X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabawsAlignCalcWorker.java;h=6bfeddf5a0c2941beced6f9aa03b5f1c2d2e9beb;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=99fc8a3da255bd5508222a9e28febd02b6ef370c;hpb=90655a5726c6f7b82048438cf66c737a6999866d;p=jalview.git
diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index 99fc8a3..6bfeddf 100644
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -1,607 +1,77 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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;
-import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-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.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
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 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;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.WrongParameterException;
-public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
+public abstract class JabawsAlignCalcWorker extends JabawsCalcWorker
{
- Jws2Instance service;
-
- @SuppressWarnings("unchecked")
- protected SequenceAnnotation aaservice;
-
- protected ScoreManager scoremanager;
-
- protected WsParamSetI preset;
-
- protected List arguments;
public JabawsAlignCalcWorker(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
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;
-
- }
-
- public WsParamSetI getPreset()
- {
- return preset;
- }
-
- public List getArguments()
- {
- return arguments;
- }
-
- /**
- * 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.
- *
- * @param newpreset
- * @param newarguments
- */
- public void updateParameters(final WsParamSetI newpreset,
- final List newarguments)
- {
- preset = newpreset;
- arguments = newarguments;
- calcMan.startWorker(this);
- }
-
- public List