-package jalview.ws;\r
-\r
-import java.util.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.datamodel.Alignment;\r
-import jalview.gui.*;\r
-import jalview.io.*;\r
-import jalview.util.*;\r
-import vamsas.objects.simple.JpredResult;\r
-\r
-class JPredThread\r
- extends WSThread implements WSClientI\r
-{\r
- // TODO: put mapping between JPredJob input and input data here - JNetAnnotation adding is done after result parsing.\r
- class JPredJob\r
- extends WSThread.WSJob\r
- {\r
- // TODO: make JPredJob deal only with what was sent to and received from a JNet service\r
- int[] predMap = null; // mapping from sequence(i) to the original sequence(predMap[i]) being predicted on\r
- vamsas.objects.simple.Sequence sequence;\r
- vamsas.objects.simple.Msfalignment msa;\r
- java.util.Hashtable SequenceInfo = null;\r
- int msaIndex = 0; // the position of the original sequence in the array of Sequences in the input object that this job holds a prediction for\r
- /**\r
- *\r
- * @return true if getResultSet will return a valid alignment and prediction result.\r
- */\r
- public boolean hasResults()\r
- {\r
- if (subjobComplete && result != null && result.isFinished()\r
- && ( (JpredResult) result).getPredfile() != null &&\r
- ( (JpredResult) result).getAligfile() != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- boolean hasValidInput()\r
- {\r
- if (sequence != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- /**\r
- *\r
- * @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.\r
- * @throws Exception\r
- */\r
- public Object[] getResultSet()\r
- throws Exception\r
- {\r
- if (result == null || !result.isFinished())\r
- {\r
- return null;\r
- }\r
- Alignment al = null;\r
- ColumnSelection alcsel = null;\r
- int FirstSeq = -1; // the position of the query sequence in Alignment al\r
-\r
- JpredResult result = (JpredResult)this.result;\r
-\r
- jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
- getPredfile(),\r
- "Paste");\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- jalview.bin.Cache.log.debug("Got prediction profile.");\r
-\r
- if ( (this.msa != null) && (result.getAligfile() != null))\r
- {\r
- jalview.bin.Cache.log.debug("Getting associated alignment.");\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = new jalview.io.IdentifyFile().Identify(result.\r
- getAligfile(),\r
- "Paste");\r
-\r
- if (jalview.io.FormatAdapter.isValidFormat(format))\r
- {\r
- SequenceI sqs[];\r
- if (predMap != null)\r
- {\r
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(\r
- alignFrame.getViewport().getGapCharacter());\r
- sqs = (SequenceI[]) alandcolsel[0];\r
- al = new Alignment(sqs);\r
- alcsel = (ColumnSelection) alandcolsel[1];\r
- }\r
- else\r
- {\r
- al = new FormatAdapter().readFile(result.getAligfile(),\r
- "Paste", format);\r
- sqs = new SequenceI[al.getHeight()];\r
-\r
- for (int i = 0, j = al.getHeight(); i < j; i++)\r
- {\r
- sqs[i] = al.getSequenceAt(i);\r
- }\r
- if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)\r
- SequenceInfo, sqs))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for alignment."));\r
- }\r
- }\r
- FirstSeq = 0;\r
- al.setDataset(null);\r
-\r
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,\r
- FirstSeq,\r
- false, predMap);\r
-\r
- }\r
- else\r
- {\r
- throw (new Exception(\r
- "Unknown format " + format + " for file : \n" +\r
- result.getAligfile()));\r
- }\r
- }\r
- else\r
- {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
- if (predMap != null)\r
- {\r
- char gc = alignFrame.getViewport().getGapCharacter();\r
- SequenceI[] sqs = (SequenceI[]) ( (java.lang.Object[]) input.\r
- getAlignmentAndColumnSelection(gc))[\r
- 0];\r
- if (this.msaIndex >= sqs.length)\r
- {\r
- throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");\r
- }\r
-\r
- /////\r
- //Uses RemoveGapsCommand\r
- /////\r
- new jalview.commands.RemoveGapsCommand("Remove Gaps",\r
- new SequenceI[]\r
- {sqs[msaIndex]},\r
- alignFrame.getCurrentView().\r
- getAlignment());\r
-\r
- SequenceI profileseq = al.getSequenceAt(FirstSeq);\r
- profileseq.setSequence(sqs[msaIndex].getSequenceAsString());\r
- }\r
-\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
- al.getSequenceAt(FirstSeq), SequenceInfo))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
- }\r
- else\r
- {\r
- al.setDataset(null);\r
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,\r
- FirstSeq,\r
- true, predMap);\r
- SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.\r
- alignToProfileSeq(al, profileseq);\r
- if (predMap != null)\r
- {\r
- // Adjust input view for gaps\r
- // propagate insertions into profile\r
- alcsel = propagateInsertions(profileseq, al, input);\r
- }\r
- }\r
- }\r
- return new Object[]\r
- {\r
- al, alcsel}; // , FirstSeq, noMsa};\r
- }\r
-\r
- /**\r
- * 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\r
- * @param al\r
- * @param profileseq\r
- */\r
- private void alignToProfileSeq(Alignment al, SequenceI profileseq)\r
- {\r
- char gc = al.getGapCharacter();\r
- int[] gapMap = profileseq.gapMap();\r
- // insert gaps into profile\r
- for (int lp = 0, r = 0; r < gapMap.length; r++)\r
- {\r
- if (gapMap[r] - lp > 1)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 1, ns = al.getHeight(); s < ns; s++)\r
- {\r
- String sq = al.getSequenceAt(s).getSequenceAsString();\r
- int diff = gapMap[r] - sq.length();\r
- if (diff > 0)\r
- {\r
- // pad gaps\r
- sq = sq + sb;\r
- while ( (diff = gapMap[r] - sq.length()) > 0)\r
- {\r
- sq = sq +\r
- ( (diff >= sb.length()) ? sb.toString() :\r
- sb.substring(0, diff));\r
- }\r
- al.getSequenceAt(s).setSequence(sq);\r
- }\r
- else\r
- {\r
- al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r]) +\r
- sb.toString() +\r
- sq.substring(gapMap[r]));\r
- }\r
- }\r
- }\r
- lp = gapMap[r];\r
- }\r
- }\r
-\r
- /**\r
- * Add gaps into the sequences aligned to profileseq under the given AlignmentView\r
- * @param profileseq\r
- * @param al\r
- * @param input\r
- */\r
- private ColumnSelection propagateInsertions(SequenceI profileseq,\r
- Alignment al,\r
- AlignmentView input)\r
- {\r
- char gc = al.getGapCharacter();\r
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);\r
- ColumnSelection nview = (ColumnSelection) alandcolsel[1];\r
- SequenceI origseq;\r
- nview.pruneDeletions(ShiftList.parseMap( (origseq = ( (SequenceI[])\r
- alandcolsel[0])[0]).gapMap())); // recover original prediction sequence's mapping to view.\r
- int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());\r
- int spos = 0;\r
- int offset = 0;\r
- // input.pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()))\r
- // add profile to visible contigs\r
- for (int v = 0; v < viscontigs.length; v += 2)\r
- {\r
- if (viscontigs[v] > spos)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 0, ns = al.getHeight(); s < ns; s++)\r
- {\r
- SequenceI sqobj = al.getSequenceAt(s);\r
- if (sqobj != profileseq)\r
- {\r
- String sq = al.getSequenceAt(s).getSequenceAsString();\r
- if (sq.length() <= spos + offset)\r
- {\r
- // pad sequence\r
- int diff = spos + offset - sq.length() - 1;\r
- if (diff > 0)\r
- {\r
- // pad gaps\r
- sq = sq + sb;\r
- while ( (diff = spos + offset - sq.length() - 1) > 0)\r
- {\r
- sq = sq +\r
- ( (diff >= sb.length()) ? sb.toString() :\r
- sb.substring(0, diff));\r
- }\r
- }\r
- sq += sb.toString();\r
- }\r
- else\r
- {\r
- al.getSequenceAt(s).setSequence(sq.substring(0, spos + offset) +\r
- sb.toString() +\r
