reading local log4j.properties file

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@283 b8ef2a07-7df7-436f-90b9-41648038564b

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

@@ -20,6 +20,7 @@ package fr.inra.pappso.xtandempipeline;
 
  */
 
+import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.MalformedURLException;
@@ -30,6 +31,7 @@ import org.apache.commons.codec.binary.Base64;
 import org.apache.log4j.Logger;
 import org.apache.log4j.PropertyConfigurator;
 
+import fr.inra.pappso.xtandempipeline.class_msms.config;
 import fr.inra.pappso.xtandempipeline.ui.swt.Main_Windows;
 
 public class XtandemPipelineMain {
@@ -53,25 +55,34 @@ public class XtandemPipelineMain {
 			+ "If a protein is identified by two peptides with an evalue of O.O1, the protein evalue is O.OOO1.\n\n"
 			+ "So, we preconise to put -4 for the protein evalue filter instead of -8.";
 
-	public static String news = "3.2.2 : Corrected report of input parameter on X!Tandem output result (thanks to T. Greko)\n\n"+
-	"3.2.1 : Add new X!Tandem paramaters for multiple search of modifications in one analyse and calculation can now be performed on z > 3"+"\n\n"+
-	"3.2.0 : Identification from Mascot dat file can now be imported and filtered."+
-	" All work as X!Tandem result excepts that protein sequence can not be retrieved : PAI and coverage are absent.\n"+
-	"Correction of FDR calculation from Reverse/Decoy search.";
+	public static String news = "3.2.2 : Corrected report of input parameter on X!Tandem output result (thanks to T. Greko)\n\n"
+			+ "3.2.1 : Add new X!Tandem paramaters for multiple search of modifications in one analyse and calculation can now be performed on z > 3"
+			+ "\n\n"
+			+ "3.2.0 : Identification from Mascot dat file can now be imported and filtered."
+			+ " All work as X!Tandem result excepts that protein sequence can not be retrieved : PAI and coverage are absent.\n"
+			+ "Correction of FDR calculation from Reverse/Decoy search.";
 
 	public static void main(String[] args) {
 
-		// Chargement en release mode
-		if (System.getProperty("os.name").contains("Linux")) {
-			PropertyConfigurator.configure(XtandemPipelineMain.class
-					.getResource("/conf/log4j.linux.properties"));
-			logger.info("Linux logging");
-			// System.out.print("Linux logging");
+		File log4jPropertyFile = new File(config.getRacinePath()
+				+ System.getProperty("file.separator") + "log4j.properties");
+		if (log4jPropertyFile.exists()) {
+			PropertyConfigurator.configure(log4jPropertyFile.getAbsolutePath());
+			logger.info("loading log4j proterties from "+log4jPropertyFile.getAbsolutePath());
+			// return (false);
 		} else {
-			PropertyConfigurator.configure(XtandemPipelineMain.class
-					.getResource("/conf/log4j.windows.properties"));
-			logger.info("Window logging");
-			// System.out.print("Window logging");
+			// Chargement en release mode
+			if (System.getProperty("os.name").contains("Linux")) {
+				PropertyConfigurator.configure(XtandemPipelineMain.class
+						.getResource("/conf/log4j.linux.properties"));
+				logger.info("Linux logging");
+				// System.out.print("Linux logging");
+			} else {
+				PropertyConfigurator.configure(XtandemPipelineMain.class
+						.getResource("/conf/log4j.windows.properties"));
+				logger.info("Window logging");
+				// System.out.print("Window logging");
+			}
 		}
 		if (args.length > 0) {
 			try {

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

@@ -144,7 +144,7 @@ public class config {
 
 	public File getXtandem_model() {
 		File file = new File(properties.getProperty(xtandem_model,
-				this.getRacinePath() + System.getProperty("file.separator")
+				config.getRacinePath() + System.getProperty("file.separator")
 						+ "xtandem_models"));
 		if (!file.exists())
 			file.mkdirs();
@@ -375,7 +375,7 @@ public class config {
 	}
 
 	public boolean loadPropertiesFromXml() throws Exception {
-		File xml = new File(this.getRacinePath()
+		File xml = new File(config.getRacinePath()
 				+ System.getProperty("file.separator") + "xtandempipeline.conf");
 		if (!xml.exists()) {
 			logger.info("New configuration file");
@@ -387,14 +387,14 @@ public class config {
 	}
 
 	public void savePropertiestoXml() throws Exception {
-		File xml = new File(this.getRacinePath()
+		File xml = new File(config.getRacinePath()
 				+ System.getProperty("file.separator") + "xtandempipeline.conf");
 		logger.info("Save properties condfiguration to : " + xml.getPath());
 		properties.storeToXML(new FileOutputStream(xml),
 				"Xtandem pipeline configuration file");
 	}
 
-	private File getRacinePath() {
+	static public File getRacinePath() {
 		File path;
 		if (System.getProperty("os.name").contains("Linux")) {
 			path = new File(System.getProperty("user.home")