/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.jws2;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
import java.util.Iterator;
import java.util.List;
import compbio.data.msa.MsaWS;
-import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.Alignment;
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.ResultNotAvailableException;
import compbio.metadata.WrongParameterException;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.util.MessageManager;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalcWorker
+public abstract class JabawsMsaInterfaceAlignCalcWorker extends
+ AbstractJabaCalcWorker
{
@SuppressWarnings("unchecked")
super(alignViewport, alignPanel);
}
- public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
+ AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
rslt = msaservice.customAlign(seqs, getJabaArguments());
} catch (WrongParameterException x)
{
- throw new JobSubmissionException(MessageManager.getString("exception.jobsubmission_invalid_params_set"), x);
+ throw new JobSubmissionException(
+ MessageManager
+ .getString("exception.jobsubmission_invalid_params_set"),
+ x);
}
}
return rslt;