- sq.substring(spos + offset));\r
- }\r
- }\r
- }\r
- //offset+=sb.length();\r
- }\r
- spos = viscontigs[v + 1] + 1;\r
- }\r
- if ( (offset + spos) < profileseq.getLength())\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 1, ns = al.getHeight(); s < ns; s++)\r
- {\r
- String sq = al.getSequenceAt(s).getSequenceAsString();\r
- // pad sequence\r
- int diff = origseq.getLength() - sq.length();\r
- while (diff > 0)\r
- {\r
- sq = sq +\r
- ( (diff >= sb.length()) ? sb.toString() : sb.substring(0, diff));\r
- diff = origseq.getLength() - sq.length();\r
- }\r
- }\r
- }\r
- return nview;\r
- }\r
-\r
- public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)\r
- {\r
- super();\r
- this.predMap = delMap;\r
- String sq = AlignSeq.extractGaps(Comparison.GapChars,\r
- seq.getSequenceAsString());\r
- if (sq.length() >= 20)\r
- {\r
- this.SequenceInfo = SequenceInfo;\r
- sequence = new vamsas.objects.simple.Sequence();\r
- sequence.setId(seq.getName());\r
- sequence.setSeq(sq);\r
- }\r
- }\r
-\r
- public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)\r
- {\r
- this(SequenceInfo, msf[0], delMap);\r
- if (sequence != null)\r
- {\r
- if (msf.length > 1)\r
- {\r
- msa = new vamsas.objects.simple.Msfalignment();\r
- jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();\r
- msa.setMsf(pileup.print(msf));\r
- }\r
- }\r
- }\r
- }\r
-\r
- ext.vamsas.Jpred server;\r
- String altitle = "";\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,\r
- String wsurl, AlignmentView alview, AlignFrame alframe)\r
- {\r
- super();\r
- this.altitle = altitle;\r
- this.server = server;\r
- this.wsInfo = wsinfo;\r
- this.input = alview;\r
- this.alignFrame = alframe;\r
- WsUrl = wsurl;\r
- }\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,\r
- String wsurl, Hashtable SequenceInfo, SequenceI seq, int[] delMap,\r
- AlignmentView alview, AlignFrame alframe)\r
- {\r
- this(wsinfo, altitle, server, wsurl, alview, alframe);\r
- JPredJob job = new JPredJob(SequenceInfo, seq, delMap);\r
- if (job.hasValidInput())\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- jobs = new WSJob[]\r
- {\r
- job};\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,\r
- Hashtable SequenceInfo, SequenceI[] msf, int[] delMap,\r
- AlignmentView alview, AlignFrame alframe, String wsurl)\r
- {\r
- this(wsinfo, altitle, server, wsurl, alview, alframe);\r
- JPredJob job = new JPredJob(SequenceInfo, msf, delMap);\r
- if (job.hasValidInput())\r
- {\r
- jobs = new WSJob[]\r
- {\r
- job};\r
- OutputHeader = wsInfo.getProgressText();\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- void StartJob(WSJob j)\r
- {\r
- if (! (j instanceof JPredJob))\r
- {\r
- throw new Error("Implementation error - StartJob(JpredJob) called on " +\r
- j.getClass());\r
- }\r
- try\r
- {\r
- JPredJob job = (JPredJob) j;\r
- if (job.msa != null)\r
- {\r
- job.jobId = server.predictOnMsa(job.msa);\r
- }\r
- else\r
- if (job.sequence != null)\r
- {\r
- job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//\r
- }\r
-\r
- if (job.jobId != null)\r
- {\r
- if (job.jobId.startsWith("Broken"))\r
- {\r
- job.result = (vamsas.objects.simple.Result)new JpredResult();\r
- job.result.setInvalid(true);\r
- job.result.setStatus("Submission " + job.jobId);\r
- }\r
- else\r
- {\r
- job.submitted = true;\r
- job.subjobComplete = false;\r
- Cache.log.info(WsUrl + " Job Id '" + job.jobId + "'");\r
- }\r
- }\r
- else\r
- {\r
- throw new Exception("Server timed out - try again later\n");\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- if (e.getMessage().indexOf("Exception") > -1)\r
- {\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo.setProgressText(j.jobnum,\r
- "Failed to submit the prediction. (Just close the window)\n"\r
