s = new StringBuilder();
+ for (; indentStep > 0; indentStep--)
+ s.append(' ');
+ setIndentStep(s.toString());
+ }
+
+ public void setIndentStep(String s) {
+ this.indentStep = s;
+ }
+
+ private void onStartElement() throws XMLStreamException {
+ stateStack.push(SEEN_ELEMENT);
+ state = SEEN_NOTHING;
+ if (depth > 0) {
+ super.writeCharacters("\n");
+ }
+ doIndent();
+ depth++;
+ }
+
+ private void onEndElement() throws XMLStreamException {
+ depth--;
+ if (state == SEEN_ELEMENT) {
+ super.writeCharacters("\n");
+ doIndent();
+ }
+ state = stateStack.pop();
+ }
+
+ private void onEmptyElement() throws XMLStreamException {
+ state = SEEN_ELEMENT;
+ if (depth > 0) {
+ super.writeCharacters("\n");
+ }
+ doIndent();
+ }
+
+ /**
+ * Print indentation for the current level.
+ *
+ * @exception org.xml.sax.SAXException
+ * If there is an error writing the indentation characters,
+ * or if a filter further down the chain raises an exception.
+ */
+ private void doIndent() throws XMLStreamException {
+ if (depth > 0) {
+ for (int i = 0; i < depth; i++)
+ super.writeCharacters(indentStep);
+ }
+ }
+
+ public void writeStartDocument() throws XMLStreamException {
+ super.writeStartDocument();
+ super.writeCharacters("\n");
+ }
+
+ public void writeStartDocument(String version) throws XMLStreamException {
+ super.writeStartDocument(version);
+ super.writeCharacters("\n");
+ }
+
+ public void writeStartDocument(String encoding, String version)
+ throws XMLStreamException {
+ super.writeStartDocument(encoding, version);
+ super.writeCharacters("\n");
+ }
+
+ public void writeStartElement(String localName) throws XMLStreamException {
+ onStartElement();
+ super.writeStartElement(localName);
+ }
+
+ public void writeStartElement(String namespaceURI, String localName)
+ throws XMLStreamException {
+ onStartElement();
+ super.writeStartElement(namespaceURI, localName);
+ }
+
+ public void writeStartElement(String prefix, String localName,
+ String namespaceURI) throws XMLStreamException {
+ onStartElement();
+ super.writeStartElement(prefix, localName, namespaceURI);
+ }
+
+ public void writeEmptyElement(String namespaceURI, String localName)
+ throws XMLStreamException {
+ onEmptyElement();
+ super.writeEmptyElement(namespaceURI, localName);
+ }
+
+ public void writeEmptyElement(String prefix, String localName,
+ String namespaceURI) throws XMLStreamException {
+ onEmptyElement();
+ super.writeEmptyElement(prefix, localName, namespaceURI);
+ }
+
+ public void writeEmptyElement(String localName) throws XMLStreamException {
+ onEmptyElement();
+ super.writeEmptyElement(localName);
+ }
+
+ public void writeEndElement() throws XMLStreamException {
+ onEndElement();
+ super.writeEndElement();
+ }
+
+ public void writeCharacters(String text) throws XMLStreamException {
+ state = SEEN_DATA;
+ super.writeCharacters(text);
+ }
+
+ public void writeCharacters(char[] text, int start, int len)
+ throws XMLStreamException {
+ state = SEEN_DATA;
+ super.writeCharacters(text, start, len);
+ }
+
+ public void writeCData(String data) throws XMLStreamException {
+ state = SEEN_DATA;
+ super.writeCData(data);
+ }
+}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlOutput.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlOutput.java
similarity index 98%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlOutput.java
rename to xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlOutput.java
index ccaae2d2f1b8993a008aaa072924ca27b48dd852..7c3b038e17a0d7fa8d7d87e40e07620c36b213fc 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlOutput.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlOutput.java
@@ -21,7 +21,7 @@
* Olivier Langella <Olivier.Langella@moulon.inra.fr>
******************************************************************************/
-package fr.inra.pappso.xtandempipeline.sax_parse;
+package fr.inra.pappso.xtandempipeline.output;
import java.io.IOException;
import java.io.OutputStream;
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlWriter.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlWriter.java
