X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabawsAlignCalcWorker.java;h=c9c1ea82836a8807776963a82669750ad1cead10;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=7ee6e08aca7bb59d7f96d1a2b8975e0769a1ea5c;hpb=f11c195585d2c4b6671b6e349fc152b8eb1fbc50;p=jalview.git
diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index 7ee6e08..c9c1ea8 100644
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jws2;
import jalview.analysis.AlignSeq;
@@ -6,10 +24,11 @@ import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.IProgressIndicator;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -17,12 +36,13 @@ import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import com.sun.xml.internal.ws.developer.ServerSideException;
import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
@@ -34,6 +54,7 @@ import compbio.metadata.WrongParameterException;
public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
{
+ Jws2Instance service;
@SuppressWarnings("unchecked")
protected SequenceAnnotation aaservice;
@@ -50,12 +71,16 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
super(alignViewport, alignPanel);
}
+ IProgressIndicator guiProgress;
+
public JabawsAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
WsParamSetI preset, List paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+ this.guiProgress = alignFrame;
this.preset = preset;
this.arguments = paramset;
+ this.service = service;
aaservice = (SequenceAnnotation) service.service;
}
@@ -71,7 +96,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
}
/**
- * reconfigure and restart the AAConsClient. This method will spawn a new
+ * reconfigure and restart the AAConClient. This method will spawn a new
* thread that will wait until any current jobs are finished, modify the
* parameters and restart the conservation calculation with the new values.
*
@@ -81,31 +106,9 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
public void updateParameters(final WsParamSetI newpreset,
final List newarguments)
{
- if (calcMan.isWorking(this))
- {
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
-
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- updateParameters(newpreset, newarguments);
- }
- }).start();
- }
- else
- {
- preset = newpreset;
- arguments = newarguments;
- calcMan.startWorker(this);
- }
+ preset = newpreset;
+ arguments = newarguments;
+ calcMan.startWorker(this);
}
public List