/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.bin.Cache;
+import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
+import jalview.bin.Console;
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;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import vamsas.objects.simple.JpredResult;
vamsas.objects.simple.Msfalignment msa;
- java.util.Hashtable SequenceInfo = null;
+ Object SequenceInfo = null;
int msaIndex = 0; // the position of the original sequence in the array of
* @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.");
+ 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(SequenceInfo, sqs))
+ if (!SeqsetUtils.deuniquify((Map<String, SequenceInfo>)SequenceInfo, sqs))
{
- throw (new Exception(
- MessageManager
- .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
+ throw (new Exception(MessageManager.getString(
+ "exception.couldnt_recover_sequence_properties_for_alignment")));
}
}
FirstSeq = 0;
{
al.setDataset(null);
}
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
- FirstSeq, false, predMap);
+ 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(
- MessageManager
- .getString("error.implementation_error_invalid_msa_index_for_job"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_invalid_msa_index_for_job"));
}
// ///
// ///
new jalview.commands.RemoveGapsCommand(
MessageManager.getString("label.remove_gaps"),
- new SequenceI[] { sqs[msaIndex] }, currentView);
+ new SequenceI[]
+ { sqs[msaIndex] }, currentView);
SequenceI profileseq = al.getSequenceAt(FirstSeq);
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
}
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
- al.getSequenceAt(FirstSeq), SequenceInfo))
+ al.getSequenceAt(FirstSeq), (SequenceInfo)SequenceInfo))
{
- throw (new Exception(
- MessageManager
- .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
+ throw (new Exception(MessageManager.getString(
+ "exception.couldnt_recover_sequence_props_for_jnet_query")));
}
else
{
{
// Adjust input view for gaps
// propagate insertions into profile
- alcsel = ColumnSelection.propagateInsertions(profileseq, al,
- input);
+ alhidden = al.propagateInsertions(profileseq, input);
}
}
}
alant.sequenceRef);
}
}
- return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
+ return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
}
/**
dsseq = dsseq.getDatasetSequence();
}
// look for same annotation on dataset and lift this one over
- List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(
- calcId, typeName);
+ List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+ typeName);
if (dsan != null && dsan.size() > 0)
{
for (AlignmentAnnotation dssan : dsan)
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]));
}
}
}
}
}
- public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
+ public JPredJob(Object SequenceInfo, SequenceI seq, int[] delMap)
{
super();
this.predMap = delMap;
}
}
- public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
+ public JPredJob(Object SequenceInfo, SequenceI[] msf, int[] delMap)
{
this(SequenceInfo, msf[0], delMap);
if (sequence != null)
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));
}
}
}
}
JPredThread(WebserviceInfo wsinfo, String altitle,
- ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
+ ext.vamsas.Jpred server, String wsurl, SequenceInfo SequenceInfo,
SequenceI seq, int[] delMap, AlignmentView alview,
AlignFrame alframe)
{
}
JPredThread(WebserviceInfo wsinfo, String altitle,
- ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
- int[] delMap, AlignmentView alview, AlignFrame alframe,
- String wsurl)
+ ext.vamsas.Jpred server, Map<String, SequenceInfo> SequenceInfo,
+ SequenceI[] msf, int[] delMap, AlignmentView alview,
+ AlignFrame alframe, String wsurl)
{
this(wsinfo, altitle, server, wsurl, alview, alframe);
JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
}
}
+ @Override
public void StartJob(AWsJob j)
{
if (!(j instanceof JPredJob))
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_error_startjob_called",
- new String[] { j.getClass().toString() }));
+ "error.implementation_error_startjob_called", new String[]
+ { j.getClass().toString() }));
}
try
{
{
job.result = new JpredResult();
job.result.setInvalid(true);
- job.result.setStatus(MessageManager.formatMessage(
- "label.submission_params", new String[] { job.getJobId()
- .toString() }));
+ 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(
- MessageManager
- .getString("exception.server_timeout_try_later"));
+ throw new Exception(MessageManager
+ .getString("exception.server_timeout_try_later"));
}
} catch (Exception e)
{
{
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setProgressText(
- j.getJobnum(),
+ 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"
+ 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(), MessageManager
- .formatMessage(
- "info.failed_to_submit_prediction",
- new String[] { 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);
+ 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);
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(
- MessageManager
- .getString("error.multiple_jnet_subjob_merge_not_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);
+ 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() }));
+ 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));
+ ((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());
}
+ @Override
public boolean isCancellable()
{
return false;
}
+ @Override
public void cancelJob()
{
throw new Error(MessageManager.getString("error.implementation_error"));
}
+ @Override
public boolean canMergeResults()
{
return false;