-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.ws;
-
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.NewickFile;
-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 WSThread implements WSClientI
-{
- String dbs=null;
- boolean profile=false;
-
- class SeqSearchWSJob
- extends WSThread.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.
- */
- 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].jobnum, jobs[j].jobnum);
- }
- wsinfo.setProgressText(jobs[j].jobnum, 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].submitted && !jobs[job].subjobComplete)
- {
- String cancelledMessage = "";
- try
- {
- vamsas.objects.simple.WsJobId cancelledJob = server
- .cancel(jobs[job].jobId);
- if (cancelledJob.getStatus() == 2)
- {
- // CANCELLED_JOB
- cancelledMessage = "Job cancelled.";
- ( (SeqSearchWSJob) jobs[job]).cancel();
- wsInfo.setStatus(jobs[job].jobnum,
- 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].jobId,
- exc);
- }
- wsInfo.setProgressText(jobs[job].jobnum, 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");
- }
- }
- }
-
- void pollJob(WSJob job)
- throws Exception
- {
- ( (SeqSearchWSJob) job).result = server.getResult( ( (SeqSearchWSJob) job).jobId);
- }
-
- void StartJob(WSJob job)
- {
- if (! (job instanceof SeqSearchWSJob))
- {
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
- job.getClass());
- }
- SeqSearchWSJob j = (SeqSearchWSJob) job;
- if (j.submitted)
- {
- if (Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
- }
- return;
- }
- if (j.seqs.getSeqs() == null)
- {
- // special case - selection consisted entirely of empty sequences...
- j.submitted = 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.jobId = jobsubmit.getJobId();
- j.submitted = true;
- j.subjobComplete = 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.allowedServerExceptions = 0;
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo
- .appendProgressText(
- j.jobnum,
- "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;
- }
-
- 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++;
- vamsas.objects.simple.Alignment valign = ( (SeqSearchResult) jobs[j].result).
- getAlignment();
- if (valign != null)
- {
- wsInfo.appendProgressText(jobs[j].jobnum,
- "\nAlignment Object Method Notes\n");
- String[] lines = valign.getMethod();
- for (int line = 0; line < lines.length; line++)
- {
- wsInfo.appendProgressText(jobs[j].jobnum, 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;
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program 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 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\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.NewickFile;\r
+import vamsas.objects.simple.MsaResult;\r
+import vamsas.objects.simple.SeqSearchResult;\r
+\r
+/**\r
+ * <p>\r
+ * Title:\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Description:\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Copyright: Copyright (c) 2004\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Company: Dundee University\r
+ * </p>\r
+ * \r
+ * @author not attributable\r
+ * @version 1.0\r
+ */\r
+class SeqSearchWSThread extends WSThread implements WSClientI\r
+{\r
+ String dbs = null;\r
+\r
+ boolean profile = false;\r
+\r
+ class SeqSearchWSJob extends WSThread.WSJob\r
+ {\r
+ // hold special input for this\r
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
+\r
+ /**\r
+ * MsaWSJob\r
+ * \r
+ * @param jobNum\r
+ * int\r
+ * @param jobId\r
+ * String\r
+ */\r
+ public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)\r
+ {\r
+ this.jobnum = jobNum;\r
+ if (!prepareInput(inSeqs, 2))\r
+ {\r
+ submitted = true;\r
+ subjobComplete = true;\r
+ result = new MsaResult();\r
+ result.setFinished(true);\r
+ result.setStatus("Job never ran - input returned to user.");\r
+ }\r
+\r
+ }\r
+\r
+ Hashtable SeqNames = new Hashtable();\r
+\r
+ Vector emptySeqs = new Vector();\r
+\r
+ /**\r
+ * prepare input sequences for service\r
+ * \r
+ * @param seqs\r
+ * jalview sequences to be prepared\r
+ * @param minlen\r
+ * minimum number of residues required for this MsaWS service\r
+ * @return true if seqs contains sequences to be submitted to service.\r
+ */\r
+ private boolean prepareInput(SequenceI[] seqs, int minlen)\r
+ {\r
+ int nseqs = 0;\r
+ if (minlen < 0)\r
+ {\r
+ throw new Error(\r
+ "Implementation error: minlen must be zero or more.");\r
+ }\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
+ {\r
+ nseqs++;\r
+ }\r
+ }\r
+ boolean valid = nseqs >= 1; // need at least one sequence for valid input\r
+ // TODO: generalise\r
+ vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]\r
+ : null;\r
+ boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted\r
+ // with gaps\r
+ for (int i = 0, n = 0; i < seqs.length; i++)\r
+ {\r
+\r
+ String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same\r
+ // for\r
+ // any\r
+ // subjob\r
+ SeqNames.put(newname, jalview.analysis.SeqsetUtils\r
+ .SeqCharacterHash(seqs[i]));\r
+ if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
+ {\r
+ seqarray[n] = new vamsas.objects.simple.Sequence();\r
+ seqarray[n].setId(newname);\r
+ seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()\r
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,\r
+ seqs[i].getSequenceAsString()));\r
+ }\r
+ else\r
+ {\r
+ String empty = null;\r
+ if (seqs[i].getEnd() >= seqs[i].getStart())\r
+ {\r
+ empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq\r
+ .extractGaps(jalview.util.Comparison.GapChars, seqs[i]\r
+ .getSequenceAsString());\r
+ }\r
+ emptySeqs.add(new String[]\r
+ { newname, empty });\r
+ }\r
+ }\r
+ if (submitGaps)\r
+ {\r
+ // almost certainly have to remove gapped columns here\r
+ }\r
+ this.seqs = new vamsas.objects.simple.SequenceSet();\r
+ this.seqs.setSeqs(seqarray);\r
+ return valid;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return true if getAlignment will return a valid alignment result.\r
+ */\r
+ public boolean hasResults()\r
+ {\r
+ if (subjobComplete\r
+ && result != null\r
+ && result.isFinished()\r
+ && ((SeqSearchResult) result).getAlignment() != null\r
+ && ((SeqSearchResult) result).getAlignment().getSeqs() != null)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * return sequence search results for display\r
+ * \r
+ * @return null or { Alignment(+features and annotation), NewickFile)}\r
+ */\r
+ public Object[] getAlignment(Alignment dataset, Hashtable featureColours)\r
+ {\r
+\r
+ if (result != null && result.isFinished())\r
+ {\r
+ SequenceI[] alseqs = null;\r
+ // char alseq_gapchar = '-';\r
+ // int alseq_l = 0;\r
+ if (((SeqSearchResult) result).getAlignment() != null)\r
+ {\r
+ alseqs = getVamsasAlignment(((SeqSearchResult) result)\r
+ .getAlignment());\r
+ // alseq_gapchar = ( (SeqSearchResult)\r
+ // result).getAlignment().getGapchar().charAt(0);\r
+ // alseq_l = alseqs.length;\r
+ }\r
+ /**\r
+ * what has to be done. 1 - annotate returned alignment with annotation\r
+ * file and sequence features file, and associate any tree-nodes. 2.\r
+ * connect alignment back to any associated dataset: 2.a. deuniquify\r
+ * recovers sequence information - but additionally, relocations must be\r
+ * made from the returned aligned sequence back to the dataset.\r
+ */\r
+ // construct annotated alignment as it would be done by the jalview\r
+ // applet\r
+ jalview.datamodel.Alignment al = new Alignment(alseqs);\r
+ // al.setDataset(dataset);\r
+ // make dataset\r
+ String inFile = null;\r
+ try\r
+ {\r
+ inFile = ((SeqSearchResult) result).getAnnotation();\r
+ if (inFile != null && inFile.length() > 0)\r
+ {\r
+ new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,\r
+ jalview.io.AppletFormatAdapter.PASTE);\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Failed to parse the annotation file associated with the alignment.");\r
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");\r
+ e.printStackTrace(System.err);\r
+ }\r
+\r
+ try\r
+ {\r
+ inFile = ((SeqSearchResult) result).getFeatures();\r
+ if (inFile != null && inFile.length() > 0)\r
+ {\r
+ jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(\r
+ inFile, jalview.io.AppletFormatAdapter.PASTE);\r
+ ff.parse(al, featureColours, false);\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Failed to parse the Features file associated with the alignment.");\r
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");\r
+ e.printStackTrace(System.err);\r
+ }\r
+ jalview.io.NewickFile nf = null;\r
+ try\r
+ {\r
+ inFile = ((SeqSearchResult) result).getNewickTree();\r
+ if (inFile != null && inFile.length() > 0)\r
+ {\r
+ nf = new jalview.io.NewickFile(inFile,\r
+ jalview.io.AppletFormatAdapter.PASTE);\r
+ if (!nf.isValid())\r
+ {\r
+ nf.close();\r
+ nf = null;\r
+ }\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Failed to parse the treeFile associated with the alignment.");\r
+ System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");\r
+ e.printStackTrace(System.err);\r
+ }\r
+\r
+ /*\r
+ * TODO: housekeeping w.r.t. recovery of dataset and annotation\r
+ * references for input sequences, and then dataset sequence creation\r
+ * for new sequences retrieved from service // finally, attempt to\r
+ * de-uniquify to recover input sequence identity, and try to map back\r
+ * onto dataset Note: this\r
+ * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will\r
+ * NOT WORK - the returned alignment may contain multiple versions of\r
+ * the input sequence, each being a subsequence of the original.\r
+ * deuniquify also removes existing annotation and features added in the\r
+ * previous step... al.setDataset(dataset); // add in new sequences\r
+ * retrieved from sequence search which are not already in dataset. //\r
+ * trigger a 'fetchDBids' to annotate sequences with database ids...\r
+ */\r
+\r
+ return new Object[]\r
+ { al, nf };\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * mark subjob as cancelled and set result object appropriatly\r
+ */\r
+ void cancel()\r
+ {\r
+ cancelled = true;\r
+ subjobComplete = true;\r
+ result = null;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return boolean true if job can be submitted.\r
+ */\r
+ boolean hasValidInput()\r
+ {\r
+ if (seqs.getSeqs() != null)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+ }\r
+\r
+ String alTitle; // name which will be used to form new alignment window.\r
+\r
+ Alignment dataset; // dataset to which the new alignment will be\r
+\r
+ // associated.\r
+\r
+ ext.vamsas.SeqSearchI server = null;\r
+\r
+ private String dbArg;\r
+\r
+ /**\r
+ * set basic options for this (group) of Msa jobs\r
+ * \r
+ * @param subgaps\r
+ * boolean\r
+ * @param presorder\r
+ * boolean\r
+ */\r
+ SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
+ AlignmentView alview, String wsname, String db)\r
+ {\r
+ super(alFrame, wsinfo, alview, wsname, wsUrl);\r
+ this.server = server;\r
+ this.dbArg = db;\r
+ }\r
+\r
+ /**\r
+ * create one or more Msa jobs to align visible seuqences in _msa\r
+ * \r
+ * @param title\r
+ * String\r
+ * @param _msa\r
+ * AlignmentView\r
+ * @param subgaps\r
+ * boolean\r
+ * @param presorder\r
+ * boolean\r
+ * @param seqset\r
+ * Alignment\r
+ */\r
+ SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
+ String wsname, String title, AlignmentView _msa, String db,\r
+ Alignment seqset)\r
+ {\r
+ this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);\r
+ OutputHeader = wsInfo.getProgressText();\r
+ alTitle = title;\r
+ dataset = seqset;\r
+\r
+ SequenceI[][] conmsa = _msa.getVisibleContigs('-');\r
+ if (conmsa != null)\r
+ {\r
+ int njobs = conmsa.length;\r
+ jobs = new SeqSearchWSJob[njobs];\r
+ for (int j = 0; j < njobs; j++)\r
+ {\r
+ if (j != 0)\r
+ {\r
+ jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);\r
+ }\r
+ else\r
+ {\r
+ jobs[j] = new SeqSearchWSJob(0, conmsa[j]);\r
+ }\r
+ if (njobs > 0)\r
+ {\r
+ wsinfo\r
+ .setProgressName("region " + jobs[j].jobnum,\r
+ jobs[j].jobnum);\r
+ }\r
+ wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);\r
+ }\r
+ }\r
+ }\r
+\r
+ public boolean isCancellable()\r
+ {\r
+ return true;\r
+ }\r
+\r
+ public void cancelJob()\r
+ {\r
+ if (!jobComplete && jobs != null)\r
+ {\r
+ boolean cancelled = true;\r
+ for (int job = 0; job < jobs.length; job++)\r
+ {\r
+ if (jobs[job].submitted && !jobs[job].subjobComplete)\r
+ {\r
+ String cancelledMessage = "";\r
+ try\r
+ {\r
+ vamsas.objects.simple.WsJobId cancelledJob = server\r
+ .cancel(jobs[job].jobId);\r
+ if (cancelledJob.getStatus() == 2)\r
+ {\r
+ // CANCELLED_JOB\r
+ cancelledMessage = "Job cancelled.";\r
+ ((SeqSearchWSJob) jobs[job]).cancel();\r
+ wsInfo.setStatus(jobs[job].jobnum,\r
+ WebserviceInfo.STATE_CANCELLED_OK);\r
+ }\r
+ else if (cancelledJob.getStatus() == 3)\r
+ {\r
+ // VALID UNSTOPPABLE JOB\r
+ cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
+ cancelled = false;\r
+ // wsInfo.setStatus(jobs[job].jobnum,\r
+ // WebserviceInfo.STATE_RUNNING);\r
+ }\r
+\r
+ if (cancelledJob.getJobId() != null)\r
+ {\r
+ cancelledMessage += ("[" + cancelledJob.getJobId() + "]");\r
+ }\r
+\r
+ cancelledMessage += "\n";\r
+ } catch (Exception exc)\r
+ {\r
+ cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"\r
+ + exc + "\n");\r
+ Cache.log.warn(\r
+ "Exception whilst cancelling " + jobs[job].jobId, exc);\r
+ }\r
+ wsInfo.setProgressText(jobs[job].jobnum, OutputHeader\r
+ + cancelledMessage + "\n");\r
+ }\r
+ }\r
+ if (cancelled)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
+ jobComplete = true;\r
+ }\r
+ this.interrupt(); // kick thread to update job states.\r
+ }\r
+ else\r
+ {\r
+ if (!jobComplete)\r
+ {\r
+ wsInfo\r
+ .setProgressText(OutputHeader\r
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
+ }\r
+ }\r
+ }\r
+\r
+ void pollJob(WSJob job) throws Exception\r
+ {\r
+ ((SeqSearchWSJob) job).result = server\r
+ .getResult(((SeqSearchWSJob) job).jobId);\r
+ }\r
+\r
+ void StartJob(WSJob job)\r
+ {\r
+ if (!(job instanceof SeqSearchWSJob))\r
+ {\r
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "\r
+ + job.getClass());\r
+ }\r
+ SeqSearchWSJob j = (SeqSearchWSJob) job;\r
+ if (j.submitted)\r
+ {\r
+ if (Cache.log.isDebugEnabled())\r
+ {\r
+ Cache.log.debug("Tried to submit an already submitted job "\r
+ + j.jobId);\r
+ }\r
+ return;\r
+ }\r
+ if (j.seqs.getSeqs() == null)\r
+ {\r
+ // special case - selection consisted entirely of empty sequences...\r
+ j.submitted = true;\r
+ j.result = new MsaResult();\r
+ j.result.setFinished(true);\r
+ j.result.setStatus("Empty Alignment Job");\r
+ ((MsaResult) j.result).setMsa(null);\r
+ }\r
+ try\r
+ {\r
+ vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs\r
+ .getSeqs()[0], dbArg);\r
+\r
+ if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))\r
+ {\r
+ j.jobId = jobsubmit.getJobId();\r
+ j.submitted = true;\r
+ j.subjobComplete = false;\r
+ // System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+ }\r
+ else\r
+ {\r
+ if (jobsubmit == null)\r
+ {\r
+ throw new Exception(\r
+ "Server at "\r
+ + WsUrl\r
+ + " returned null object, it probably cannot be contacted. Try again later ?");\r
+ }\r
+\r
+ throw new Exception(jobsubmit.getJobId());\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ // TODO: JBPNote catch timeout or other fault types explicitly\r
+ // For unexpected errors\r
+ System.err\r
+ .println(WebServiceName\r
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"\r
+ + "When contacting Server:" + WsUrl + "\n"\r
+ + e.toString() + "\n");\r
+ j.allowedServerExceptions = 0;\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo\r
+ .appendProgressText(\r
+ j.jobnum,\r
+ "Failed to submit sequences for alignment.\n"\r
+ + "It is most likely that there is a problem with the server.\n"\r
+ + "Just close the window\n");\r
+\r
+ // e.printStackTrace(); // TODO: JBPNote DEBUG\r
+ }\r
+ }\r
+\r
+ private jalview.datamodel.Sequence[] getVamsasAlignment(\r
+ vamsas.objects.simple.Alignment valign)\r
+ {\r
+ vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
+ jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
+\r
+ for (int i = 0, j = seqs.length; i < j; i++)\r
+ {\r
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]\r
+ .getSeq());\r
+ }\r
+\r
+ return msa;\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\r
+ && jobs[j].hasResults())\r
+ {\r
+ results++;\r
+ vamsas.objects.simple.Alignment valign = ((SeqSearchResult) jobs[j].result)\r
+ .getAlignment();\r
+ if (valign != null)\r
+ {\r
+ wsInfo.appendProgressText(jobs[j].jobnum,\r
+ "\nAlignment Object Method Notes\n");\r
+ String[] lines = valign.getMethod();\r
+ for (int line = 0; line < lines.length; line++)\r
+ {\r
+ wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");\r
+ }\r
+ // JBPNote The returned files from a webservice could be\r
+ // hidden behind icons in the monitor window that,\r
+ // when clicked, pop up their corresponding data\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(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 newFrame)\r
+ {\r
+ if (!newFrame)\r
+ {\r
+ System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");\r
+ return;\r
+ }\r
+ // each subjob is an independent alignment for the moment\r
+ // Alignment al[] = new Alignment[jobs.length];\r
+ // NewickFile nf[] = new NewickFile[jobs.length];\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+ Hashtable featureColours = new Hashtable();\r
+ Alignment al = null;\r
+ NewickFile nf = null;\r
+ if (jobs[j].hasResults())\r
+ {\r
+ Object[] res = ((SeqSearchWSJob) jobs[j]).getAlignment(dataset,\r
+ featureColours);\r
+ if (res == null)\r
+ {\r
+ continue;\r
+ }\r
+ ;\r
+ al = (Alignment) res[0];\r
+ nf = (NewickFile) res[1];\r
+ }\r
+ else\r
+ {\r
+ al = null;\r
+ nf = null;\r
+ continue;\r
+ }\r
+ /*\r
+ * We can't map new alignment back with insertions from input's hidden\r
+ * regions until dataset mapping is sorted out... but basically it goes\r
+ * like this: 1. Merge each domain hit back onto the visible segments in\r
+ * the same way as a Jnet prediction is mapped back\r
+ * \r
+ * Object[] newview = input.getUpdatedView(results, orders, getGapChar()); //\r
+ * trash references to original result data for (int j = 0; j <\r
+ * jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]\r
+ * alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =\r
+ * (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);\r
+ * \r
+ * if (dataset != null) { al.setDataset(dataset); }\r
+ * \r
+ * propagateDatasetMappings(al); }\r
+ */\r
+\r
+ AlignFrame af = new AlignFrame(al,// columnselection,\r
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+ if (nf != null)\r
+ {\r
+ af.ShowNewickTree(nf, "Tree from " + this.alTitle);\r
+ }\r
+ // initialise with same renderer settings as in parent alignframe.\r
+ af.getFeatureRenderer().transferSettings(this.featureSettings);\r
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+\r
+ public boolean canMergeResults()\r
+ {\r
+ return false;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff