/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.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.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.io.FormatAdapter;
+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 null;
}
- Alignment al = null;
+ AlignmentI al = null;
ColumnSelection alcsel = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
{
sqs[i] = al.getSequenceAt(i);
}
- if (!jalview.analysis.SeqsetUtils.deuniquify(
- (Hashtable) SequenceInfo, sqs))
+ if (!jalview.analysis.SeqsetUtils.deuniquify(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;
}
else
{
- throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()})));
+ throw (new Exception(MessageManager.formatMessage(
+ "exception.unknown_format_for_file", new String[] {
+ format, result.getAligfile() })));
}
}
else
if (predMap != null)
{
char gc = getGapChar();
- SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input
- .getAlignmentAndColumnSelection(gc))[0];
+ SequenceI[] sqs = (SequenceI[]) input
+ .getAlignmentAndColumnSelection(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"));
}
// ///
// Uses RemoveGapsCommand
// ///
- new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.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());
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
al.getSequenceAt(FirstSeq), 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
{
if (alant.sequenceRef != null)
{
replaceAnnotationOnAlignmentWith(alant, alant.label,
- "jalview.jws1.Jpred", alant.sequenceRef);
+ "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
+ alant.sequenceRef);
}
}
- return new Object[]
- { al, alcsel }; // , FirstSeq, noMsa};
+ return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
}
/**
* @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();
if (job.hasValidInput())
{
OutputHeader = wsInfo.getProgressText();
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
job.setJobnum(0);
}
else
JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
if (job.hasValidInput())
{
- jobs = new WSJob[]
- { job };
+ jobs = new WSJob[] { job };
OutputHeader = wsInfo.getProgressText();
job.setJobnum(0);
}
{
if (!(j instanceof JPredJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()}));
+ 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(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
}
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_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);
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)
{
"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));
if (input == null)
{
if (res[1] != null)