similarity index 97%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlWriter.java
rename to xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlWriter.java
index aaa2a3f2152487843ab475b961d80f90443e9b44..f20cfb84db0baf205ea22ae9962fde9b33802756 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQmlWriter.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlWriter.java
@@ -21,7 +21,7 @@
* Olivier Langella <Olivier.Langella@moulon.inra.fr>
******************************************************************************/
-package fr.inra.pappso.xtandempipeline.sax_parse;
+package fr.inra.pappso.xtandempipeline.output;
import java.util.ArrayList;
import java.util.HashSet;
@@ -294,7 +294,7 @@ public class MassChroQmlWriter {
logger.debug("write begin");
try {
writer.writeStartElement("rawdata");
- for (MsRun sample : ident.get_samples().getMsRunList()) {
+ for (MsRun sample : ident.getMsRunSet().getMsRunList()) {
String id_samp = "samp" + this.sample2xmlId.size();
// ajout dans les hashtable
sample2xmlId.put(sample, id_samp);
@@ -328,7 +328,7 @@ public class MassChroQmlWriter {
writer.writeEmptyElement("group");
writer.writeAttribute("id", this.groupe_id);
String raw_list = "";
- for (MsRun sample : ident.get_samples().getMsRunList()) {
+ for (MsRun sample : ident.getMsRunSet().getMsRunList()) {
raw_list = raw_list + " " + sample2xmlId.get(sample);
}
writer.writeAttribute("data_ids", raw_list.trim());
@@ -401,10 +401,10 @@ public class MassChroQmlWriter {
Match top = (Match) sgList.get(0)
.getHashSampleScanSetProtList().get(0)
.getGrpProtMatch();
- Peptide pep = (Peptide) top.getBestPeptideToHashSampleScan(hash);
+ Peptide pep = (Peptide) top
+ .getBestPeptideToHashSampleScan(hash);
- String seqMod = pep
- .get_LI_sequenceModifsWithoutMs3();
+ String seqMod = pep.get_LI_sequenceModifsWithoutMs3();
if (seqMod2protIds.containsKey(seqMod)) {
} else {
// Add new peptide id
@@ -419,8 +419,8 @@ public class MassChroQmlWriter {
HashSet<String> temp = new HashSet<String>();
seqMod2protIds.put(seqMod, temp);
- seqMod2PeptideList.put(seqMod,
- new ArrayList<Peptide>());
+ seqMod2PeptideList
+ .put(seqMod, new ArrayList<Peptide>());
}
seqMod2PeptideList.get(seqMod).add(pep);
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
new file mode 100644
index 0000000000000000000000000000000000000000..e9d41ba6500ee5b8971d1fb17b11c06394ada388
--- /dev/null
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
@@ -0,0 +1,188 @@
+/*******************************************************************************
+ * Copyright (c) 2012 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:
+ * Benoit Valot <Benoit.Valot@moulon.inra.fr>
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr>
+ ******************************************************************************/
+
+package fr.inra.pappso.xtandempipeline.output;
+
+import java.io.IOException;
+import java.io.OutputStream;
+
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.pappso.libodsstream.OdsDocWriter;
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.class_msms.Match;
+import fr.inra.pappso.xtandempipeline.class_msms.Protein;
+import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
+import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
+import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
+
+public class OdsRedundantPeptideOutput {
+ private static final Logger logger = Logger
+ .getLogger(OdsRedundantPeptideOutput.class);
+
+ protected OdsDocWriter odsTable;
+
+ protected OdsRedundantPeptideOutput() {
+
+ }
+
+ public OdsRedundantPeptideOutput(OutputStream outputStream)
+ throws MSMSException {
+ try {
+ odsTable = new OdsDocWriter(outputStream);
+ } catch (IOException e) {
+ String message = "IOException " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ } catch (XMLStreamException e) {
+ String message = "XMLStreamException " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ } catch (DatatypeConfigurationException e) {
+ String message = "DatatypeConfigurationException " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ }
+
+ public void close() throws MSMSException {
+ try {
+ odsTable.close();
