XPIP file kick start

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@356 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/debian/changelog

   * fixed xml header problem on PROTICdbML export
+  * xpip file kick start
 
 xtandempipeline (3.3.0-1) lucid; urgency=low
 

xtandempipeline/share/applications/xtandempipeline.desktop.cmake

@@ -3,7 +3,7 @@ Name=Xtandem pipeline @XTANDEMPIPELINE_VERSION@
 Categories=Education;Science;Math;
 Comment=loads and parses the xml results product by X!Tandem
 Comment[fr]=chargement et exploitation des résultats du logiciel X!Tandem
-Exec=@CMAKE_INSTALL_PREFIX@/bin/xtandempipeline.sh
+Exec=@CMAKE_INSTALL_PREFIX@/bin/xtandempipeline.sh %U
 Icon=@CMAKE_INSTALL_PREFIX@/share/xtandempipeline/xtandempipeline_icon.svg
 Terminal=false
 Type=Application

xtandempipeline/share/xtandempipeline/xtandempipeline.sh.cmake

 #!/bin/bash
 
 if [ $(uname -m) == "x86_64" ]; then
-	@CMAKE_Java_COMPILER@ -Xmx3000m -Xms256m -jar @CMAKE_INSTALL_PREFIX@/share/xtandempipeline/XtandemPipeline.jar
+	@CMAKE_Java_COMPILER@ -Xmx3000m -Xms256m -jar @CMAKE_INSTALL_PREFIX@/share/xtandempipeline/XtandemPipeline.jar $1
 else
-	@CMAKE_Java_COMPILER@ -Xmx1500m -Xms256m -jar @CMAKE_INSTALL_PREFIX@/share/xtandempipeline/XtandemPipeline.jar
+	@CMAKE_Java_COMPILER@ -Xmx1500m -Xms256m -jar @CMAKE_INSTALL_PREFIX@/share/xtandempipeline/XtandemPipeline.jar $1
 fi
 
 

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

@@ -21,6 +21,8 @@ package fr.inra.pappso.xtandempipeline;
  */
 
 import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.MalformedURLException;
@@ -109,11 +111,30 @@ public class XtandemPipelineMain {
 				} catch (IOException e) {
 					logger.error("unable to open URL "
 							+ urlOfXpipData.toString());
-					new Main_Windows(null);
+					// Perhaps that the first argument is a local path to an
+					// XPIP file ?
+					InputStream in = null;
+					try {
+						in = new FileInputStream(args[0]);
+					} catch (FileNotFoundException e1) {
+						logger.error("unable to open XPIP file ");
+						in = null;
+					}
+					new Main_Windows(in);
+
 				}
 			} catch (MalformedURLException e) {
 				logger.error("MalformedURLException on " + args[0]);
-				new Main_Windows(null);
+				// Perhaps that the first argument is a local path to an
+				// XPIP file ?
+				InputStream in = null;
+				try {
+					in = new FileInputStream(args[0]);
+				} catch (FileNotFoundException e1) {
+					logger.error("unable to open XPIP file ");
+					in = null;
+				}
+				new Main_Windows(in);
 			}
 		} else {
 			logger.info("Starting new main in classic mode");