/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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.Console;
+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
* @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;
}
- 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.");
+ Console.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.");
+ Console.debug("Got prediction profile.");
if ((this.msa != null) && (result.getAligfile() != null))
{
- jalview.bin.Cache.log.debug("Getting associated alignment.");
+ Console.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."));
+ throw (new Exception(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,
- FirstSeq, false, predMap);
+ }
+ 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
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!");
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_invalid_msa_index_for_job"));
}
// ///
// Uses RemoveGapsCommand
// ///
- new jalview.commands.RemoveGapsCommand("Remove Gaps",
+ new jalview.commands.RemoveGapsCommand(
+ MessageManager.getString("label.remove_gaps"),
new SequenceI[]
{ sqs[msaIndex] }, currentView);
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
}
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al
- .getSequenceAt(FirstSeq), SequenceInfo))
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+ al.getSequenceAt(FirstSeq), SequenceInfo))
{
- throw (new Exception(
- "Couldn't recover sequence properties for JNet Query sequence!"));
+ throw (new Exception(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.
{
// Adjust input view for gaps
// propagate insertions into profile
- alcsel = propagateInsertions(profileseq, al, input);
+ alhidden = al.propagateInsertions(profileseq, 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<AlignmentAnnotation> 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();
}
/**
* @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();
sq = sq + sb;
while ((diff = gapMap[r] - sq.length()) > 0)
{
- sq = sq
- + ((diff >= sb.length()) ? sb.toString() : sb
- .substring(0, diff));
+ sq = sq + ((diff >= sb.length()) ? sb.toString()
+ : sb.substring(0, diff));
}
al.getSequenceAt(s).setSequence(sq);
}
else
{
- al.getSequenceAt(s).setSequence(
- sq.substring(0, gapMap[r]) + sb.toString()
- + sq.substring(gapMap[r]));
+ al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r])
+ + sb.toString() + sq.substring(gapMap[r]));
}
}
}
}
}
- /**
- * Add gaps into the sequences aligned to profileseq under the given
- * AlignmentView
- *
- * @param profileseq
- * @param al
- * @param input
- */
- private ColumnSelection propagateInsertions(SequenceI profileseq,
- Alignment al, AlignmentView input)
- {
- char gc = al.getGapCharacter();
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
- ColumnSelection nview = (ColumnSelection) alandcolsel[1];
- SequenceI origseq;
- nview.pruneDeletions(ShiftList
- .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])
- .gapMap())); // recover original prediction sequence's
- // mapping to view.
- int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());
- int spos = 0;
- int offset = 0;
- // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
- // alandcolsel[0])[0].gapMap()))
- // add profile to visible contigs
- for (int v = 0; v < viscontigs.length; v += 2)
- {
- if (viscontigs[v] > spos)
- {
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
- {
- sb.append(gc);
- }
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
- {
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj != profileseq)
- {
- String sq = al.getSequenceAt(s).getSequenceAsString();
- if (sq.length() <= spos + offset)
- {
- // pad sequence
- int diff = spos + offset - sq.length() - 1;
- if (diff > 0)
- {
- // pad gaps
- sq = sq + sb;
- while ((diff = spos + offset - sq.length() - 1) > 0)
- {
- sq = sq
- + ((diff >= sb.length()) ? sb.toString() : sb
- .substring(0, diff));
- }
- }
- sq += sb.toString();
- }
- else
- {
- al.getSequenceAt(s).setSequence(
- sq.substring(0, spos + offset) + sb.toString()
- + sq.substring(spos + offset));
- }
- }
- }
- // offset+=sb.length();
- }
- spos = viscontigs[v + 1] + 1;
- }
- if ((offset + spos) < profileseq.getLength())
- {
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
- {
- sb.append(gc);
- }
- for (int s = 1, ns = al.getHeight(); s < ns; s++)
- {
- String sq = al.getSequenceAt(s).getSequenceAsString();
- // pad sequence
- int diff = origseq.getLength() - sq.length();
- while (diff > 0)
- {
- sq = sq
- + ((diff >= sb.length()) ? sb.toString() : sb
- .substring(0, diff));
- diff = origseq.getLength() - sq.length();
- }
- }
- }
- return nview;
- }
-
public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
{
super();
this.predMap = delMap;