+ } catch (Exception e) {
+ String message = "Exception closing OdsRedundantPeptideOutput "
+ + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ }
+
+ public void write(Identification ident) throws MSMSException {
+ try {
+ odsTable.writeSheet("peptides");
+
+ this.writeHeaders();
+ for (Group group : ident.getGrouping().getGroupList()) {
+ for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+
+ for (HashSampleScanSetProt hashProt : sg
+ .getHashSampleScanSetProtList()) {
+ Protein prot = (Protein) hashProt.getGrpProtMatch()
+ .getGrpProtein();
+ // peptidesHitRef
+ for (Peptide peptide : ((Match) hashProt
+ .getGrpProtMatch())
+ .get_peptide_order_inclus_redon()) {
+
+ this.writeOnePeptide(group, sg, prot, peptide);
+ }
+ }
+ }
+ }
+ odsTable.writeLine();
+ odsTable.writeLine();
+
+ } catch (XMLStreamException e) {
+ String message = "XMLStreamException in write(Identification ident) "
+ + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ }
+
+ private void writeHeaders() throws MSMSException {
+ try {
+ odsTable.writeLine();
+ odsTable.writeCell("Group");
+ odsTable.writeCell("Subgroup");
+ odsTable.writeCell("Protein accession");
+ odsTable.writeCell("Protein description");
+ odsTable.writeCell("MS Sample");
+ odsTable.writeCell("Scan");
+ odsTable.writeCell("Rt (s)");
+ odsTable.writeCell("Sequence");
+ odsTable.writeCell("Modifs");
+ odsTable.writeCell("Start");
+ odsTable.writeCell("Stop");
+
+ odsTable.writeCell("E-value");
+ odsTable.writeCell("Charge");
+ odsTable.writeCell("MH+ Obs");
+ odsTable.writeCell("MH+ theo");
+ odsTable.writeCell("DeltaMH+");
+ odsTable.writeCell("Delta-ppm");
+ } catch (XMLStreamException e) {
+ String message = "XMLStreamException in writeHeaders() "
+ + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+
+ }
+
+ private void writeOnePeptide(Group group, SubGroup sg, Protein prot,
+ Peptide peptide) throws MSMSException {
+ try {
+ odsTable.writeLine();
+ odsTable.writeCell(group.getNumber());
+ odsTable.writeCell(sg.getNumber());
+ odsTable.writeCell(prot.getAccession());
+ odsTable.writeCell(prot.get_description());
+ odsTable.writeCell(peptide.get_sample());
+ odsTable.writeCell(peptide.getSampleScan().getScan());
+ odsTable.writeCell(peptide.get_RT_in_sec());
+ odsTable.writeCell(peptide.getSequence());
+ odsTable.writeCell(peptide.get_Modifs_formater());
+ odsTable.writeCell(peptide.get_start());
+ odsTable.writeCell(peptide.get_stop());
+
+ odsTable.writeCell(peptide.get_evalue());
+ // S.append("\t" + pep.get_evalue());
+ odsTable.writeCell(peptide.get_charge());
+ // S.append("\t" + pep.get_charge());
+ odsTable.writeCell(peptide.get_mhplus_obser());
+ // S.append("\t" + pep.get_mhplus_obser());
+ odsTable.writeCell(peptide.get_mhplus_theo());
+ // S.append("\t" + pep.get_mhplus_theo());
+ odsTable.writeCell(peptide.get_deltamass());
+ // S.append("\t" + pep.get_deltamass());
+ odsTable.writeCell(((peptide.get_deltamass() / peptide
+ .get_mhplus_theo()) * 1000000));
+
+ } catch (XMLStreamException e) {
+ String message = "XMLStreamException in writeOnePeptide(Group group, SubGroup sg, Protein prot, Peptide peptide) "
+ + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ } catch (Exception e) {
+ String message = "Exception in writeOnePeptide(Protein prot, Peptide peptide) "
+ + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ }
+}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/ProticDbMlOutput.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlOutput.java
similarity index 98%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/ProticDbMlOutput.java
rename to xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlOutput.java
index ae9c3d9983372197cecdb5d0b29f22f2def4834e..e63e3e22daf13ee81bc62f1b5e094f4ca8c719af 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/ProticDbMlOutput.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlOutput.java
@@ -21,7 +21,7 @@
* Olivier Langella <Olivier.Langella@moulon.inra.fr>
******************************************************************************/
-package fr.inra.pappso.xtandempipeline.sax_parse;
