X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=dc245ae6c7559fa0d0f11ca1cbc94ac08ebdcbb7;hb=5c3e1272c6bf1e145a65050c0cc73737eee788b5;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..dc245ae 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -1,19 +1,22 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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;
@@ -137,21 +140,26 @@ class JPredThread extends JWS1Thread implements WSClientI
if (!jalview.analysis.SeqsetUtils.deuniquify(
(Hashtable) 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());
+ }
+ else
+ {
+ al.setDataset(null);
+ }
jalview.io.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[]{format,result.getAligfile()})));
}
}
else
@@ -165,14 +173,13 @@ class JPredThread extends JWS1Thread implements WSClientI
.getAlignmentAndColumnSelection(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);
@@ -183,12 +190,19 @@ class JPredThread extends JWS1Thread implements WSClientI
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.
@@ -202,11 +216,52 @@ class JPredThread extends JWS1Thread implements WSClientI
}
}
}
+ // transfer to dataset
+ for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
+ {
+ if (alant.sequenceRef != null)
+ {
+ replaceAnnotationOnAlignmentWith(alant, alant.label,
+ "jalview.jws1.Jpred", alant.sequenceRef);
+ }
+ }
return new Object[]
{ al, alcsel }; // , 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();
+ }
+
+ /**
* Given an alignment where all other sequences except profileseq are
* aligned to the ungapped profileseq, insert gaps in the other sequences to
* realign them with the residues in profileseq
@@ -354,9 +409,7 @@ class JPredThread extends JWS1Thread implements WSClientI
{
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
{
@@ -377,7 +430,7 @@ class JPredThread extends JWS1Thread implements WSClientI
{
job.result = (vamsas.objects.simple.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 +442,7 @@ 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 +466,7 @@ 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);
@@ -505,8 +556,7 @@ class JPredThread extends JWS1Thread implements WSClientI
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)
{
@@ -514,9 +564,7 @@ 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);
}
}
@@ -584,7 +632,7 @@ class JPredThread extends JWS1Thread implements WSClientI
public void cancelJob()
{
- throw new Error("Implementation error!");
+ throw new Error(MessageManager.getString("error.implementation_error"));
}
public boolean canMergeResults()