X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=b0210d8668cb175282c6dc803d68ada1438c3458;hb=c70905eb5589c7622a2c7cf8a008ba0863b5c010;hp=52c2145b89a189d4ff45a43e5fef5ae2f703d204;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 52c2145..b0210d8 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -1,33 +1,53 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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 .
+ * 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.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.util.*;
+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.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;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.List;
+
import vamsas.objects.simple.JpredResult;
class JPredThread extends JWS1Thread implements WSClientI
@@ -58,6 +78,7 @@ class JPredThread extends JWS1Thread implements WSClientI
* @return true if getResultSet will return a valid alignment and prediction
* result.
*/
+ @Override
public boolean hasResults()
{
if (subjobComplete && result != null && result.isFinished()
@@ -69,6 +90,7 @@ class JPredThread extends JWS1Thread implements WSClientI
return false;
}
+ @Override
public boolean hasValidInput()
{
if (sequence != null)
@@ -91,67 +113,75 @@ class JPredThread extends JWS1Thread implements WSClientI
{
return null;
}
- Alignment al = null;
- ColumnSelection alcsel = null;
+ AlignmentI al = 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(
- (Hashtable) SequenceInfo, sqs))
+ if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
{
throw (new Exception(
- "Couldn't recover sequence properties for alignment."));
+ MessageManager
+ .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
}
}
FirstSeq = 0;
- al.setDataset(null);
+ if (currentView.getDataset() != null)
+ {
+ al.setDataset(currentView.getDataset());
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
+ }
+ else
+ {
+ al.setDataset(null);
+ }
+ JnetAnnotationMaker.add_annotation(prediction, al,
FirstSeq, false, predMap);
}
else
{
- throw (new Exception("Unknown format " + format
- + " for file : \n" + result.getAligfile()));
+ throw (new Exception(MessageManager.formatMessage(
+ "exception.unknown_format_for_file", new String[] { "",
+ result.getAligfile() })));
}
}
else
@@ -161,20 +191,21 @@ class JPredThread extends JWS1Thread implements WSClientI
if (predMap != null)
{
char gc = getGapChar();
- SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input
- .getAlignmentAndColumnSelection(gc))[0];
+ SequenceI[] sqs = (SequenceI[]) input
+ .getAlignmentAndHiddenColumns(gc)[0];
if (this.msaIndex >= sqs.length)
{
throw new Error(
- "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
+ MessageManager
+ .getString("error.implementation_error_invalid_msa_index_for_job"));
}
// ///
// Uses RemoveGapsCommand
// ///
- new jalview.commands.RemoveGapsCommand("Remove Gaps",
- new SequenceI[]
- { sqs[msaIndex] }, currentView);
+ new jalview.commands.RemoveGapsCommand(
+ MessageManager.getString("label.remove_gaps"),
+ new SequenceI[] { sqs[msaIndex] }, currentView);
SequenceI profileseq = al.getSequenceAt(FirstSeq);
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
@@ -184,11 +215,20 @@ class JPredThread extends JWS1Thread implements WSClientI
al.getSequenceAt(FirstSeq), SequenceInfo))
{
throw (new Exception(
- "Couldn't recover sequence properties for JNet Query sequence!"));
+ MessageManager
+ .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
}
else
{
- al.setDataset(null);
+ if (currentView.getDataset() != null)
+ {
+ al.setDataset(currentView.getDataset());
+
+ }
+ else
+ {
+ al.setDataset(null);
+ }
jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
FirstSeq, true, predMap);
SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
@@ -197,13 +237,54 @@ class JPredThread extends JWS1Thread implements WSClientI
{
// Adjust input view for gaps
// propagate insertions into profile
- alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+ alhidden = HiddenColumns.propagateInsertions(profileseq, al,
input);
}
}
}
- return new Object[]
- { al, alcsel }; // , FirstSeq, noMsa};
+ // transfer to dataset
+ for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
+ {
+ if (alant.sequenceRef != null)
+ {
+ replaceAnnotationOnAlignmentWith(alant, alant.label,
+ "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
+ alant.sequenceRef);
+ }
+ }
+ return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
+ }
+
+ /**
+ * copied from JabawsCalcWorker
+ *
+ * @param newAnnot
+ * @param typeName
+ * @param calcId
+ * @param aSeq
+ */
+ protected void replaceAnnotationOnAlignmentWith(
+ AlignmentAnnotation newAnnot, String typeName, String calcId,
+ SequenceI aSeq)
+ {
+ SequenceI dsseq = aSeq.getDatasetSequence();
+ while (dsseq.getDatasetSequence() != null)
+ {
+ dsseq = dsseq.getDatasetSequence();
+ }
+ // look for same annotation on dataset and lift this one over
+ List dsan = dsseq.getAlignmentAnnotations(