+package fr.inra.pappso.xtandempipeline.output;
import java.io.IOException;
import java.io.OutputStream;
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/ProticDbMlWriter.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlWriter.java
similarity index 94%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/ProticDbMlWriter.java
rename to xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlWriter.java
index 72db150ca05517e94c1216618c687dd8423e0686..51a1109b52f800717af17765cb065223f1e35264 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/ProticDbMlWriter.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlWriter.java
@@ -21,7 +21,7 @@
* Olivier Langella <Olivier.Langella@moulon.inra.fr>
******************************************************************************/
-package fr.inra.pappso.xtandempipeline.sax_parse;
+package fr.inra.pappso.xtandempipeline.output;
import java.util.ArrayList;
import java.util.Hashtable;
@@ -285,7 +285,8 @@ public class ProticDbMlWriter {
writer.writeAttribute("display_id", prot
.get_description().substring(0, 59));
} else {
- writer.writeAttribute("display_id",
+ writer.writeAttribute(
+ "display_id",
prot.get_description()
.substring(
0,
@@ -296,10 +297,10 @@ public class ProticDbMlWriter {
// dbname="AGI_LocusCode"></dbxref>
if (prot.get_dbxref_type().equals("no") == false) {
writer.writeStartElement("dbxref");
- writer.writeAttribute("key", prot
- .get_dbxref_accession());
- writer.writeAttribute("dbname", prot
- .get_dbxref_type());
+ writer.writeAttribute("key",
+ prot.get_dbxref_accession());
+ writer.writeAttribute("dbname",
+ prot.get_dbxref_type());
writer.writeEndElement();// dbxref
}
writer.writeStartElement("description");
@@ -403,9 +404,8 @@ public class ProticDbMlWriter {
writer.writeAttribute("value", ""
+ XtandemPipelineSession.getInstance().getConfig()
.get_peptide_number());
- writer
- .writeAttribute("name",
- "X!TandemPipeline filter on minimal number of peptide per protein");
+ writer.writeAttribute("name",
+ "X!TandemPipeline filter on minimal number of peptide per protein");
writer.writeAttribute("cvLabel", "PROTICdbO");
writer.writeAttribute("accession", "PROTICdbO:0000325");
writer.writeEndElement();// cvParam
@@ -435,19 +435,15 @@ public class ProticDbMlWriter {
String pep_hit_id = "pep" + pep_to_id.size();
// param par default
writer.writeStartElement("peptideHit");
- writer
- .writeAttribute("calc_mr", ""
- + (pep.get_mhplus_theo() - 1.00794));
+ writer.writeAttribute("calc_mr", "" + (pep.get_mhplus_theo() - 1.00794));
double exp_mz = (pep.get_mhplus_obser() + (1.00794 * (pep.get_charge() - 1)))
/ pep.get_charge();
writer.writeAttribute("exp_mz", "" + exp_mz);
writer.writeAttribute("delta", "" + pep.get_deltamass());
- writer
- .writeAttribute("exp_mr", ""
- + (pep.get_mhplus_obser() - 1.00794));
+ writer.writeAttribute("exp_mr", "" + (pep.get_mhplus_obser() - 1.00794));
writer.writeAttribute("acq_number", "" + pep.get_scan());
- writer.writeAttribute("ms_run_id", ""
- + msrun_to_id.get(pep.get_sample()));
+ writer.writeAttribute("ms_run_id",
+ "" + msrun_to_id.get(pep.get_sample()));
writer.writeAttribute("id", pep_hit_id);
writer.writeAttribute("exp_z", "" + pep.get_charge());
@@ -612,9 +608,11 @@ public class ProticDbMlWriter {
for (MsRun sample : match.get_sample_matchs()) {
if (!view.containsKey(sample.getSampleName())) {
writer.writeStartElement("matchSample");
- writer.writeAttribute("sample_id", ""
- + sample_to_id.get(sample
- .getSampleName()));
+ writer.writeAttribute(
+ "sample_id",
+ ""
+ + sample_to_id.get(sample
+ .getSampleName()));
String name = sample.getSampleName();
name = name.replaceAll(".xml", "");
writer.writeAttribute("name", "" + name);
@@ -631,8 +629,8 @@ public class ProticDbMlWriter {
writer.writeStartElement("proteinHit");
Protein prot = (Protein) hashProt.getGrpProtMatch()
.getGrpProtein();
- writer.writeAttribute("sequence_id", ""
- + prot_to_id.get(prot.get_description()));
+ writer.writeAttribute("sequence_id",
+ "" + prot_to_id.get(prot.get_description()));
// proteinHit.setAttribute("score", "");
writer.writeAttribute("rank", "" + k);
