--- /dev/null
+package jalview.ws;\r
+\r
+import java.util.*;\r
+\r
+import javax.swing.*;\r
+\r
+import vamsas.objects.simple.JpredResult;\r
+\r
+import ext.vamsas.*;\r
+import jalview.analysis.*;\r
+import jalview.bin.*;\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
+import jalview.io.*;\r
+import jalview.util.*;\r
+import jalview.ws.WSThread.*;\r
+\r
+class JPredThread\r
+extends WSThread\r
+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
+ * @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
+ Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
+ sqs = (SequenceI[]) alandcolsel[0];\r
+ al = new Alignment(sqs);\r
+ alcsel=(ColumnSelection) alandcolsel[1];\r
+ } else {\r
+ al = new Alignment(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, 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
+ char gc = alignFrame.getViewport().getGapCharacter();\r
+ SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input.getAlignmentAndColumnSelection(gc))[0];\r
+ if (this.msaIndex>=sqs.length)\r
+ throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");\r
+ sqs[msaIndex].removeGaps();\r
+ SequenceI profileseq=al.getSequenceAt(FirstSeq);\r
+ profileseq.setSequence(sqs[msaIndex].getSequence());\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
+ } else {\r
+ al.setDataset(null);\r
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,\r
+ true, predMap);\r
+ SequenceI profileseq=al.getSequenceAt(0); // this includes any gaps.\r
+ alignToProfileSeq(al, profileseq);\r
+ if (predMap!=null) {\r
+ // Adjust input view for gaps\r
+ // propagate insertions into profile\r
+ alcsel=propagateInsertions(profileseq, al, input);\r
+ }\r
+ }\r
+ }\r
+ return new Object[] { al, alcsel}; // , FirstSeq, noMsa};\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
+ 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
+ if (gapMap[r]-lp>1) {\r
+ StringBuffer sb=new StringBuffer();\r
+ for (int s=0, ns=gapMap[r]-lp; s<ns; s++) {\r
+ sb.append(gc);\r
+ }\r
+ for (int s=1,ns=al.getHeight(); s<ns; s++) {\r
+ String sq = al.getSequenceAt(s).getSequence();\r
+ int diff=gapMap[r]-sq.length();\r
+ if (diff>0) {\r
+ // pad gaps\r
+ sq=sq+sb;\r
+ while ((diff=gapMap[r]-sq.length())>0) {\r
+ sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));\r
+ }\r
+ al.getSequenceAt(s).setSequence(sq);\r
+ } else {\r
+ al.getSequenceAt(s).setSequence(sq.substring(0,gapMap[r])+sb.toString()+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, Alignment al, AlignmentView input) {\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[]) 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
+ if (viscontigs[v]>spos) {\r
+ StringBuffer sb=new StringBuffer();\r
+ for (int s=0, ns=viscontigs[v]-spos; s<ns; s++) {\r
+ sb.append(gc);\r
+ }\r
+ for (int s=0,ns=al.getHeight(); s<ns; s++) {\r
+ SequenceI sqobj = al.getSequenceAt(s);\r
+ if (sqobj!=profileseq) {\r
+ String sq = al.getSequenceAt(s).getSequence();\r
+ if (sq.length()<=spos+offset) {\r
+ // pad sequence\r
+ int diff=spos+offset-sq.length()-1;\r
+ if (diff>0) {\r
+ // pad gaps\r
+ sq=sq+sb;\r
+ while ((diff=spos+offset-sq.length()-1)>0) {\r
+ sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));\r
+ }\r
+ }\r
+ sq+=sb.toString();\r
+ } else {\r
+ al.getSequenceAt(s).setSequence(sq.substring(0,spos+offset)+sb.toString()+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
+ StringBuffer sb=new StringBuffer();\r
+ for (int s=0, ns=profileseq.getLength()-spos-offset; s<ns; s++) {\r
+ sb.append(gc);\r
+ }\r
+ for (int s=1,ns=al.getHeight(); s<ns; s++) {\r
+ String sq = al.getSequenceAt(s).getSequence();\r
+ // pad sequence\r
+ int diff=origseq.getLength()-sq.length();\r
+ while (diff>0) {\r
+ sq=sq+((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, seq.getSequence());\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
+ ext.vamsas.Jpred server;\r
+ String altitle = "";\r
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, String wsurl, AlignmentView alview, AlignFrame alframe) {\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
+\r
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,SequenceI seq, int[] delMap, 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, Hashtable SequenceInfo, SequenceI[] msf, int[] delMap, 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
+ 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
+ res = jobres;\r
+ else {\r
+ // do merge with other job results\r
+ throw new Error("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
+ if (res[1]!=null) {\r
+ af = new AlignFrame((Alignment)res[0], (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ } else {\r
+ af = new AlignFrame((Alignment)res[0], AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ }\r
+ } else {\r
+ /*java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
+\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],AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ }\r
+ Desktop.addInternalFrame(af, altitle,\r
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ Cache.log.info("Append results onto existing alignment.");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ void pollJob(WSJob job)\r
+ throws Exception\r
+ {\r
+ job.result = server.getresult(job.jobId);\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
+\r
+\r
git://source.jalview.org / jalview.git / blobdiff