Change svn eclipse plugin

Only search y/b phospho loss on MS2


git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@178 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
 	<classpathentry kind="lib" path="lib"/>
 	<classpathentry kind="lib" path="lib/libodsstream.jar"/>
 	<classpathentry kind="lib" path="lib/libproteomicsvg.jar"/>
@@ -30,6 +30,5 @@
 	<classpathentry kind="lib" path="lib/http/commons-httpclient-3.1.jar"/>
 	<classpathentry kind="lib" path="lib/http/commons-logging-1.0.4.jar"/>
 	<classpathentry kind="lib" path="lib/swt/swt-gtk-linux-x86_64.jar"/>
-	<classpathentry kind="lib" path="lib/swt/swt-gtk-linux-x86.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

xtandempipeline/.settings/org.eclipse.jdt.core.prefs

+#Mon Jan 02 11:06:48 CET 2012
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6

xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_Details_item.java

@@ -33,7 +33,6 @@ import fr.inra.moulon.proticport.model.entities.Spectrum;
 import fr.inra.moulon.proticport.model.exceptions.ProticDataNotFoundException;
 import fr.inra.moulon.svgutils.svgspectrum.SvgAaMod;
 import fr.inra.moulon.svgutils.svgspectrum.SvgAaModPhospho;
-import fr.inra.moulon.svgutils.svgspectrum.SvgAminoAcid;
 import fr.inra.moulon.svgutils.svgspectrum.SvgPeptideSequence;
 import fr.inra.moulon.svgutils.svgspectrum.SvgSpectrumDocument;
 import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
@@ -363,7 +362,7 @@ public class Peptide_Details_item extends CTabItem {
 		SvgPeptideSequence mon_peptide = new SvgPeptideSequence(
 				pep.get_sequence());
 		for (Modifs mod : pep.get_Modifs()) {
-			if (mod.is_phopho_modifs()) {
+			if (mod.is_phopho_modifs() && mod.get_modvalue()>0) {
 				SvgAaMod themod = new SvgAaModPhospho(); // phosphorylated
 															// residue
 				mon_peptide.getAA(mod.get_posi()).addModification(themod);