+ calcId, typeName);
+ if (dsan != null && dsan.size() > 0)
+ {
+ for (AlignmentAnnotation dssan : dsan)
+ {
+ dsseq.removeAlignmentAnnotation(dssan);
+ }
+ }
+ AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+ dsseq.addAlignmentAnnotation(dssan);
+ dssan.adjustForAlignment();
}
/**
@@ -214,7 +295,7 @@ class JPredThread extends JWS1Thread implements WSClientI
* @param al
* @param profileseq
*/
- private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+ private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
{
char gc = al.getGapCharacter();
int[] gapMap = profileseq.gapMap();
@@ -283,8 +364,8 @@ class JPredThread extends JWS1Thread implements WSClientI
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));
}
}
}
@@ -320,8 +401,7 @@ class JPredThread extends JWS1Thread implements WSClientI
if (job.hasValidInput())
{
OutputHeader = wsInfo.getProgressText();
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
job.setJobnum(0);
}
else
@@ -339,8 +419,7 @@ class JPredThread extends JWS1Thread implements WSClientI
JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
if (job.hasValidInput())
{
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
OutputHeader = wsInfo.getProgressText();
job.setJobnum(0);
}
@@ -350,13 +429,14 @@ class JPredThread extends JWS1Thread implements WSClientI
}
}
+ @Override
public void StartJob(AWsJob j)
{
if (!(j instanceof JPredJob))
{
- throw new Error(
- "Implementation error - StartJob(JpredJob) called on "
- + j.getClass());
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_startjob_called",
+ new String[] { j.getClass().toString() }));
}
try
{
@@ -375,9 +455,11 @@ class JPredThread extends JWS1Thread implements WSClientI
{
if (job.getJobId().startsWith("Broken"))
{
- job.result = (vamsas.objects.simple.Result) new JpredResult();
+ job.result = new JpredResult();
job.result.setInvalid(true);
- job.result.setStatus("Submission " + job.getJobId());
+ job.result.setStatus(MessageManager.formatMessage(
+ "label.submission_params", new String[] { job.getJobId()
+ .toString() }));
throw new Exception(job.getJobId());
}
else
@@ -389,7 +471,9 @@ class JPredThread extends JWS1Thread implements WSClientI
}
else
{
- throw new Exception("Server timed out - try again later\n");
+ throw new Exception(
+ MessageManager
+ .getString("exception.server_timeout_try_later"));
}
} catch (Exception e)
{
@@ -413,9 +497,11 @@ class JPredThread extends JWS1Thread implements WSClientI
{
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
// JBPNote - this could be a popup informing the user of the problem.
- wsInfo.appendProgressText(j.getJobnum(),
- "Failed to submit the prediction:\n" + e.getMessage()
- + wsInfo.getProgressText());
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .formatMessage(
+ "info.failed_to_submit_prediction",
+ new String[] { e.getMessage(),
+ wsInfo.getProgressText() }));
jalview.bin.Cache.log.debug(
"Failed Submission of job " + j.getJobnum(), e);
@@ -426,6 +512,7 @@ class JPredThread extends JWS1Thread implements WSClientI
}
}
+ @Override
public void parseResult()
{
int results = 0; // number of result sets received
@@ -453,6 +540,7 @@ class JPredThread extends JWS1Thread implements WSClientI
wsInfo.showResultsNewFrame
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(true);
@@ -461,6 +549,7 @@ class JPredThread extends JWS1Thread implements WSClientI
wsInfo.mergeResults
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(false);
@@ -506,7 +595,8 @@ class JPredThread extends JWS1Thread implements WSClientI
{
// do merge with other job results
throw new Error(
- "Multiple JNet subjob merging not yet implemented.");
+ MessageManager
+ .getString("error.multiple_jnet_subjob_merge_not_implemented"));
}
} catch (Exception e)
{
@@ -514,9 +604,10 @@ class JPredThread extends JWS1Thread implements WSClientI
"JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(j.getJobnum(), OutputHeader + "\n"
- + j.result.getStatus()
- + "\nInvalid JNet job result data!\n" + e.getMessage());
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager
+ .formatMessage("info.invalid_jnet_job_result_data",
+ new String[] { OutputHeader.toString(),
+ j.result.getStatus(), e.getMessage() }));
j.result.setBroken(true);
}
}
@@ -527,12 +618,14 @@ class JPredThread extends JWS1Thread implements WSClientI
if (newWindow)
{
AlignFrame af;
+ ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0])
+ .getSequenceAt(0));
if (input == null)
{
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
@@ -558,7 +651,8 @@ class JPredThread extends JWS1Thread implements WSClientI
*/
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,
@@ -572,21 +666,25 @@ class JPredThread extends JWS1Thread implements WSClientI
}
}
+ @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("Implementation error!");
+ throw new Error(MessageManager.getString("error.implementation_error"));
}
+ @Override
public boolean canMergeResults()
{
return false;