--- /dev/null
+/*
+ * 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.NewickFile;
+import jalview.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import vamsas.objects.simple.MsaResult;
+import vamsas.objects.simple.SeqSearchResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ *
+ * <p>
+ * Description:
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+class SeqSearchWSThread extends JWS1Thread implements WSClientI
+{
+ String dbs = null;
+
+ boolean profile = false;
+
+ class SeqSearchWSJob extends WSJob
+ {
+ // hold special input for this
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
+
+ /**
+ * MsaWSJob
+ *
+ * @param jobNum
+ * int
+ * @param jobId
+ * String
+ */
+ public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
+ {
+ this.jobnum = jobNum;
+ if (!prepareInput(inSeqs, 2))
+ {
+ submitted = true;
+ subjobComplete = true;
+ result = new MsaResult();
+ result.setFinished(true);
+ result.setStatus("Job never ran - input returned to user.");
+ }
+
+ }
+
+ Hashtable SeqNames = new Hashtable();
+
+ Vector emptySeqs = new Vector();
+
+ /**
+ * prepare input sequences for service
+ *
+ * @param seqs
+ * jalview sequences to be prepared
+ * @param minlen
+ * minimum number of residues required for this MsaWS service
+ * @return true if seqs contains sequences to be submitted to service.
+ */
+ private boolean prepareInput(SequenceI[] seqs, int minlen)
+ {
+ int nseqs = 0;
+ if (minlen < 0)
+ {
+ throw new Error(
+ "Implementation error: minlen must be zero or more.");
+ }
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
+ nseqs++;
+ }
+ }
+ boolean valid = nseqs >= 1; // need at least one sequence for valid input
+ // TODO: generalise
+ vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+ : null;
+ boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted
+ // with gaps
+ for (int i = 0, n = 0; i < seqs.length; i++)
+ {
+
+ String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+ // for
+ // any
+ // subjob
+ SeqNames.put(newname, jalview.analysis.SeqsetUtils
+ .SeqCharacterHash(seqs[i]));
+ if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
+ seqarray[n] = new vamsas.objects.simple.Sequence();
+ seqarray[n].setId(newname);
+ seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ seqs[i].getSequenceAsString()));
+ }
+ else
+ {
+ String empty = null;
+ if (seqs[i].getEnd() >= seqs[i].getStart())
+ {
+ empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
+ .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
+ .getSequenceAsString());
+ }
+ emptySeqs.add(new String[]
+ { newname, empty });
+ }
+ }
+ if (submitGaps)
+ {
+ // almost certainly have to remove gapped columns here
+ }
+ this.seqs = new vamsas.objects.simple.SequenceSet();
+ this.seqs.setSeqs(seqarray);
+ return valid;
+ }
+
+ /**
+ *
+ * @return true if getAlignment will return a valid alignment result.
+ */
+ public boolean hasResults()
+ {
+ if (subjobComplete
+ && result != null
+ && result.isFinished()
+ && ((SeqSearchResult) result).getAlignment() != null
+ && ((SeqSearchResult) result).getAlignment().getSeqs() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * return sequence search results for display
+ *
+ * @return null or { Alignment(+features and annotation), NewickFile)}
+ */
+ public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+ {
+
+ if (result != null && result.isFinished())
+ {
+ SequenceI[] alseqs = null;
+ // char alseq_gapchar = '-';
+ // int alseq_l = 0;
+ if (((SeqSearchResult) result).getAlignment() != null)
+ {
+ alseqs = getVamsasAlignment(((SeqSearchResult) result)
+ .getAlignment());
+ // alseq_gapchar = ( (SeqSearchResult)
+ // result).getAlignment().getGapchar().charAt(0);
+ // alseq_l = alseqs.length;
+ }
+ /**
+ * what has to be done. 1 - annotate returned alignment with annotation
+ * file and sequence features file, and associate any tree-nodes. 2.
+ * connect alignment back to any associated dataset: 2.a. deuniquify
+ * recovers sequence information - but additionally, relocations must be
+ * made from the returned aligned sequence back to the dataset.
