/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.jws1;
import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.PileUpfile;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
* @return true if getResultSet will return a valid alignment and prediction
* result.
*/
+ @Override
public boolean hasResults()
{
if (subjobComplete && result != null && result.isFinished()
return false;
}
+ @Override
public boolean hasValidInput()
{
if (sequence != null)
return null;
}
AlignmentI al = null;
- ColumnSelection alcsel = null;
+ HiddenColumns alhidden = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
JpredResult result = (JpredResult) this.result;
- jalview.bin.Cache.log.debug("Parsing output from JNet job.");
+ Cache.log.debug("Parsing output from JNet job.");
// JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
// "File");
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(
- result.getPredfile(), "Paste");
+ JPredFile prediction = new JPredFile(
+ result.getPredfile(), DataSourceType.PASTE);
SequenceI[] preds = prediction.getSeqsAsArray();
- jalview.bin.Cache.log.debug("Got prediction profile.");
+ Cache.log.debug("Got prediction profile.");
if ((this.msa != null) && (result.getAligfile() != null))
{
- jalview.bin.Cache.log.debug("Getting associated alignment.");
+ Cache.log.debug("Getting associated alignment.");
// we ignore the returned alignment if we only predicted on a single
// sequence
- String format = new jalview.io.IdentifyFile().Identify(
- result.getAligfile(), "Paste");
+ FileFormatI format = new IdentifyFile().identify(
+ result.getAligfile(), DataSourceType.PASTE);
- if (jalview.io.FormatAdapter.isValidFormat(format))
+ if (format != null)
{
SequenceI sqs[];
if (predMap != null)
{
Object[] alandcolsel = input
- .getAlignmentAndColumnSelection(getGapChar());
+ .getAlignmentAndHiddenColumns(getGapChar());
sqs = (SequenceI[]) alandcolsel[0];
al = new Alignment(sqs);
- alcsel = (ColumnSelection) alandcolsel[1];
+ alhidden = (HiddenColumns) alandcolsel[1];
}
else
{
al = new FormatAdapter().readFile(result.getAligfile(),
- "Paste", format);
+ DataSourceType.PASTE, format);
sqs = new SequenceI[al.getHeight()];
for (int i = 0, j = al.getHeight(); i < j; i++)
{
sqs[i] = al.getSequenceAt(i);
}
- if (!jalview.analysis.SeqsetUtils.deuniquify(SequenceInfo, sqs))
+ if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
{
throw (new Exception(
MessageManager
{
al.setDataset(null);
}
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
+ JnetAnnotationMaker.add_annotation(prediction, al,
FirstSeq, false, predMap);
}
else
{
throw (new Exception(MessageManager.formatMessage(
- "exception.unknown_format_for_file", new String[] {
- format, result.getAligfile() })));
+ "exception.unknown_format_for_file", new String[] { "",
+ result.getAligfile() })));
}
}
else
{
char gc = getGapChar();
SequenceI[] sqs = (SequenceI[]) input
- .getAlignmentAndColumnSelection(gc)[0];
+ .getAlignmentAndHiddenColumns(gc)[0];
if (this.msaIndex >= sqs.length)
{
throw new Error(
{
// Adjust input view for gaps
// propagate insertions into profile
- alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+ alhidden = HiddenColumns.propagateInsertions(profileseq, al,
input);
}
}
alant.sequenceRef);
}
}
- return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
+ return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
}
/**
if (msf.length > 1)
{
msa = new vamsas.objects.simple.Msfalignment();
- jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
- msa.setMsf(pileup.print(msf));
+ PileUpfile pileup = new PileUpfile();
+ msa.setMsf(pileup.print(msf, true));
}
}
}
}
}
+ @Override
public void StartJob(AWsJob j)
{
if (!(j instanceof JPredJob))
}
}
+ @Override
public void parseResult()
{
int results = 0; // number of result sets received
wsInfo.showResultsNewFrame
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(true);
wsInfo.mergeResults
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(false);
if (res[1] != null)
{
af = new AlignFrame((Alignment) res[0],
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
else
*/
af = new AlignFrame((Alignment) res[0],
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ (HiddenColumns) res[1],
+ AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
}
}
+ @Override
public void pollJob(AWsJob job) throws Exception
{
((JPredJob) job).result = server.getresult(job.getJobId());
}
+ @Override
public boolean isCancellable()
{
return false;
}
+ @Override
public void cancelJob()
{
throw new Error(MessageManager.getString("error.implementation_error"));
}
+ @Override
public boolean canMergeResults()
{
return false;