- String sq = AlignSeq.extractGaps(Comparison.GapChars, seq
- .getSequenceAsString());
+ String sq = AlignSeq.extractGaps(Comparison.GapChars,
+ seq.getSequenceAsString());
if (sq.length() >= 20)
{
this.SequenceInfo = SequenceInfo;
sequence.setId(seq.getName());
sequence.setSeq(sq);
}
+ else
+ {
+ errorMessage = "Sequence is too short to predict with JPred - need at least 20 amino acids.";
+ }
}
public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
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));
}
}
}
+
+ String errorMessage = "";
+
+ public String getValidationMessages()
+ {
+ return errorMessage + "\n";
+ }
}
ext.vamsas.Jpred server;
if (job.hasValidInput())
{
OutputHeader = wsInfo.getProgressText();
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
job.setJobnum(0);
}
+ else
+ {
+ wsInfo.appendProgressText(job.getValidationMessages());
+ }
}
JPredThread(WebserviceInfo wsinfo, String altitle,
JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
if (job.hasValidInput())
{
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
OutputHeader = wsInfo.getProgressText();
job.setJobnum(0);
}
+ else
+ {
+ wsInfo.appendProgressText(job.getValidationMessages());
+ }
}
+ @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
{
{
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
{
job.setSubmitted(true);
job.setSubjobComplete(false);
- Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+ Console.info(WsUrl + " Job Id '" + job.getJobId() + "'");
}
}
else
{
- throw new Exception("Server timed out - try again later\n");
+ throw new Exception(MessageManager
+ .getString("exception.server_timeout_try_later"));
}
} catch (Exception e)
{
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
if (e.getMessage().indexOf("Exception") > -1)
{
- wsInfo
- .setStatus(j.getJobnum(),
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo
- .setProgressText(
- j.getJobnum(),
- "Failed to submit the prediction. (Just close the window)\n"
- + "It is most likely that there is a problem with the server.\n");
- System.err
- .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setProgressText(j.getJobnum(),
+ "Failed to submit the prediction. (Just close the window)\n"
+ + "It is most likely that there is a problem with the server.\n");
+ System.err.println(
+ "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+ e.getMessage() + "\n");
- jalview.bin.Cache.log.warn("Server Exception", e);
+ Console.warn("Server Exception", e);
}
else
{
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());
+ 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);
+ Console.debug("Failed Submission of job " + j.getJobnum(), e);
}
j.setAllowedServerExceptions(-1);
}
}
+ @Override
public void parseResult()
{
int results = 0; // number of result sets received
} catch (Exception ex)
{
- Cache.log.error("Unexpected exception when processing results for "
- + altitle, ex);
+ Console.error(
+ "Unexpected exception when processing results for " + altitle,
+ ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
if (results > 0)
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);
}
else
{
+ wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
+ wsInfo.appendInfoText("No jobs ran.");
wsInfo.setFinishedNoResults();
}
}
msa = (j.msa != null) ? true : msa;
try
{
- jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ Console.debug("Parsing output of job " + jn);
jobres = j.getResultSet();
- jalview.bin.Cache.log.debug("Finished parsing output.");
+ Console.debug("Finished parsing output.");
if (jobs.length == 1)
{
res = jobres;
else
{
// do merge with other job results
- throw new Error(
- "Multiple JNet subjob merging not yet implemented.");
+ throw new Error(MessageManager.getString(
+ "error.multiple_jnet_subjob_merge_not_implemented"));
}
} catch (Exception e)
{
- jalview.bin.Cache.log.error(
- "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());
+ Console.error("JNet Client: JPred Annotation Parse Error", e);
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_ERROR);
+ 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);
}
}
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
* alandcolsel[0])[0].gapMap())); }
*/
- af = new AlignFrame((Alignment) res[0],
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ af = new AlignFrame((Alignment) res[0], (HiddenColumns) res[1],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
else
{
- Cache.log.info("Append results onto existing alignment.");
+ Console.info("Append results onto existing alignment.");
}
}
}
}
+ @Override
public void pollJob(AWsJob job) throws Exception
{
- ((JPredJob)job).result = server.getresult(job.getJobId());
+ ((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;
git://source.jalview.org / jalview.git / blobdiff