- +\r
- "It is most likely that there is a problem with the server.\n");\r
- System.err.println(\r
- "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +\r
- e.getMessage() + "\n");\r
-\r
- jalview.bin.Cache.log.warn("Server Exception", e);\r
- }\r
- else\r
- {\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- // JBPNote - this could be a popup informing the user of the problem.\r
- wsInfo.appendProgressText(j.jobnum,\r
- "Failed to submit the prediction:\n"\r
- + e.getMessage() +\r
- wsInfo.getProgressText());\r
-\r
- jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);\r
-\r
- }\r
- j.allowedServerExceptions = -1;\r
- j.subjobComplete = true;\r
- }\r
- }\r
-\r
- void parseResult()\r
- {\r
- int results = 0; // number of result sets received\r
- JobStateSummary finalState = new JobStateSummary();\r
- try\r
- {\r
- for (int j = 0; j < jobs.length; j++)\r
- {\r
- finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);\r
- if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())\r
- {\r
- results++;\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
-\r
- Cache.log.error("Unexpected exception when processing results for " +\r
- altitle, ex);\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
- if (results > 0)\r
- {\r
- wsInfo.showResultsNewFrame\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(\r
- java.awt.event.ActionEvent evt)\r
- {\r
- displayResults(true);\r
- }\r
- });\r
- wsInfo.mergeResults\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(\r
- java.awt.event.ActionEvent evt)\r
- {\r
- displayResults(false);\r
- }\r
- });\r
- wsInfo.setResultsReady();\r
- }\r
- else\r
- {\r
- wsInfo.setFinishedNoResults();\r
- }\r
- }\r
-\r
- void displayResults(boolean newWindow)\r
- {\r
- // TODO: cope with multiple subjobs.\r
- if (jobs != null)\r
- {\r
- Object[] res = null;\r
- boolean msa = false;\r
- for (int jn = 0; jn < jobs.length; jn++)\r
- {\r
- Object[] jobres = null;\r
- JPredJob j = (JPredJob) jobs[jn];\r
-\r
- if (j.hasResults())\r
- {\r
- // hack - we only deal with all single seuqence predictions or all profile predictions\r
- msa = (j.msa != null) ? true : msa;\r
- try\r
- {\r
- jalview.bin.Cache.log.debug("Parsing output of job " + jn);\r
- jobres = j.getResultSet();\r
- jalview.bin.Cache.log.debug("Finished parsing output.");\r
- if (jobs.length == 1)\r
- {\r
- res = jobres;\r
- }\r
- else\r
- {\r
- // do merge with other job results\r
- throw new Error(\r
- "Multiple JNet subjob merging not yet implemented.");\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- jalview.bin.Cache.log.error(\r
- "JNet Client: JPred Annotation Parse Error",\r
- e);\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- wsInfo.appendProgressText(j.jobnum,\r
- OutputHeader + "\n" +\r
- j.result.getStatus() +\r
- "\nInvalid JNet job result data!\n" +\r
- e.getMessage());\r
- j.result.setBroken(true);\r
- }\r
- }\r
- }\r
-\r
- if (res != null)\r
- {\r
- if (newWindow)\r
- {\r
- AlignFrame af;\r
- if (input == null)\r
- {\r
- if (res[1] != null)\r
- {\r
- af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- else\r
- {\r
- af = new AlignFrame( (Alignment) res[0], AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- }\r
- else\r
- {\r
- /*java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
- if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
- if (msa) {\r
- throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");\r
- }\r
- }\r
- if (!msa) {\r
- // update hidden regions to account for loss of gaps in profile. - if any\r
- // gapMap returns insert list, interpreted as delete list by pruneDeletions\r
- //((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));\r
- }*/\r
-\r
