From 54d1ccf2e66492fba71ef21cf8d3765e88124c9f Mon Sep 17 00:00:00 2001
From: langella <langella@b8ef2a07-7df7-436f-90b9-41648038564b>
Date: Fri, 15 Apr 2011 12:18:44 +0000
Subject: [PATCH] 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 | 8 ++++----
xtandempipeline/debian/changelog | 7 +++++++
xtandempipeline/debian/control | 4 ++--
.../share/xtandempipeline/xtandempipeline.jnlp | 5 +++--
.../share/xtandempipeline/xtandempipeline.sh.cmake | 2 +-
.../inra/pappso/xtandempipeline/XtandemPipelineMain.java | 2 +-
.../pappso/xtandempipeline/class_msms/Identification.java | 3 +--
7 files changed, 19 insertions(+), 12 deletions(-)
diff --git a/xtandempipeline/CMakeLists.txt b/xtandempipeline/CMakeLists.txt
index b9c6b19e7..936f921ba 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 957d3d2f9..fde3348a4 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 bd789b4d3..5d0238d4b 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 1c0641d13..ca554b2ba 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 40401b8b1..705b9d75a 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 c8b8c145b..0f9936e6b 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 7f53e5aea..6c3ee0c1f 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);
--
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