+ */
+ // construct annotated alignment as it would be done by the jalview
+ // applet
+ jalview.datamodel.Alignment al = new Alignment(alseqs);
+ // al.setDataset(dataset);
+ // make dataset
+ String inFile = null;
+ try
+ {
+ inFile = ((SeqSearchResult) result).getAnnotation();
+ if (inFile != null && inFile.length() > 0)
+ {
+ new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
+ jalview.io.AppletFormatAdapter.PASTE);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Failed to parse the annotation file associated with the alignment.");
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ e.printStackTrace(System.err);
+ }
+
+ try
+ {
+ inFile = ((SeqSearchResult) result).getFeatures();
+ if (inFile != null && inFile.length() > 0)
+ {
+ jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
+ inFile, jalview.io.AppletFormatAdapter.PASTE);
+ ff.parse(al, featureColours, false);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Failed to parse the Features file associated with the alignment.");
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ e.printStackTrace(System.err);
+ }
+ jalview.io.NewickFile nf = null;
+ try
+ {
+ inFile = ((SeqSearchResult) result).getNewickTree();
+ if (inFile != null && inFile.length() > 0)
+ {
+ nf = new jalview.io.NewickFile(inFile,
+ jalview.io.AppletFormatAdapter.PASTE);
+ if (!nf.isValid())
+ {
+ nf.close();
+ nf = null;
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Failed to parse the treeFile associated with the alignment.");
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+ e.printStackTrace(System.err);
+ }
+
+ /*
+ * TODO: housekeeping w.r.t. recovery of dataset and annotation
+ * references for input sequences, and then dataset sequence creation
+ * for new sequences retrieved from service // finally, attempt to
+ * de-uniquify to recover input sequence identity, and try to map back
+ * onto dataset Note: this
+ * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will
+ * NOT WORK - the returned alignment may contain multiple versions of
+ * the input sequence, each being a subsequence of the original.
+ * deuniquify also removes existing annotation and features added in the
+ * previous step... al.setDataset(dataset); // add in new sequences
+ * retrieved from sequence search which are not already in dataset. //
+ * trigger a 'fetchDBids' to annotate sequences with database ids...
+ */
+
+ return new Object[]
+ { al, nf };
+ }
+ return null;
+ }
+
+ /**
+ * mark subjob as cancelled and set result object appropriatly
+ */
+ void cancel()
+ {
+ cancelled = true;
+ subjobComplete = true;
+ result = null;
+ }
+
+ /**
+ *
+ * @return boolean true if job can be submitted.
+ */
+ public boolean hasValidInput()
+ {
+ if (seqs.getSeqs() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+ }
+
+ String alTitle; // name which will be used to form new alignment window.
+
+ Alignment dataset; // dataset to which the new alignment will be
+
+ // associated.
+
+ ext.vamsas.SeqSearchI server = null;
+
+ private String dbArg;
+
+ /**
+ * set basic options for this (group) of Msa jobs
+ *
+ * @param subgaps
+ * boolean
+ * @param presorder
+ * boolean
+ */
+ SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ AlignmentView alview, String wsname, String db)
+ {
+ super(alFrame, wsinfo, alview, wsname, wsUrl);
+ this.server = server;
+ this.dbArg = db;
+ }
+
+ /**
+ * create one or more Msa jobs to align visible seuqences in _msa
+ *
+ * @param title
+ * String
+ * @param _msa
+ * AlignmentView
+ * @param subgaps
+ * boolean
+ * @param presorder
+ * boolean
+ * @param seqset
+ * Alignment
+ */
+ SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ String wsname, String title, AlignmentView _msa, String db,
+ Alignment seqset)
+ {
+ this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
+ OutputHeader = wsInfo.getProgressText();
+ alTitle = title;
+ dataset = seqset;
+
+ SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+ if (conmsa != null)
+ {
+ int njobs = conmsa.length;
+ jobs = new SeqSearchWSJob[njobs];
+ for (int j = 0; j < njobs; j++)
+ {
+ if (j != 0)
+ {
+ jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
+ }
+ else
+ {
+ jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
+ }
+ if (njobs > 0)
+ {
+ wsinfo
+ .setProgressName("region " + jobs[j].getJobnum(),
+ jobs[j].getJobnum());
+ }
+ wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
+ }
+ }
+ }
+
+ public boolean isCancellable()
+ {
+ return true;
+ }
+
+ public void cancelJob()
+ {
+ if (!jobComplete && jobs != null)
+ {
+ boolean cancelled = true;
+ for (int job = 0; job < jobs.length; job++)
+ {
+ if (jobs[job].isSubmitted() && !jobs[job].isSubjobComplete())
+ {
+ String cancelledMessage = "";
+ try
+ {
+ vamsas.objects.simple.WsJobId cancelledJob = server
+ .cancel(jobs[job].getJobId());
+ if (cancelledJob.getStatus() == 2)
+ {
+ // CANCELLED_JOB
+ cancelledMessage = "Job cancelled.";
+ ((SeqSearchWSJob) jobs[job]).cancel();
+ wsInfo.setStatus(jobs[job].getJobnum(),
+ WebserviceInfo.STATE_CANCELLED_OK);
+ }
+ else if (cancelledJob.getStatus() == 3)
+ {
+ // VALID UNSTOPPABLE JOB
+ cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+ cancelled = false;
+ // wsInfo.setStatus(jobs[job].jobnum,
+ // WebserviceInfo.STATE_RUNNING);
+ }
+
+ if (cancelledJob.getJobId() != null)
+ {
+ cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+ }
+
+ cancelledMessage += "\n";
+ } catch (Exception exc)
+ {
+ cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ + exc + "\n");
+ Cache.log.warn(
+ "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+ }
+ wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ + cancelledMessage + "\n");
+ }
+ }
+ if (cancelled)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+ jobComplete = true;
+ }
+ this.interrupt(); // kick thread to update job states.
