new version 3.1.0

modifying debian package
not working at this momment : complete refactoring with new grouping package

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@45 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/CMakeLists.txt

@@ -20,7 +20,7 @@ MESSAGE("Java_JAVAC_EXECUTABLE : ${Java_JAVAC_EXECUTABLE} ")
 
 cmake_minimum_required(VERSION 2.6)
 
-SET (XTANDEMPIPELINE_VERSION "3.0.2")
+SET (XTANDEMPIPELINE_VERSION "3.1.0")
 
 SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
 SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
@@ -38,8 +38,8 @@ SET(CPACK_PACKAGE_VENDOR "INRA")
 
 SET(CPACK_PACKAGE_VERSION ${XTANDEMPIPELINE_VERSION})
 SET(CPACK_PACKAGE_VERSION_MAJOR "3")
-SET(CPACK_PACKAGE_VERSION_MINOR "0")
-SET(CPACK_PACKAGE_VERSION_PATCH "2")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
 #SET(CPACK_RESOURCE_FILE_LICENSE ${xtandemparser_SOURCE_DIR}/COPYING)
 #SET(CPACK_RESOURCE_FILE_README ${xtandemparser_SOURCE_DIR}/README)
 #SET(CPACK_RESOURCE_FILE_WELCOME ${xtandemparser_SOURCE_DIR}/INSTALL)
@@ -154,7 +154,7 @@ INSTALL(FILES share/applications/xtandempipeline.desktop DESTINATION share/appli
 #INSTALL(FILES share/beads/beads_silver_small.conf DESTINATION share/beads)
 INSTALL(PROGRAMS share/xtandempipeline/xtandempipeline.sh DESTINATION bin)
 INSTALL(FILES share/xtandempipeline/xtandempipeline.jnlp DESTINATION share/xtandempipeline)
-INSTALL(FILES share/xtandempipeline/XTandem_Pipeline.jar DESTINATION share/xtandempipeline)
+INSTALL(FILES share/xtandempipeline/XtandemPipeline.jar DESTINATION share/xtandempipeline)
 INSTALL(FILES share/xtandempipeline/proticws_svgutils.jar DESTINATION share/xtandempipeline)
 INSTALL(FILES share/xtandempipeline/xtandempipeline_icon.svg DESTINATION share/xtandempipeline)
 

xtandempipeline/debian/changelog

+xtandempipeline (3.1.0-1) maverick; urgency=low
+
+  * complete rewrite of the grouping algorithm with Benoit Valot
+  * log4j introduced
+
+ --  Olivier Langella <Olivier.Langella@moulon.inra.fr>  Fri, 15 Apr 2011 12:18:51 +0200
+
 xtandempipeline (3.0.2-2) maverick; urgency=low
 
   * fixed bash script to launch XtandemPipeline

xtandempipeline/debian/control

@@ -6,13 +6,13 @@ Homepage: http://pappso.inra.fr/
 DM-Upload-Allowed: yes
 Uploaders: Olivier Langella <olivier.langella@moulon.inra.fr>
 Standards-Version: 1.0
-Build-Depends: debhelper (>= 5), cmake (>= 2.6), ant (>=1.8), openjdk-6-jdk (>=1.6), libswt-gtk-3.5-java (>=3.5.1), libbatik-java (>=1.7), libswt-mozilla-gtk-3.5-jni
+Build-Depends: debhelper (>= 5), cmake (>= 2.6), ant (>=1.8), openjdk-6-jdk (>=1.6), libswt-gtk-3.5-java (>=3.5.1), libbatik-java (>=1.7), libswt-mozilla-gtk-3.5-jni, liblog4j1.2-java (>=1.2.15)
 
 Package: xtandempipeline
 Architecture: all
 Replaces: xtandemparser (<< 2.9.8-2~)
 Conflicts: xtandemparser (<< 2.9.8-2~)
-Depends: ${shlibs:Depends}, openjdk-6-jre (>=1.6), libswt-gtk-3.5-java (>=3.5.1), libbatik-java (>=1.7), libswt-mozilla-gtk-3.5-jni, xtandem-cyclone | xtandem-tornado
+Depends: ${shlibs:Depends}, openjdk-6-jre (>=1.6), libswt-gtk-3.5-java (>=3.5.1), libbatik-java (>=1.7), libswt-mozilla-gtk-3.5-jni, xtandem-cyclone | xtandem-tornado, liblog4j1.2-java (>=1.2.15)
 Description: loads and parses the xml results product by X!Tandem
  This Java application loads and parses the xml results product by X!Tandem, applies filters on 
  E-value at peptide and protein levels, filters proteins on the basis of a minimun number of 

xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp

@@ -17,7 +17,7 @@
   </security>
   <resources>
     <j2se version="1.6+" java-vm-args="-ea -Xincgc -verbose -Xmx1024m -Xms256m" />
-    <jar href="XTandem_Pipeline.jar" main="true" download="eager" />
+    <jar href="XtandemPipeline.jar" main="true" download="eager" />
         
     <!--	  	    
 	 ***************************************
@@ -47,6 +47,7 @@
 	 others
 	      **************************   
     -->
+    <jar href="lib/log4j-1.2.jar" main="true" download="eager" />
     <jar href="lib/xalan-2.6.0.jar" main="true" download="eager" />
     <jar href="lib/xercesImpl-2.9.1.jar" main="true" download="eager" />
     <jar href="lib/xml-apis-1.3.04.jar" main="true" download="eager" />
@@ -81,7 +82,7 @@
     <jar href="lib/swt/swt-gtk-linux-x86.jar" />
   </resources>
   
-	<application-desc main-class="My_XTandem_Pipeline" >
+	<application-desc main-class="XtandemPipelineMain" >
 	</application-desc>
 
   <update check="always" policy="prompt-update"></update>

xtandempipeline/share/xtandempipeline/xtandempipeline.sh.cmake

 #!/bin/bash
 
-@CMAKE_Java_COMPILER@ -jar @CMAKE_INSTALL_PREFIX@/share/xtandempipeline/XTandem_Pipeline.jar
+@CMAKE_Java_COMPILER@ -Xmx3000m -Xms256m -jar @CMAKE_INSTALL_PREFIX@/share/xtandempipeline/XtandemPipeline.jar

xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java

@@ -15,7 +15,7 @@ public class XtandemPipelineMain {
 	 * @return 
 	 * @return 
 	 */
-	static public String version = "3.0.3";
+	static public String version = "3.1.0";
 	
 	public static void main(String[] args) {
 		PropertyConfigurator.configure("conf/log4j.properties");

xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java

@@ -12,7 +12,6 @@ import fr.inra.pappso.xtandempipeline.filter_print.print_base;
 import fr.inra.pappso.xtandempipeline.filter_print.swt_table_base;
 import fr.inra.pappso.xtandempipeline.grouping.Group;
 import fr.inra.pappso.xtandempipeline.grouping.GroupSet;
-import fr.inra.pappso.xtandempipeline.grouping.HashKey4Groups;
 import fr.inra.pappso.xtandempipeline.grouping.HashPeptide;
 import fr.inra.pappso.xtandempipeline.grouping.HashPeptideSet;
 import fr.inra.pappso.xtandempipeline.grouping.HashProtein;
@@ -160,7 +159,7 @@ public class Identification {
 		}
 
 		for (Group group : grouping.getGroupList()) {
-			for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
+			for (SubGroup sg : group.getSubGroupSet()) {
 				for (HashSampleScanSetProt hk : sg
 						.getHashSampleScanSetProtSet()) {
 					hk.getMatch().setIsvalidate(true);