- af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- Desktop.addInternalFrame(af, altitle,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- else\r
- {\r
- Cache.log.info("Append results onto existing alignment.");\r
- }\r
- }\r
- }\r
- }\r
-\r
- void pollJob(WSJob job)\r
- throws Exception\r
- {\r
- job.result = server.getresult(job.jobId);\r
- }\r
-\r
- public boolean isCancellable()\r
- {\r
- return false;\r
- }\r
-\r
- public void cancelJob()\r
- {\r
- throw new Error("Implementation error!");\r
- }\r
-\r
- public boolean canMergeResults()\r
- {\r
- return false;\r
- }\r
-\r
-}\r
+package jalview.ws;
+
+import static java.lang.String.format;
+
+import java.util.Hashtable;
+import java.util.List;
+
+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.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.util.MessageManager;
+import jalview.ws.api.CancellableI;
+import jalview.ws.api.JPredMutlipleAlignmentServiceI;
+import jalview.ws.gui.WsJob;
+import jalview.ws.gui.WsJob.JobState;
+
+
+class JPredJob extends WsJob
+{
+ Hashtable<?, ?> sequenceInfo;
+ List<SequenceI> msf;
+ int[] delMap;
+ AlignmentI alignment = null;
+ HiddenColumns hiddenCols = null;
+
+ public JPredJob(Hashtable<?, ?> sequenceInfo, SequenceI[] msf, int[] delMap)
+ {
+ this.sequenceInfo = sequenceInfo;
+ this.msf = List.of(msf);
+ this.delMap = delMap;
+ }
+
+ @Override
+ public boolean hasValidInput()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean hasResults()
+ {
+ return (isSubjobComplete() && alignment != null);
+ }
+}
+
+
+public class JPredThread extends AWSThread implements WSClientI
+{
+
+ private JPredMutlipleAlignmentServiceI server;
+ private String title;
+ private Hashtable<?, ?> sequenceInfo;
+ private SequenceI[] msf;
+ private int[] delMap;
+
+ public JPredThread(WebserviceInfo wsInfo, String title,
+ JPredMutlipleAlignmentServiceI server, Hashtable<?, ?> sequenceInfo,
+ SequenceI[] msf, int[] delMap, AlignmentView view, AlignFrame frame,
+ String wsURL)
+ {
+ super(frame, wsInfo, view, wsURL);
+ this.server = server;
+ this.title = title;
+ this.sequenceInfo = sequenceInfo;
+ this.msf = msf;
+ this.delMap = delMap;
+ JPredJob job = new JPredJob(sequenceInfo, msf, delMap);
+ this.jobs = new JPredJob[] { job };
+ }
+
+ @Override
+ public boolean isCancellable()
+ {
+ return server instanceof CancellableI;
+ }
+
+ @Override
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+
+ @Override
+ public void cancelJob()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void pollJob(AWsJob job_) throws Exception
+ {
+ var job = (JPredJob) job_;
+ server.updateStatus(job);
+ server.updateJobProgress(job);
+ }
+
+ @Override
+ public void StartJob(AWsJob job_)
+ {
+ if (!(job_ instanceof JPredJob))
+ throw new RuntimeException("Invalid job type");
+ var job = (JPredJob) job_;
+ if (job.isSubmitted())
+ {
+ return;
+ }
+ try {
+ try
+ {
+ var jobHandle = server.align(job.msf);
+ if (jobHandle != null)
+ job.setJobHandle(jobHandle);
+ }
+ catch (Throwable th) {
+ if (!server.handleSubmitError(th, job, wsInfo)) {
+ throw th;
+ }
+ }
+ if (job.getJobId() != null) {
+ job.setSubmitted(true);
+ job.setSubjobComplete(false);
+ return;
+ }
+ else {
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[]
+ { WsUrl }));
+ }
+ }
+ catch (Throwable th)
+ {
+ // For unexpected errors
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
+ th.printStackTrace(System.err);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(job.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+
+ }
+ finally
+ {
+ if (!job.isSubmitted())
+ {
+ job.setAllowedServerExceptions(0);
+ wsInfo.appendProgressText(job.getJobnum(), MessageManager.getString(
+ "info.failed_to_submit_sequences_for_alignment"));