@@ -660,9 +658,12 @@ public class ProticDbMlWriter {
if (samples.size() == 1) {
writer.writeStartElement("cvParam");
- writer.writeAttribute("value", ""
- + ((Match) hashProt.getGrpProtMatch())
- .get_coverage());
+ writer.writeAttribute(
+ "value",
+ ""
+ + ((Match) hashProt
+ .getGrpProtMatch())
+ .get_coverage());
writer.writeAttribute("name",
"Coverage determination by Benuch");
writer.writeAttribute("cvLabel", "PROTICdbO");
@@ -681,20 +682,19 @@ public class ProticDbMlWriter {
for (Peptide pep : ((Match) hashProt.getGrpProtMatch())
.get_peptide_order_inclus_redon()) {
writer.writeStartElement("peptideHitRef");
- writer
- .writeAttribute(
- "peptide_hit_id",
- ""
- + pep_to_id
- .get(pep
- .get_sample_scan_sequencepeptide_cle()));
+ writer.writeAttribute(
+ "peptide_hit_id",
+ ""
+ + pep_to_id.get(pep
+ .get_sample_scan_sequencepeptide_cle()));
writer.writeStartElement("fromSeq");
- writer.writeAttribute("seq_id", ""
- + prot_to_id.get(prot2.get_description()));
- writer
- .writeAttribute("start", ""
- + pep.get_start());
+ writer.writeAttribute(
+ "seq_id",
+ ""
+ + prot_to_id.get(prot2
+ .get_description()));
+ writer.writeAttribute("start", "" + pep.get_start());
writer.writeAttribute("stop", "" + pep.get_stop());
String res1 = pep.get_pre();
res1 = res1.replaceAll("]", "-");
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/IndentingXMLStreamWriter.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/IndentingXMLStreamWriter.java
deleted file mode 100644
index e0e30ec9ea194119b296de44da74b2bf5bb9316f..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/IndentingXMLStreamWriter.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package fr.inra.pappso.xtandempipeline.sax_parse;
-
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamWriter;
-
-import org.apache.cxf.staxutils.DelegatingXMLStreamWriter;
-
-import java.util.Stack;
-
-/**
- * @author Kohsuke Kawaguchi
- */
-public class IndentingXMLStreamWriter extends DelegatingXMLStreamWriter {
- private final static Object SEEN_NOTHING = new Object();
- private final static Object SEEN_ELEMENT = new Object();
- private final static Object SEEN_DATA = new Object();
-
- private Object state = SEEN_NOTHING;
- private Stack<Object> stateStack = new Stack<Object>();
-
- private String indentStep = " ";
- private int depth = 0;
-
- public IndentingXMLStreamWriter(XMLStreamWriter writer) {
- super(writer);
- }
-
- /**
- * Return the current indent step.
- *
- * <p>Return the current indent step: each start tag will be
- * indented by this number of spaces times the number of
- * ancestors that the element has.</p>
- *
- * @return The number of spaces in each indentation step,
- * or 0 or less for no indentation.
- * @see #setIndentStep(int)
- *
- * @deprecated
- * Only return the length of the indent string.
- */
- public int getIndentStep() {
- return indentStep.length();
- }
-
-
- /**
- * Set the current indent step.
- *
- * @param indentStep The new indent step (0 or less for no
- * indentation).
- * @see #getIndentStep()
- *
- * @deprecated
- * Should use the version that takes string.
- */
- public void setIndentStep(int indentStep) {
- StringBuilder s = new StringBuilder();
- for (; indentStep > 0; indentStep--) s.append(' ');
- setIndentStep(s.toString());
- }
-
- public void setIndentStep(String s) {
- this.indentStep = s;
- }
-
- private void onStartElement() throws XMLStreamException {
- stateStack.push(SEEN_ELEMENT);
- state = SEEN_NOTHING;
- if (depth > 0) {
- super.writeCharacters("\n");
- }
- doIndent();
- depth++;
- }
-
- private void onEndElement() throws XMLStreamException {
- depth--;
- if (state == SEEN_ELEMENT) {
- super.writeCharacters("\n");
- doIndent();
- }
- state = stateStack.pop();
- }
-
- private void onEmptyElement() throws XMLStreamException {
- state = SEEN_ELEMENT;
- if (depth > 0) {
- super.writeCharacters("\n");
- }
- doIndent();
- }
-
- /**
- * Print indentation for the current level.
- *
- * @exception org.xml.sax.SAXException If there is an error
- * writing the indentation characters, or if a filter
- * further down the chain raises an exception.
