diff --git a/xtandempipeline/CMakeLists.txt b/xtandempipeline/CMakeLists.txt
index b9c6b19e7a98ee557bbf48fe113fbd2e632aa205..936f921babb98dc48319d6519465168a17b0c06b 100644
--- a/xtandempipeline/CMakeLists.txt
+++ b/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)
diff --git a/xtandempipeline/debian/changelog b/xtandempipeline/debian/changelog
index 957d3d2f9f72090b6c3381affc6943e213ff6fa0..fde3348a476ea3ebbe2b1532fc8c16102681e83d 100644
--- a/xtandempipeline/debian/changelog
+++ b/xtandempipeline/debian/changelog
@@ -1,3 +1,10 @@
+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
diff --git a/xtandempipeline/debian/control b/xtandempipeline/debian/control
index bd789b4d31b9b04feb51ee3cea4ac116bf97210c..5d0238d4bae4e0601bfe7e9814306670e71a941d 100644
--- a/xtandempipeline/debian/control
+++ b/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
diff --git a/xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp b/xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp
index 1c0641d139408d0b1a99674f2c0a96d43d318231..ca554b2ba3556ba4266636d22810ad1754a05487 100644
--- a/xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp
+++ b/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>
diff --git a/xtandempipeline/share/xtandempipeline/xtandempipeline.sh.cmake b/xtandempipeline/share/xtandempipeline/xtandempipeline.sh.cmake
index 40401b8b1ed491bf958a04d57765218fcbfae583..705b9d75a05525baff976f9a70a6b028c24867da 100644
--- a/xtandempipeline/share/xtandempipeline/xtandempipeline.sh.cmake
+++ b/xtandempipeline/share/xtandempipeline/xtandempipeline.sh.cmake
@@ -1,3 +1,3 @@
#!/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
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java
index c8b8c145b70cbd54ca4ada67348276dcbb1fc4f6..0f9936e6b18accb45eae70d77d8d7cfca4a385b0 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java
+++ b/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");
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
index 7f53e5aea12b50d3ef5861179f2b0064f73300ba..6c3ee0c1f6a844181f345e7d68e0f970425593a2 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
+++ b/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);