/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.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(
- "Invalid parameter set. Check Jalview implementation.", x);
-
+ throw new JobSubmissionException(MessageManager.getString(
+ "exception.jobsubmission_invalid_params_set"), x);
}
}
return rslt;
List<AlignmentAnnotation> ourAnnot, String typeName,
String calcId, SequenceI dseq, int base, Score scr)
{
- System.out.println("Creating annotation on dseq:" + dseq.getStart()
- + " base is " + base + " and length=" + dseq.getLength()
- + " == " + scr.getScores().size());
+ jalview.bin.Console.outPrintln("Creating annotation on dseq:"
+ + dseq.getStart() + " base is " + base + " and length="
+ + dseq.getLength() + " == " + scr.getScores().size());
// AlignmentAnnotation annotation = new AlignmentAnnotation(
// scr.getMethod(), typeName, new Annotation[]
// {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);