- */
- private void doIndent() throws XMLStreamException {
- if (depth > 0) {
- for (int i = 0; i < depth; i++)
- super.writeCharacters(indentStep);
- }
- }
-
-
- public void writeStartDocument() throws XMLStreamException {
- super.writeStartDocument();
- super.writeCharacters("\n");
- }
-
- public void writeStartDocument(String version) throws XMLStreamException {
- super.writeStartDocument(version);
- super.writeCharacters("\n");
- }
-
- public void writeStartDocument(String encoding, String version) throws XMLStreamException {
- super.writeStartDocument(encoding, version);
- super.writeCharacters("\n");
- }
-
- public void writeStartElement(String localName) throws XMLStreamException {
- onStartElement();
- super.writeStartElement(localName);
- }
-
- public void writeStartElement(String namespaceURI, String localName) throws XMLStreamException {
- onStartElement();
- super.writeStartElement(namespaceURI, localName);
- }
-
- public void writeStartElement(String prefix, String localName, String namespaceURI) throws XMLStreamException {
- onStartElement();
- super.writeStartElement(prefix, localName, namespaceURI);
- }
-
- public void writeEmptyElement(String namespaceURI, String localName) throws XMLStreamException {
- onEmptyElement();
- super.writeEmptyElement(namespaceURI, localName);
- }
-
- public void writeEmptyElement(String prefix, String localName, String namespaceURI) throws XMLStreamException {
- onEmptyElement();
- super.writeEmptyElement(prefix, localName, namespaceURI);
- }
-
- public void writeEmptyElement(String localName) throws XMLStreamException {
- onEmptyElement();
- super.writeEmptyElement(localName);
- }
-
- public void writeEndElement() throws XMLStreamException {
- onEndElement();
- super.writeEndElement();
- }
-
- public void writeCharacters(String text) throws XMLStreamException {
- state = SEEN_DATA;
- super.writeCharacters(text);
- }
-
- public void writeCharacters(char[] text, int start, int len) throws XMLStreamException {
- state = SEEN_DATA;
- super.writeCharacters(text, start, len);
- }
-
- public void writeCData(String data) throws XMLStreamException {
- state = SEEN_DATA;
- super.writeCData(data);
- }
-}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
index e87f0c4d8e8da56b4975e12e9dc59efa5888c561..53df785da0a6e65757935f514feab8e69cfb348a 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
@@ -4,7 +4,6 @@ import java.util.ArrayList;
import java.util.Vector;
import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
-import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
@@ -46,7 +45,7 @@ public class individual extends process {
// Is sample exist? Get previous identification
Identification identtemp = null;
for (int m = 0; m < identifications.size(); m++) {
- logger.debug("identifications.size() "+identifications.size());
+ logger.debug("identifications.size() " + identifications.size());
MsRunSet samples = identifications.get(m).getMsRunSet();
for (MsRun sample : samples) {
logger.debug("msRun name : " + sample.getSampleName());
@@ -67,7 +66,8 @@ public class individual extends process {
// identifications.add(handler.get_identifications());
// Load identification from datasource
- identifications.add(dataSourceToParse.loadIdentification(identtemp));
+ identifications
+ .add(dataSourceToParse.loadIdentification(identtemp));
// verification pas arreté
if (this.isStop())
@@ -81,7 +81,7 @@ public class individual extends process {
// filtering
this.set_view("Analysing file : " + (j + 1) + "/"
+ identifications.size() + "\n" + "Filtering file : "
- + ident.get_samples().getMsRunList().get(0).getSampleName());
+ + ident.getMsRunSet().getMsRunList().get(0).getSampleName());
// on mets à jour les liens
ident.filtered_match(new filter_index_and_order_match_scan());
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
index 05ab57d13a887372c216e1087d868cbc589ab0f8..907552a866b2ed16acb2de41aea13efc6c5dd03e 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
@@ -17,8 +17,10 @@ import fr.inra.pappso.xtandempipeline.filter_print.calculation_protein_fdr_distr
import fr.inra.pappso.xtandempipeline.filter_print.filter_isotopic_modifs;
import fr.inra.pappso.xtandempipeline.filter_print.print_fasta;
import fr.inra.pappso.xtandempipeline.filter_print.print_pepnovo;
-import fr.inra.pappso.xtandempipeline.sax_parse.MassChroQmlOutput;
-import fr.inra.pappso.xtandempipeline.sax_parse.ProticDbMlOutput;
+import fr.inra.pappso.xtandempipeline.output.CsvRedundantPeptideOutput;
+import fr.inra.pappso.xtandempipeline.output.MassChroQmlOutput;
+import fr.inra.pappso.xtandempipeline.output.OdsRedundantPeptideOutput;
+import fr.inra.pappso.xtandempipeline.output.ProticDbMlOutput;
import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