+ }
+ else
+ {
+ if (!jobComplete)
+ {
+ wsInfo
+ .setProgressText(OutputHeader
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+ }
+ }
+ }
+
+ public void pollJob(AWsJob job) throws Exception
+ {
+ ((SeqSearchWSJob) job).result = server
+ .getResult(((SeqSearchWSJob) job).getJobId());
+ }
+
+ public void StartJob(AWsJob job)
+ {
+ if (!(job instanceof SeqSearchWSJob))
+ {
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
+ + job.getClass());
+ }
+ SeqSearchWSJob j = (SeqSearchWSJob) job;
+ if (j.isSubmitted())
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Tried to submit an already submitted job "
+ + j.getJobId());
+ }
+ return;
+ }
+ if (j.seqs.getSeqs() == null)
+ {
+ // special case - selection consisted entirely of empty sequences...
+ j.setSubmitted(true);
+ j.result = new MsaResult();
+ j.result.setFinished(true);
+ j.result.setStatus("Empty Alignment Job");
+ ((MsaResult) j.result).setMsa(null);
+ }
+ try
+ {
+ vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs
+ .getSeqs()[0], dbArg);
+
+ if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
+ {
+ j.setJobId(jobsubmit.getJobId());
+ j.setSubmitted(true);
+ j.setSubjobComplete(false);
+ // System.out.println(WsURL + " Job Id '" + jobId + "'");
+ }
+ else
+ {
+ if (jobsubmit == null)
+ {
+ throw new Exception(
+ "Server at "
+ + WsUrl
+ + " returned null object, it probably cannot be contacted. Try again later ?");
+ }
+
+ throw new Exception(jobsubmit.getJobId());
+ }
+ } catch (Exception e)
+ {
+ // TODO: JBPNote catch timeout or other fault types explicitly
+ // 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"
+ + e.toString() + "\n");
+ j.setAllowedServerExceptions(0);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo
+ .appendProgressText(
+ j.getJobnum(),
+ "Failed to submit sequences for alignment.\n"
+ + "It is most likely that there is a problem with the server.\n"
+ + "Just close the window\n");
+
+ // e.printStackTrace(); // TODO: JBPNote DEBUG
+ }
+ }
+
+ private jalview.datamodel.Sequence[] getVamsasAlignment(
+ vamsas.objects.simple.Alignment valign)
+ {
+ vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+ jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+
+ for (int i = 0, j = seqs.length; i < j; i++)
+ {
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
+ .getSeq());
+ }
+
+ return msa;
+ }
+
+ 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++;
+ vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob)jobs[j]).result)
+ .getAlignment();
+ if (valign != null)
+ {
+ wsInfo.appendProgressText(jobs[j].getJobnum(),
+ "\nAlignment Object Method Notes\n");
+ String[] lines = valign.getMethod();
+ for (int line = 0; line < lines.length; line++)
+ {
+ wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n");
+ }
+ // JBPNote The returned files from a webservice could be
+ // hidden behind icons in the monitor window that,
+ // when clicked, pop up their corresponding data
+ }
+ }
+ }
+ } 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 newFrame)
+ {
+ if (!newFrame)
+ {
+ System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+ return;
+ }
+ // each subjob is an independent alignment for the moment
+ // Alignment al[] = new Alignment[jobs.length];
+ // NewickFile nf[] = new NewickFile[jobs.length];
+ for (int j = 0; j < jobs.length; j++)
+ {
+ Hashtable featureColours = new Hashtable();
+ Alignment al = null;
+ NewickFile nf = null;
+ if (jobs[j].hasResults())
+ {
+ Object[] res = ((SeqSearchWSJob) jobs[j]).getAlignment(dataset,
+ featureColours);
+ if (res == null)
+ {
+ continue;
+ }
+ ;
+ al = (Alignment) res[0];
+ nf = (NewickFile) res[1];
+ }
+ else
+ {
+ al = null;
+ nf = null;
+ continue;
+ }
+ /*
+ * We can't map new alignment back with insertions from input's hidden
+ * regions until dataset mapping is sorted out... but basically it goes
+ * like this: 1. Merge each domain hit back onto the visible segments in
+ * the same way as a Jnet prediction is mapped back
+ *
+ * Object[] newview = input.getUpdatedView(results, orders, getGapChar());
+ * // trash references to original result data for (int j = 0; j <
+ * jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]
+ * alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =
+ * (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);
+ *
+ * if (dataset != null) { al.setDataset(dataset); }
+ *
+ * propagateDatasetMappings(al); }
+ */
+
+ AlignFrame af = new AlignFrame(al,// columnselection,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ if (nf != null)
+ {
+ af.ShowNewickTree(nf, "Tree from " + this.alTitle);
+ }
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff