import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.WrongParameterException;
-public abstract class JabawsMsaInterfaceAlignCalcWorker extends
- AbstractJabaCalcWorker
+public abstract class JabawsMsaInterfaceAlignCalcWorker
+ extends AbstractJabaCalcWorker
{
@SuppressWarnings("unchecked")
}
public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
- AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+ 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;
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);