public class printing_base extends process {
@@ -54,8 +56,7 @@ public class printing_base extends process {
this.set_view("Printing Open Document Spreadsheet file results");
OdsDocWriter doc = this.ods_specific_printing(this.getfileout()
- .getAbsolutePath()
- + ".ods");
+ .getAbsolutePath() + ".ods");
doc.close();
}
@@ -64,8 +65,7 @@ public class printing_base extends process {
this.set_view("Printing PROTICdbML file results");
FileOutputStream outputStream = new FileOutputStream(new File(this
- .getfileout().getAbsolutePath()
- + "_protic.xml"));
+ .getfileout().getAbsolutePath() + "_protic.xml"));
ProticDbMlOutput protidDbMlOutput = new ProticDbMlOutput();
protidDbMlOutput.open(outputStream);
@@ -109,7 +109,7 @@ public class printing_base extends process {
+ "<tandem_to_pepnovo>" + "\n");
for (Identification ident : this.identifications) {
ident.print_result(new print_pepnovo(output, ident
- .get_samples()));
+ .getMsRunSet()));
}
output.write("</tandem_to_pepnovo>" + "\n");
output.close();
@@ -146,19 +146,38 @@ public class printing_base extends process {
this.set_view("Printing MassChroQ xml file results");
Identification ident = this.identifications.get(0);
// modification isotopic
- ident
- .filtered_match(new filter_isotopic_modifs(
- this.isotopic_mods));
+ ident.filtered_match(new filter_isotopic_modifs(this.isotopic_mods));
MassChroQmlOutput massChroQmlOutput = new MassChroQmlOutput(
this.isotopic_mods, ident);
FileOutputStream outputStream = new FileOutputStream(new File(this
- .getfileout().getAbsolutePath()
- + ".masschroqML"));
- ;
+ .getfileout().getAbsolutePath() + ".masschroqML"));
+
massChroQmlOutput.write(outputStream);
}
+ // redundant peptide output (containing start and stop positions on
+ // proteins)
+ if (true) {
+ FileOutputStream outputStream = new FileOutputStream(new File(this
+ .getfileout().getAbsolutePath() + "_pep_redundant.ods"));
+ OdsRedundantPeptideOutput odsRedOutput = new OdsRedundantPeptideOutput(
+ outputStream);
+ for (Identification ident : this.identifications) {
+ odsRedOutput.write(ident);
+ }
+ odsRedOutput.close();
+
+ FileOutputStream csvStream = new FileOutputStream(new File(this
+ .getfileout().getAbsolutePath() + "_pep_redundant.csv"));
+ CsvRedundantPeptideOutput csvRedOutput = new CsvRedundantPeptideOutput(
+ csvStream);
+ for (Identification ident : this.identifications) {
+ csvRedOutput.write(ident);
+ }
+ csvRedOutput.close();
+ }
+
if (this.isStop())
throw new StopException("");
this.add_current_progress();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
index b1f4f14e7f0cad0746f0bd5f47b62c15ff46d8d6..9ae88a6e00f9c1c7c02b17d2ebe4dac1b8d033bb 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
@@ -18,21 +18,22 @@ public class printing_combine extends printing_base {
super(conf);
}
- protected OdsDocWriter ods_specific_printing(String filename) throws Exception {
+ protected OdsDocWriter ods_specific_printing(String filename)
+ throws Exception {
logger.info("Print combine results in ODS");
OdsDocWriter odsDoc = new OdsDocWriter(filename);
this.set_view("Printing protein file results");
-
+
odsDoc.writeSheet("proteins");
- //msms_output output = new msms_output();
- //output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
+ // msms_output output = new msms_output();
+ // output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_combined(odsDoc));
}
- //output.close();
+ // output.close();
// Verification pas arrete
if (this.isStop())
@@ -41,13 +42,13 @@ public class printing_combine extends printing_base {
this.set_view("Printing peptide file results");
odsDoc.writeSheet("peptides");
- //output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
+ // output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
// peptide list
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_peptide_list(odsDoc));
}
- //output.close();
+ // output.close();
// Verification pas arrete
if (this.isStop())
@@ -55,17 +56,17 @@ public class printing_combine extends printing_base {
this.add_current_progress();
this.set_view("Printing compar file results");
- //odsDoc.writeSheet("compar");
- //output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
+ // odsDoc.writeSheet("compar");
+ // output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
for (Identification ident : this.identifications) {
- ident.print_result(new print_ods_compar(odsDoc, ident.get_samples()));
+ ident.print_result(new print_ods_compar(odsDoc, ident.getMsRunSet()));
}
- //output.close();
+ // output.close();
this.add_current_progress();
return odsDoc;
}
-
+
protected void specific_printing() throws Exception {
logger.info("Print combine results");
@@ -101,7 +102,7 @@ public class printing_combine extends printing_base {
this.set_view("Printing compar file results");
