-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws;\r
-\r
-import java.util.*;\r
-\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 vamsas.objects.simple.JpredResult;\r
-\r
-class JPredThread extends JWS1Thread implements WSClientI\r
-{\r
- // TODO: put mapping between JPredJob input and input data here -\r
- // JNetAnnotation adding is done after result parsing.\r
- class JPredJob extends WSJob\r
- {\r
- // TODO: make JPredJob deal only with what was sent to and received from a\r
- // JNet service\r
- int[] predMap = null; // mapping from sequence(i) to the original\r
-\r
- // sequence(predMap[i]) being predicted on\r
-\r
- vamsas.objects.simple.Sequence sequence;\r
-\r
- vamsas.objects.simple.Msfalignment msa;\r
-\r
- java.util.Hashtable SequenceInfo = null;\r
-\r
- int msaIndex = 0; // the position of the original sequence in the array of\r
-\r
- // Sequences in the input object that this job holds a\r
- // prediction for\r
-\r
- /**\r
- * \r
- * @return true if getResultSet will return a valid alignment and prediction\r
- * 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
- public 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,\r
- * ColumnSelection for this prediction} or null if no results\r
- * available.\r
- * @throws Exception\r
- */\r
- public Object[] getResultSet() 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",\r
- // "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result\r
- .getPredfile(), "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\r
- // sequence\r
- String format = new jalview.io.IdentifyFile().Identify(result\r
- .getAligfile(), "Paste");\r
-\r
- if (jalview.io.FormatAdapter.isValidFormat(format))\r
- {\r
- SequenceI sqs[];\r
- if (predMap != null)\r
- {\r
- Object[] alandcolsel = input\r
- .getAlignmentAndColumnSelection(getGapChar());\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(\r
- (Hashtable) 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, false, predMap);\r
-\r
- }\r
- else\r
- {\r
- throw (new Exception("Unknown format " + format\r
- + " for file : \n" + result.getAligfile()));\r
- }\r
- }\r
- else\r
- {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
- if (predMap != null)\r
- {\r
- char gc = getGapChar();\r
- SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input\r
- .getAlignmentAndColumnSelection(gc))[0];\r
- if (this.msaIndex >= sqs.length)\r
- {\r
- throw new Error(\r
- "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] }, currentView);\r
-\r
- SequenceI profileseq = al.getSequenceAt(FirstSeq);\r
- profileseq.setSequence(sqs[msaIndex].getSequenceAsString());\r
- }\r
-\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al\r
- .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, 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
- { al, alcsel }; // , FirstSeq, noMsa};\r
- }\r
-\r
- /**\r
- * Given an alignment where all other sequences except profileseq are\r
- * aligned to the ungapped profileseq, insert gaps in the other sequences to\r
- * realign them with the residues in profileseq\r
- * \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() : sb\r
- .substring(0, diff));\r
- }\r
- al.getSequenceAt(s).setSequence(sq);\r
- }\r
- else\r
- {\r
- al.getSequenceAt(s).setSequence(\r
- sq.substring(0, gapMap[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\r
- * AlignmentView\r
- * \r
- * @param profileseq\r
- * @param al\r
- * @param input\r
- */\r
- private ColumnSelection propagateInsertions(SequenceI profileseq,\r
- Alignment al, 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\r
- .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])\r
- .gapMap())); // recover original prediction sequence's\r
- // 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[])\r
- // 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() : sb\r
- .substring(0, diff));\r
- }\r
- }\r
- sq += sb.toString();\r
- }\r
- else\r
- {\r
- al.getSequenceAt(s).setSequence(\r
- sq.substring(0, spos + offset) + 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\r
- .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\r
- .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
-\r
- String altitle = "";\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle,\r
- ext.vamsas.Jpred server, String wsurl, AlignmentView alview,\r
- AlignFrame alframe)\r
- {\r
- super(alframe, wsinfo, alview, wsurl);\r
- this.altitle = altitle;\r
- this.server = server;\r
- }\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle,\r
- ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,\r
- SequenceI seq, int[] delMap, AlignmentView alview,\r
- 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
- { job };\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle,\r
- ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,\r
- int[] delMap, AlignmentView alview, AlignFrame alframe,\r
- 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
- { job };\r
- OutputHeader = wsInfo.getProgressText();\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- public void StartJob(AWsJob j)\r
- {\r
- if (!(j instanceof JPredJob))\r
- {\r
- throw new Error(\r
- "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 if (job.sequence != null)\r
- {\r
- job.jobId = server.predict(job.sequence); // debug like : job.jobId =\r
- // "/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
- throw new Exception(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
- } catch (Exception e)\r
- {\r
- // kill the whole job.\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- if (e.getMessage().indexOf("Exception") > -1)\r
- {\r
- wsInfo\r
- .setStatus(j.jobnum,\r
- WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo\r
- .setProgressText(\r
- j.jobnum,\r
- "Failed to submit the prediction. (Just close the window)\n"\r
- + "It is most likely that there is a problem with the server.\n");\r
- System.err\r
- .println("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" + e.getMessage()\r
- + wsInfo.getProgressText());\r
-\r
- jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum,\r
- e);\r
-\r
- }\r
- j.allowedServerExceptions = -1;\r
- j.subjobComplete = true;\r
- }\r
- }\r
-\r
- public 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\r
- && jobs[j].hasResults())\r
- {\r
- results++;\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(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(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\r
- // 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
- } catch (Exception e)\r
- {\r
- jalview.bin.Cache.log.error(\r
- "JNet Client: JPred Annotation Parse Error", e);\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- wsInfo.appendProgressText(j.jobnum, OutputHeader + "\n"\r
- + j.result.getStatus()\r
- + "\nInvalid JNet job result data!\n" + 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],\r
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- else\r
- {\r
- af = new AlignFrame((Alignment) res[0],\r
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- }\r
- else\r
- {\r
- /*\r
- * java.lang.Object[] alandcolsel =\r
- * input.getAlignmentAndColumnSelection\r
- * (alignFrame.getViewport().getGapCharacter()); if\r
- * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
- * if (msa) { throw new Error("Implementation Error! ColumnSelection\r
- * from input alignment will not map to result alignment!"); } } if\r
- * (!msa) { // update hidden regions to account for loss of gaps in\r
- * profile. - if any // gapMap returns insert list, interpreted as\r
- * delete list by pruneDeletions //((ColumnSelection)\r
- * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])\r
- * alandcolsel[0])[0].gapMap())); }\r
- */\r
-\r
- af = new AlignFrame((Alignment) res[0],\r
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- }\r
- Desktop.addInternalFrame(af, altitle, 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
- public void pollJob(AWsJob job) throws Exception\r
- {\r
- ((JPredJob)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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+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.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import vamsas.objects.simple.JpredResult;
+
+class JPredThread extends JWS1Thread implements WSClientI
+{
+ // TODO: put mapping between JPredJob input and input data here -
+ // JNetAnnotation adding is done after result parsing.
+ class JPredJob extends WSJob
+ {
+ // TODO: make JPredJob deal only with what was sent to and received from a
+ // JNet service
+ int[] predMap = null; // mapping from sequence(i) to the original
+
+ // sequence(predMap[i]) being predicted on
+
+ vamsas.objects.simple.Sequence sequence;
+
+ vamsas.objects.simple.Msfalignment msa;
+
+ java.util.Hashtable SequenceInfo = null;
+
+ 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
+
+ /**
+ *
+ * @return true if getResultSet will return a valid alignment and prediction
+ * result.
+ */
+ public boolean hasResults()
+ {
+ if (subjobComplete && result != null && result.isFinished()
+ && ((JpredResult) result).getPredfile() != null
+ && ((JpredResult) result).getAligfile() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ public boolean hasValidInput()
+ {
+ if (sequence != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ *
+ * @return null or Object[] { annotated alignment for this prediction,
+ * ColumnSelection for this prediction} or null if no results
+ * available.
