X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;fp=src%2Fjalview%2Fws%2FJPredThread.java;h=a0036fe2a164b2af437833c848ecad5b2ec5c15b;hb=add30afdc46a14e61ccf55881fa91b9ca9abfe80;hp=3589c165b48f1a8bb8d06b3adea3ef06d9db05cb;hpb=9b2272a1679b87760b193ecc87f994d7f5141c75;p=jalview.git
diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
similarity index 92%
rename from src/jalview/ws/JPredThread.java
rename to src/jalview/ws/jws1/JPredThread.java
index 3589c16..a0036fe 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -1,664 +1,667 @@
-/*
- * 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 .
- */
-package jalview.ws;
-
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.util.*;
-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.jobnum = 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.jobnum = 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.jobId = server.predictOnMsa(job.msa);
- }
- else if (job.sequence != null)
- {
- job.jobId = server.predict(job.sequence); // debug like : job.jobId =
- // "/jobs/www-jpred/jp_Yatat29";//
- }
-
- if (job.jobId != null)
- {
- if (job.jobId.startsWith("Broken"))
- {
- job.result = (vamsas.objects.simple.Result) new JpredResult();
- job.result.setInvalid(true);
- job.result.setStatus("Submission " + job.jobId);
- throw new Exception(job.jobId);
- }
- else
- {
- job.submitted = true;
- job.subjobComplete = false;
- Cache.log.info(WsUrl + " Job Id '" + job.jobId + "'");
- }
- }
- 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.jobnum,
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo
- .setProgressText(
- j.jobnum,
- "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.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
- // JBPNote - this could be a popup informing the user of the problem.
- wsInfo.appendProgressText(j.jobnum,
- "Failed to submit the prediction:\n" + e.getMessage()
- + wsInfo.getProgressText());
-
- jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum,
- e);
-
- }
- j.allowedServerExceptions = -1;
- j.subjobComplete = 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].submitted && jobs[j].subjobComplete
- && 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.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(j.jobnum, 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.jobId);
- }
-
- public boolean isCancellable()
- {
- return false;
- }
-
- public void cancelJob()
- {
- throw new Error("Implementation error!");
- }
-
- public boolean canMergeResults()
- {
- return false;
- }
-
-}
+/*
+ * 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 .
+ */
+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;
+ }
+
+}