output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
for (Identification ident : this.identifications) {
- ident.print_result(new print_compar(output, ident.get_samples()));
+ ident.print_result(new print_compar(output, ident.getMsRunSet()));
}
output.close();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
index 448e899c62784040f64dd81fd957470042d80109..259aabc2ba83a6dd6a9bb14c068aa8165f90db72 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
@@ -1,6 +1,5 @@
package fr.inra.pappso.xtandempipeline.thread;
-
import fr.inra.pappso.libodsstream.OdsDocWriter;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
@@ -11,23 +10,24 @@ import fr.inra.pappso.xtandempipeline.filter_print.print_peptide_list;
import fr.inra.pappso.xtandempipeline.filter_print.print_protein_to_indiv;
import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
public class printing_indiv extends printing_base {
public printing_indiv(config conf) {
super(conf);
}
-
- protected OdsDocWriter ods_specific_printing(String filename) throws Exception {
+
+ protected OdsDocWriter ods_specific_printing(String filename)
+ throws Exception {
logger.info("Print individual results in ODS");
OdsDocWriter odsDoc = new OdsDocWriter(filename);
-
+
this.set_view("Printing protein file results");
-
+
odsDoc.writeSheet("proteins");
// protein view
for (Identification ident : this.identifications) {
- ident.print_result(new print_ods_protein_to_indiv(odsDoc, ident.get_samples()));
+ ident.print_result(new print_ods_protein_to_indiv(odsDoc, ident
+ .getMsRunSet()));
}
// Verification pas arrete
@@ -46,19 +46,20 @@ public class printing_indiv extends printing_base {
if (this.isStop())
throw new StopException("");
this.add_current_progress();
-
+
return odsDoc;
}
- protected void specific_printing () throws Exception {
+ protected void specific_printing() throws Exception {
logger.info("Print individual results");
-
+
this.set_view("Printing protein file results");
msms_output output = new msms_output();
output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
- ident.print_result(new print_protein_to_indiv(output, ident.get_samples()));
+ ident.print_result(new print_protein_to_indiv(output, ident
+ .getMsRunSet()));
}
output.close();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
index ef274d8325039994b4d162458a57627f84560e0b..cbae3ca8f2141e871cee575a46625ba4f7400962 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
@@ -18,20 +18,21 @@ public class printing_phosphopeptide extends printing_base {
super(conf);
}
- protected OdsDocWriter ods_specific_printing(String filename) throws Exception {
+ protected OdsDocWriter ods_specific_printing(String filename)
+ throws Exception {
OdsDocWriter odsDoc = new OdsDocWriter(filename);
logger.info("Print phophopeptide results ODS");
this.set_view("Printing protein file results");
odsDoc.writeSheet("proteins");
- //msms_output output = new msms_output();
- //output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
+ // msms_output output = new msms_output();
+ // output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_protein_to_phosphopeptide(odsDoc));
}
- //output.close();
+ // output.close();
// Verification pas arrete
if (this.isStop())
@@ -39,14 +40,15 @@ public class printing_phosphopeptide extends printing_base {
this.add_current_progress();
this.set_view("Printing peptide file results");
- //output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
+ // output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
odsDoc.writeSheet("peptides");
// peptide list
for (Identification ident : this.identifications) {
- ident.print_result(new print_ods_peptide_list_to_phosphopeptide(odsDoc));
+ ident.print_result(new print_ods_peptide_list_to_phosphopeptide(
+ odsDoc));
}
- //output.close();
+ // output.close();
// Verification pas arrete
if (this.isStop())
@@ -54,13 +56,13 @@ public class printing_phosphopeptide extends printing_base {
this.add_current_progress();
this.set_view("Printing compar file results");
- //odsDoc.writeSheet("compar");
- //output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
+ // odsDoc.writeSheet("compar");
+ // output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
for (Identification ident : this.identifications) {
ident.print_result(new print_ods_compar_phospho(odsDoc, ident
- .get_samples()));
+ .getMsRunSet()));
}
- //output.close();
+ // output.close();
this.add_current_progress();
return odsDoc;
@@ -101,7 +103,7 @@ public class printing_phosphopeptide extends printing_base {
output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
for (Identification ident : this.identifications) {
ident.print_result(new print_compar_phospho(output, ident
- .get_samples()));
+ .getMsRunSet()));
}
output.close();