+ * @throws Exception
+ */
+ public Object[] getResultSet() throws Exception
+ {
+ if (result == null || !result.isFinished())
+ {
+ return null;
+ }
+ Alignment al = null;
+ ColumnSelection alcsel = 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.");
+ // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
+ // "File");
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result
+ .getPredfile(), "Paste");
+ SequenceI[] preds = prediction.getSeqsAsArray();
+ jalview.bin.Cache.log.debug("Got prediction profile.");
+
+ if ((this.msa != null) && (result.getAligfile() != null))
+ {
+ jalview.bin.Cache.log.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");
+
+ if (jalview.io.FormatAdapter.isValidFormat(format))
+ {
+ SequenceI sqs[];
+ if (predMap != null)
+ {
+ Object[] alandcolsel = input
+ .getAlignmentAndColumnSelection(getGapChar());
+ sqs = (SequenceI[]) alandcolsel[0];
+ al = new Alignment(sqs);
+ alcsel = (ColumnSelection) alandcolsel[1];
+ }
+ else
+ {
+ al = new FormatAdapter().readFile(result.getAligfile(),
+ "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(
+ (Hashtable) SequenceInfo, sqs))
+ {
+ throw (new Exception(
+ "Couldn't recover sequence properties for alignment."));
+ }
+ }
+ FirstSeq = 0;
+ 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()));
+ }
+ }
+ else
+ {
+ al = new Alignment(preds);
+ FirstSeq = prediction.getQuerySeqPosition();
+ if (predMap != null)
+ {
+ char gc = getGapChar();
+ SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input
+ .getAlignmentAndColumnSelection(gc))[0];
+ if (this.msaIndex >= sqs.length)
+ {
+ throw new Error(
+ "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
+ }
+
+ // ///
+ // Uses RemoveGapsCommand
+ // ///
+ new jalview.commands.RemoveGapsCommand("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(
+ "Couldn't recover sequence properties for JNet Query sequence!"));
+ }
+ else
+ {
+ al.setDataset(null);
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
+ FirstSeq, true, predMap);
+ SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
+ alignToProfileSeq(al, profileseq);
+ if (predMap != null)
+ {
+ // Adjust input view for gaps
+ // propagate insertions into profile
+ alcsel = propagateInsertions(profileseq, al, input);
+ }
+ }
+ }
+ return new Object[]
+ { al, alcsel }; // , FirstSeq, noMsa};
+ }
+
+ /**
+ * 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
+ *
+ * @param al
+ * @param profileseq
+ */
+ private void alignToProfileSeq(Alignment al, SequenceI profileseq)
+ {
+ char gc = al.getGapCharacter();
+ int[] gapMap = profileseq.gapMap();
+ // insert gaps into profile
+ for (int lp = 0, r = 0; r < gapMap.length; r++)
+ {
+ if (gapMap[r] - lp > 1)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 1, ns = al.getHeight(); s < ns; s++)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ int diff = gapMap[r] - sq.length();
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = gapMap[r] - sq.length()) > 0)
+ {
+ 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]));
+ }
+ }
+ }
+ lp = gapMap[r];
+ }
+ }
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * @param al
+ * @param input
+ */
+ private ColumnSelection propagateInsertions(SequenceI profileseq,
+ Alignment al, AlignmentView input)
+ {
+ char gc = al.getGapCharacter();
+ Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+ ColumnSelection nview = (ColumnSelection) alandcolsel[1];
+ SequenceI origseq;
+ nview.pruneDeletions(ShiftList
+ .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])
+ .gapMap())); // recover original prediction sequence's
+ // mapping to view.
+ int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());
+ int spos = 0;
+ int offset = 0;
+ // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+ // alandcolsel[0])[0].gapMap()))
+ // add profile to visible contigs
+ for (int v = 0; v < viscontigs.length; v += 2)
+ {
+ if (viscontigs[v] > spos)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= spos + offset)
+ {
+ // pad sequence
+ int diff = spos + offset - sq.length() - 1;
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = spos + offset - sq.length() - 1) > 0)
+ {
+ sq = sq
+ + ((diff >= sb.length()) ? sb.toString() : sb
+ .substring(0, diff));
+ }
+ }
+ sq += sb.toString();
+ }
+ else
+ {
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, spos + offset) + sb.toString()
+ + sq.substring(spos + offset));
+ }
+ }
+ }
+ // offset+=sb.length();
+ }
+ spos = viscontigs[v + 1] + 1;
+ }
+ if ((offset + spos) < profileseq.getLength())
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 1, ns = al.getHeight(); s < ns; s++)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ // pad sequence
+ int diff = origseq.getLength() - sq.length();
+ while (diff > 0)
+ {
+ sq = sq
+ + ((diff >= sb.length()) ? sb.toString() : sb
+ .substring(0, diff));
+ diff = origseq.getLength() - sq.length();
+ }
+ }
+ }
+ return nview;
+ }
+
+ public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
+ {
+ super();
+ this.predMap = delMap;
+ String sq = AlignSeq.extractGaps(Comparison.GapChars, seq
+ .getSequenceAsString());
+ if (sq.length() >= 20)
+ {
+ this.SequenceInfo = SequenceInfo;
+ sequence = new vamsas.objects.simple.Sequence();
+ sequence.setId(seq.getName());
+ sequence.setSeq(sq);
+ }
+ }
+
+ public JPredJob(Hashtable 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));
+ }
+ }
+ }
+ }
+
+ ext.vamsas.Jpred server;
+
+ String altitle = "";
+
+ JPredThread(WebserviceInfo wsinfo, String altitle,
+ ext.vamsas.Jpred server, String wsurl, AlignmentView alview,
+ AlignFrame alframe)
+ {
+ super(alframe, wsinfo, alview, wsurl);
+ this.altitle = altitle;
+ this.server = server;
+ }
+
+ JPredThread(WebserviceInfo wsinfo, String altitle,
+ ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
+ SequenceI seq, int[] delMap, AlignmentView alview,
+ AlignFrame alframe)
+ {
+ this(wsinfo, altitle, server, wsurl, alview, alframe);
+ JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
+ if (job.hasValidInput())
+ {
+ OutputHeader = wsInfo.getProgressText();
+ jobs = new WSJob[]
+ { job };
+ job.setJobnum(0);
+ }
+ }
+
+ JPredThread(WebserviceInfo wsinfo, String altitle,
+ ext.vamsas.Jpred server, Hashtable 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);
+ if (job.hasValidInput())
+ {
+ jobs = new WSJob[]
+ { job };
+ OutputHeader = wsInfo.getProgressText();
+ job.setJobnum(0);
+ }
+ }
+
+ public void StartJob(AWsJob j)
+ {
+ if (!(j instanceof JPredJob))
+ {
+ throw new Error(
+ "Implementation error - StartJob(JpredJob) called on "
+ + j.getClass());
+ }
+ try
+ {
+ JPredJob job = (JPredJob) j;
+ if (job.msa != null)
+ {
+ job.setJobId(server.predictOnMsa(job.msa));
+ }
+ else if (job.sequence != null)
+ {
+ job.setJobId(server.predict(job.sequence)); // debug like : job.jobId =
+ // "/jobs/www-jpred/jp_Yatat29";//
+ }
+
+ if (job.getJobId() != null)
+ {
+ if (job.getJobId().startsWith("Broken"))
+ {
+ job.result = (vamsas.objects.simple.Result) new JpredResult();
+ job.result.setInvalid(true);
+ job.result.setStatus("Submission " + job.getJobId());
+ throw new Exception(job.getJobId());
+ }
+ else
+ {
+ job.setSubmitted(true);
+ job.setSubjobComplete(false);
+ Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+ }
+ }
+ else
+ {
+ throw new Exception("Server timed out - try again later\n");
+ }
+ } catch (Exception e)
+ {
+ // kill the whole job.
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ if (e.getMessage().indexOf("Exception") > -1)
+ {
+ wsInfo
+ .setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ 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"
+ + e.getMessage() + "\n");
+
+ jalview.bin.Cache.log.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(),
+ "Failed to submit the prediction:\n" + e.getMessage()
+ + wsInfo.getProgressText());
+
+ jalview.bin.Cache.log.debug("Failed Submission of job " + j.getJobnum(),
+ e);
+
+ }
+ j.setAllowedServerExceptions(-1);
+ j.setSubjobComplete(true);
+ }
+ }
+
+ public void parseResult()
+ {
+ int results = 0; // number of result sets received
+ JobStateSummary finalState = new JobStateSummary();
+ try
+ {
+ for (int j = 0; j < jobs.length; j++)
+ {
+ finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+ if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete()
+ && jobs[j].hasResults())
+ {
+ results++;
+ }
+ }
+ } catch (Exception ex)
+ {
+
+ Cache.log.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()
+ {
+ public void actionPerformed(java.awt.event.ActionEvent evt)
+ {
+ displayResults(true);
+ }
+ });
+ wsInfo.mergeResults
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(java.awt.event.ActionEvent evt)
+ {
+ displayResults(false);
+ }
+ });
+ wsInfo.setResultsReady();
+ }
+ else
+ {
+ wsInfo.setFinishedNoResults();
+ }
+ }
+
+ void displayResults(boolean newWindow)
+ {
+ // TODO: cope with multiple subjobs.
+ if (jobs != null)
+ {
+ Object[] res = null;
+ boolean msa = false;
+ for (int jn = 0; jn < jobs.length; jn++)
+ {
+ Object[] jobres = null;
+ JPredJob j = (JPredJob) jobs[jn];
+
+ if (j.hasResults())
+ {
+ // hack - we only deal with all single seuqence predictions or all
+ // profile predictions
+ msa = (j.msa != null) ? true : msa;
+ try
+ {
+ jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ jobres = j.getResultSet();
+ jalview.bin.Cache.log.debug("Finished parsing output.");
+ if (jobs.length == 1)
+ {
+ res = jobres;
+ }
+ else
+ {
+ // do merge with other job results
+ throw new Error(
+ "Multiple JNet subjob merging not yet implemented.");
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.error(
+ "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());
+ j.result.setBroken(true);
+ }
+ }
+ }
+
+ if (res != null)
+ {
+ if (newWindow)
+ {
+ AlignFrame af;
+ if (input == null)
+ {
+ if (res[1] != null)
+ {
+ af = new AlignFrame((Alignment) res[0],
+ (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ else
+ {
+ af = new AlignFrame((Alignment) res[0],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+ else
+ {
+ /*
+ * java.lang.Object[] alandcolsel =
+ * input.getAlignmentAndColumnSelection
+ * (alignFrame.getViewport().getGapCharacter()); if
+ * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
+ * if (msa) { throw new Error("Implementation Error! ColumnSelection
+ * from input alignment will not map to result alignment!"); } } if
+ * (!msa) { // update hidden regions to account for loss of gaps in
+ * profile. - if any // gapMap returns insert list, interpreted as
+ * delete list by pruneDeletions //((ColumnSelection)
+ * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])
+ * alandcolsel[0])[0].gapMap())); }
+ */
+
+ af = new AlignFrame((Alignment) res[0],
+ (ColumnSelection) 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.");
+ }
+ }
+ }
+ }
+
+ public void pollJob(AWsJob job) throws Exception
+ {
+ ((JPredJob)job).result = server.getresult(job.getJobId());
+ }
+
+ public boolean isCancellable()
+ {
+ return false;
+ }
+
+ public void cancelJob()
+ {
+ throw new Error("Implementation error!");
+ }
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff