From 2a60631fc35cb237924541926f8693b1dbed373b Mon Sep 17 00:00:00 2001
From: langella <langella@b8ef2a07-7df7-436f-90b9-41648038564b>
Date: Sun, 10 Feb 2013 12:21:14 +0000
Subject: [PATCH] force instanciation of MsRun throught MsRunSet
git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@336 b8ef2a07-7df7-436f-90b9-41648038564b
---
.../xtandempipeline/class_msms/MsRun.java | 2 +-
.../xtandempipeline/thread/individual.java | 38 +++++++++++--------
2 files changed, 24 insertions(+), 16 deletions(-)
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
index 5d8a456f6..89929923a 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
@@ -14,7 +14,7 @@ public class MsRun implements GrpMsSample {
private HashSet<IdentificationDataSource> files = new HashSet<IdentificationDataSource>(
0);
- public MsRun(String sample_name) {
+ protected MsRun(String sample_name) {
logger.debug("MsRun begin "+sample_name);
sampleName = sample_name;
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
index 485ddfcbf..a3ffa0477 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
@@ -4,6 +4,7 @@ import java.util.ArrayList;
import java.util.Vector;
import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
@@ -37,29 +38,36 @@ public class individual extends process {
// Ecrire le process et penser à relever des StopException
for (int i = 0; i < dataSources.size(); i++) {
// parsing
- this.set_view("Analysing file : " + (i + 1) + "/" + dataSources.size()
- + "\n" + "Parsing file : " + dataSources.get(i).getName());
-
+ this.set_view("Analysing file : " + (i + 1) + "/"
+ + dataSources.size() + "\n" + "Parsing file : "
+ + dataSources.get(i).getName());
+
// Is sample exist? Get previous identification
Identification identtemp = null;
for (int m = 0; m < identifications.size(); m++) {
MsRunSet samples = identifications.get(m).get_samples();
- MsRun test = new MsRun(dataSources.get(i).getName());
+ MsRun test = samples.getInstance(dataSources.get(i));
+ if (test == null) {
+ String message = "MsRun test is null";
+ logger.error(message);
+ throw new MSMSException(message);
+ }
if (samples.contains(test))
identtemp = identifications.get(m);
}
- //xtandem handler;
- //if (identtemp != null)
- // handler = new xtandem(identtemp, dataSources.get(i));
- //else
- // handler = new xtandem(dataSources.get(i));
- //new parse_file(handler, dataSources.get(i).);
+ // xtandem handler;
+ // if (identtemp != null)
+ // handler = new xtandem(identtemp, dataSources.get(i));
+ // else
+ // handler = new xtandem(dataSources.get(i));
+ // new parse_file(handler, dataSources.get(i).);
//
- //if (identtemp == null)
- // identifications.add(handler.get_identifications());
-
- //Load identification from datasource
- identifications.add(dataSources.get(i).loadIdentification(identtemp));
+ // if (identtemp == null)
+ // identifications.add(handler.get_identifications());
+
+ // Load identification from datasource
+ identifications.add(dataSources.get(i)
+ .loadIdentification(identtemp));
// verification pas arreté
if (this.isStop())
--
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