+ }
+ }
+ }
+
+ @Override
+ public void parseResult()
+ {
+ long progbar = (long) (Math.random() * ~(1L << 63));
+ wsInfo.setProgressBar(
+ MessageManager.getString("status.collecting_job_results"), progbar);
+ int results = 0;
+ var finalState = new JobStateSummary();
+ try
+ {
+ for (int i = 0; i < jobs.length; i++) {
+ final var job = (JPredJob) jobs[i];
+ finalState.updateJobPanelState(wsInfo, OutputHeader, job);
+ if (job.isFinished()) {
+ try {
+ server.updateJobProgress(job);
+ }
+ catch (Exception e) {
+ Cache.log.warn(format(
+ "Exception when retrieving remaining Job progress data " +
+ "for job %s on server %s", job.getJobId(), WsUrl));
+ e.printStackTrace();
+ }
+ // removed the waiting loop
+ Cache.log.debug(format("Job Execution file for job: %s " +
+ "on server %s%n%s", job.getJobId(), WsUrl, job.getStatus()));
+ try {
+ prepareJobResult(job);
+ }
+ catch (Exception e) {
+ if (!server.handleCollectionException(e, job, wsInfo)) {
+ Cache.log.error("Could not get alignment for job.", e);
+ job.setState(JobState.SERVERERROR);
+ }
+ }
+ }
+ finalState.updateJobPanelState(wsInfo, OutputHeader, job);
+ if (job.isSubmitted() && job.isSubjobComplete() && job.hasResults()) {
+ results++;
+ }
+ }
+ }
+ catch (Exception e) {
+ Cache.log.error(
+ "Unexpected exception when processing results for " + title, e);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ if (results > 0) {
+ wsInfo.showResultsNewFrame.addActionListener(
+ (evt) -> displayResults(true));
+ wsInfo.mergeResults.addActionListener(
+ (evt) -> displayResults(false));
+ wsInfo.setResultsReady();
+ }
+ else {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.appendInfoText("No jobs ran.");
+ wsInfo.setFinishedNoResults();
+ }
+ updateGlobalStatus(finalState);
+ wsInfo.removeProgressBar(progbar);
+ }
+
+ private void prepareJobResult(JPredJob job) throws Exception
+ {
+ HiddenColumns hiddenCols = null;
+ int firstSeq = -1;
+ AlignmentI alignment;
+ var prediction = server.getPrediction(job.getJobHandle());
+ var preds = prediction.getSeqsAsArray();
+
+ if (job.delMap != null)
+ {
+ Object[] alandcolsel = input
+ .getAlignmentAndHiddenColumns(getGapChar());
+ alignment = new Alignment((SequenceI[]) alandcolsel[0]);
+ hiddenCols = (HiddenColumns) alandcolsel[1];
+ }
+ else
+ {
+ alignment = server.getAlignment(job.getJobHandle());
+ var seqs = new SequenceI[alignment.getHeight()];
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ seqs[i] = alignment.getSequenceAt(i);
+ }
+ if (!SeqsetUtils.deuniquify(sequenceInfo, seqs))
+ {
+ throw (new Exception(MessageManager.getString(
+ "exception.couldnt_recover_sequence_properties_for_alignment")));
+ }
+ }
+ firstSeq = 0;
+ if (currentView.getDataset() != null)
+ {
+ alignment.setDataset(currentView.getDataset());
+ }
+ else
+ {
+ alignment.setDataset(null);
+ }
+ JnetAnnotationMaker.add_annotation(prediction, alignment, firstSeq, false,
+ job.delMap);
+
+ for (var annot : alignment.getAlignmentAnnotation())
+ {
+ if (annot.sequenceRef != null)
+ {
+ replaceAnnotationOnAlignmentWith(annot, annot.label,
+ "jalview.ws.JPred", annot.sequenceRef);
+ }
+ }
+ job.alignment = alignment;
+ job.hiddenCols = hiddenCols;
+ }
+
+ private static 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();
+ }
+
+ private void displayResults(boolean newWindow)
+ {
+ if (jobs == null || jobs.length == 0)
+ {
+ return;
+ }
+ var job = (JPredJob) jobs[0];
+ if (job.hasResults() && newWindow)
+ {
+ AlignFrame frame;
+ job.alignment.setSeqrep(job.alignment.getSequenceAt(0));
+ frame = new AlignFrame(job.alignment, job.hiddenCols,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(frame, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff