-/*
- * 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.datamodel.Alignment;
-import jalview.gui.*;
-import vamsas.objects.simple.MsaResult;
-
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
-class MsaWSThread
- extends WSThread implements WSClientI
-{
- boolean submitGaps = false; // pass sequences including gaps to alignment
-
- // service
-
- boolean preserveOrder = true; // and always store and recover sequence
-
- // order
-
- class MsaWSJob
- 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 MsaWSJob(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 MsaWS 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 two seqs
- vamsas.objects.simple.Sequence[] seqarray =
- (valid)
- ? new vamsas.objects.simple.Sequence[nseqs]
- : null;
- 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});
- }
- }
- 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()
- && ( (MsaResult) result).getMsa() != null &&
- ( (MsaResult) result).getMsa().getSeqs() != null)
- {
- return true;
- }
- return false;
- }
-
- public Object[] getAlignment()
- {
-
- if (result != null && result.isFinished())
- {
- SequenceI[] alseqs = null;
- char alseq_gapchar = '-';
- int alseq_l = 0;
- if ( ( (MsaResult) result).getMsa() != null)
- {
- alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());
- alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);
- alseq_l = alseqs.length;
- }
- if (emptySeqs.size() > 0)
- {
- SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
- // get width
- int i, w = 0;
- if (alseq_l > 0)
- {
- for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
- {
- if (w < alseqs[i].getLength())
- {
- w = alseqs[i].getLength();
- }
- t_alseqs[i] = alseqs[i];
- alseqs[i] = null;
- }
- }
- // check that aligned width is at least as wide as emptySeqs width.
- int ow = w, nw = w;
- for (i = 0, w = emptySeqs.size(); i < w; i++)
- {
- String[] es = (String[]) emptySeqs.get(i);
- if (es != null && es[1] != null)
- {
- int sw = es[1].length();
- if (nw < sw)
- {
- nw = sw;
- }
- }
- }
- // make a gapped string.
- StringBuffer insbuff = new StringBuffer(w);
- for (i = 0; i < nw; i++)
- {
- insbuff.append(alseq_gapchar);
- }
- if (ow < nw)
- {
- for (i = 0; i < alseq_l; i++)
- {
- int sw = t_alseqs[i].getLength();
- if (nw > sw)
- {
- // pad at end
- alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() +
- insbuff.substring(0, sw - nw));
- }
- }
- }
- for (i = 0, w = emptySeqs.size(); i < w; i++)
- {
- String[] es = (String[]) emptySeqs.get(i);
- if (es[1] == null)
- {
- t_alseqs[i +
- alseq_l] = new jalview.datamodel.Sequence(es[0],
- insbuff.toString(), 1, 0);
- }
- else
- {
- if (es[1].length() < nw)
- {
- t_alseqs[i +
- alseq_l] = new jalview.datamodel.Sequence(es[0],
- es[1] + insbuff.substring(0, nw - es[1].length()), 1,
- 1 + es[1].length());
- }
- else
- {
- t_alseqs[i +
- alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
- }
- }
- }
- alseqs = t_alseqs;
- }
- AlignmentOrder msaorder = new AlignmentOrder(alseqs);
- // always recover the order - makes parseResult()'s life easier.
- jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
- // account for any missing sequences
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[]
- {
- alseqs, msaorder};
- }
- 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.MuscleWS server = null;
- /**
- * set basic options for this (group) of Msa jobs
- *
- * @param subgaps
- * boolean
- * @param presorder
- * boolean
- */
- MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
- AlignmentView alview,
- String wsname, boolean subgaps, boolean presorder)
- {
- super(alFrame, wsinfo, alview, wsname, wsUrl);
- this.server = server;
- this.submitGaps = subgaps;
- this.preserveOrder = presorder;
- }
-
- /**
- * 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
- */
- MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
- String wsname, String title, AlignmentView _msa, boolean subgaps,
- boolean presorder, Alignment seqset)
- {
- this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
- OutputHeader = wsInfo.getProgressText();
- alTitle = title;
- dataset = seqset;
-
- SequenceI[][] conmsa = _msa.getVisibleContigs('-');
- if (conmsa != null)
- {
- int njobs = conmsa.length;
- jobs = new MsaWSJob[njobs];
- for (int j = 0; j < njobs; j++)
- {
- if (j != 0)
- {
- jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
- }
- else
- {
- jobs[j] = new MsaWSJob(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.";
- ( (MsaWSJob) 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
- {
- ( (MsaWSJob) job).result = server.getResult( ( (MsaWSJob) job).jobId);
- }
-
- void StartJob(WSJob job)
- {
- if (! (job instanceof MsaWSJob))
- {
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
- job.getClass());
- }
- MsaWSJob j = (MsaWSJob) 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.align(j.seqs);
-
- 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)
- {
- // TODO: refactor to helper class for vamsas.objects.simple objects
- 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 = ( (MsaResult) jobs[j].result).
- getMsa();
- 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)
- {
- // view input or result data for each block
- Vector alorders = new Vector();
- SequenceI[][] results = new SequenceI[jobs.length][];
- AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
- for (int j = 0; j < jobs.length; j++)
- {
- if (jobs[j].hasResults())
- {
- Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
- alorders.add(res[1]);
- results[j] = (SequenceI[]) res[0];
- orders[j] = (AlignmentOrder) res[1];
-
-// SequenceI[] alignment = input.getUpdated
- }
- else
- {
- results[j] = null;
- }
- }
- 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);
- // TODO: add 'provenance' property to alignment from the method notes accompanying each subjob
- if (dataset != null)
- {
- al.setDataset(dataset);
- }
-
- propagateDatasetMappings(al);
- // JBNote- TODO: warn user if a block is input rather than aligned data ?
-
- if (newFrame)
- {
- AlignFrame af = new AlignFrame(al, columnselection,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
-
- // initialise with same renderer settings as in parent alignframe.
- af.getFeatureRenderer().transferSettings(
- this.featureSettings);
- // update orders
- if (alorders.size() > 0)
- {
- if (alorders.size() == 1)
- {
- af.addSortByOrderMenuItem(WebServiceName + " Ordering",
- (AlignmentOrder) alorders.get(0));
- }
- else
- {
- // construct a non-redundant ordering set
- Vector names = new Vector();
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- String orderName = new String(" Region " + i);
- int j = i + 1;
-
- while (j < l)
- {
- if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
- AlignmentOrder) alorders.get(j))))
- {
- alorders.remove(j);
- l--;
- orderName += "," + j;
- }
- else
- {
- j++;
- }
- }
-
- if (i == 0 && j == 1)
- {
- names.add(new String(""));
- }
- else
- {
- names.add(orderName);
- }
- }
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- af.addSortByOrderMenuItem(WebServiceName
- + ( (String) names.get(i)) +
- " Ordering",
- (AlignmentOrder) alorders.get(i));
- }
- }
- }
-
- Desktop.addInternalFrame(af, alTitle,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
-
- }
- else
- {
- System.out.println("MERGE WITH OLD FRAME");
- // TODO: modify alignment in original frame, replacing old for new alignment using the commands.EditCommand model to ensure the update can be undone
- }
- }
-
- 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.datamodel.Alignment;\r
+import jalview.gui.*;\r
+import vamsas.objects.simple.MsaResult;\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 MsaWSThread extends WSThread implements WSClientI\r
+{\r
+ boolean submitGaps = false; // pass sequences including gaps to alignment\r
+\r
+ // service\r
+\r
+ boolean preserveOrder = true; // and always store and recover sequence\r
+\r
+ // order\r
+\r
+ class MsaWSJob 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 MsaWSJob(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 MsaWS 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 two seqs\r
+ vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]\r
+ : null;\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
+ 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 && result != null && result.isFinished()\r
+ && ((MsaResult) result).getMsa() != null\r
+ && ((MsaResult) result).getMsa().getSeqs() != null)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ public Object[] getAlignment()\r
+ {\r
+\r
+ if (result != null && result.isFinished())\r
+ {\r
+ SequenceI[] alseqs = null;\r
+ char alseq_gapchar = '-';\r
+ int alseq_l = 0;\r
+ if (((MsaResult) result).getMsa() != null)\r
+ {\r
+ alseqs = getVamsasAlignment(((MsaResult) result).getMsa());\r
+ alseq_gapchar = ((MsaResult) result).getMsa().getGapchar()\r
+ .charAt(0);\r
+ alseq_l = alseqs.length;\r
+ }\r
+ if (emptySeqs.size() > 0)\r
+ {\r
+ SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];\r
+ // get width\r
+ int i, w = 0;\r
+ if (alseq_l > 0)\r
+ {\r
+ for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)\r
+ {\r
+ if (w < alseqs[i].getLength())\r
+ {\r
+ w = alseqs[i].getLength();\r
+ }\r
+ t_alseqs[i] = alseqs[i];\r
+ alseqs[i] = null;\r
+ }\r
+ }\r
+ // check that aligned width is at least as wide as emptySeqs width.\r
+ int ow = w, nw = w;\r
+ for (i = 0, w = emptySeqs.size(); i < w; i++)\r
+ {\r
+ String[] es = (String[]) emptySeqs.get(i);\r
+ if (es != null && es[1] != null)\r
+ {\r
+ int sw = es[1].length();\r
+ if (nw < sw)\r
+ {\r
+ nw = sw;\r
+ }\r
+ }\r
+ }\r
+ // make a gapped string.\r
+ StringBuffer insbuff = new StringBuffer(w);\r
+ for (i = 0; i < nw; i++)\r
+ {\r
+ insbuff.append(alseq_gapchar);\r
+ }\r
+ if (ow < nw)\r
+ {\r
+ for (i = 0; i < alseq_l; i++)\r
+ {\r
+ int sw = t_alseqs[i].getLength();\r
+ if (nw > sw)\r
+ {\r
+ // pad at end\r
+ alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()\r
+ + insbuff.substring(0, sw - nw));\r
+ }\r
+ }\r
+ }\r
+ for (i = 0, w = emptySeqs.size(); i < w; i++)\r
+ {\r
+ String[] es = (String[]) emptySeqs.get(i);\r
+ if (es[1] == null)\r
+ {\r
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],\r
+ insbuff.toString(), 1, 0);\r
+ }\r
+ else\r
+ {\r
+ if (es[1].length() < nw)\r
+ {\r
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(\r
+ es[0],\r
+ es[1] + insbuff.substring(0, nw - es[1].length()),\r
+ 1, 1 + es[1].length());\r
+ }\r
+ else\r
+ {\r
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(\r
+ es[0], es[1]);\r
+ }\r
+ }\r
+ }\r
+ alseqs = t_alseqs;\r
+ }\r
+ AlignmentOrder msaorder = new AlignmentOrder(alseqs);\r
+ // always recover the order - makes parseResult()'s life easier.\r
+ jalview.analysis.AlignmentSorter.recoverOrder(alseqs);\r
+ // account for any missing sequences\r
+ jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);\r
+ return new Object[]\r
+ { alseqs, msaorder };\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.MuscleWS server = null;\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
+ MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
+ AlignmentView alview, String wsname, boolean subgaps,\r
+ boolean presorder)\r
+ {\r
+ super(alFrame, wsinfo, alview, wsname, wsUrl);\r
+ this.server = server;\r
+ this.submitGaps = subgaps;\r
+ this.preserveOrder = presorder;\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
+ MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
+ String wsname, String title, AlignmentView _msa, boolean subgaps,\r
+ boolean presorder, Alignment seqset)\r
+ {\r
+ this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);\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 MsaWSJob[njobs];\r
+ for (int j = 0; j < njobs; j++)\r
+ {\r
+ if (j != 0)\r
+ {\r
+ jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);\r
+ }\r
+ else\r
+ {\r
+ jobs[j] = new MsaWSJob(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
+ ((MsaWSJob) 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
+ ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);\r
+ }\r
+\r
+ void StartJob(WSJob job)\r
+ {\r
+ if (!(job instanceof MsaWSJob))\r
+ {\r
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "\r
+ + job.getClass());\r
+ }\r
+ MsaWSJob j = (MsaWSJob) 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.align(j.seqs);\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
+ // TODO: refactor to helper class for vamsas.objects.simple objects\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 = ((MsaResult) jobs[j].result)\r
+ .getMsa();\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
+ // view input or result data for each block\r
+ Vector alorders = new Vector();\r
+ SequenceI[][] results = new SequenceI[jobs.length][];\r
+ AlignmentOrder[] orders = new AlignmentOrder[jobs.length];\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+ if (jobs[j].hasResults())\r
+ {\r
+ Object[] res = ((MsaWSJob) jobs[j]).getAlignment();\r
+ alorders.add(res[1]);\r
+ results[j] = (SequenceI[]) res[0];\r
+ orders[j] = (AlignmentOrder) res[1];\r
+\r
+ // SequenceI[] alignment = input.getUpdated\r
+ }\r
+ else\r
+ {\r
+ results[j] = null;\r
+ }\r
+ }\r
+ Object[] newview = input.getUpdatedView(results, orders, getGapChar());\r
+ // trash references to original result data\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+ results[j] = null;\r
+ orders[j] = null;\r
+ }\r
+ SequenceI[] alignment = (SequenceI[]) newview[0];\r
+ ColumnSelection columnselection = (ColumnSelection) newview[1];\r
+ Alignment al = new Alignment(alignment);\r
+ // TODO: add 'provenance' property to alignment from the method notes\r
+ // accompanying each subjob\r
+ if (dataset != null)\r
+ {\r
+ al.setDataset(dataset);\r
+ }\r
+\r
+ propagateDatasetMappings(al);\r
+ // JBNote- TODO: warn user if a block is input rather than aligned data ?\r
+\r
+ if (newFrame)\r
+ {\r
+ AlignFrame af = new AlignFrame(al, columnselection,\r
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+\r
+ // initialise with same renderer settings as in parent alignframe.\r
+ af.getFeatureRenderer().transferSettings(this.featureSettings);\r
+ // update orders\r
+ if (alorders.size() > 0)\r
+ {\r
+ if (alorders.size() == 1)\r
+ {\r
+ af.addSortByOrderMenuItem(WebServiceName + " Ordering",\r
+ (AlignmentOrder) alorders.get(0));\r
+ }\r
+ else\r
+ {\r
+ // construct a non-redundant ordering set\r
+ Vector names = new Vector();\r
+ for (int i = 0, l = alorders.size(); i < l; i++)\r
+ {\r
+ String orderName = new String(" Region " + i);\r
+ int j = i + 1;\r
+\r
+ while (j < l)\r
+ {\r
+ if (((AlignmentOrder) alorders.get(i))\r
+ .equals(((AlignmentOrder) alorders.get(j))))\r
+ {\r
+ alorders.remove(j);\r
+ l--;\r
+ orderName += "," + j;\r
+ }\r
+ else\r
+ {\r
+ j++;\r
+ }\r
+ }\r
+\r
+ if (i == 0 && j == 1)\r
+ {\r
+ names.add(new String(""));\r
+ }\r
+ else\r
+ {\r
+ names.add(orderName);\r
+ }\r
+ }\r
+ for (int i = 0, l = alorders.size(); i < l; i++)\r
+ {\r
+ af.addSortByOrderMenuItem(WebServiceName\r
+ + ((String) names.get(i)) + " Ordering",\r
+ (AlignmentOrder) alorders.get(i));\r
+ }\r
+ }\r
+ }\r
+\r
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+\r
+ }\r
+ else\r
+ {\r
+ System.out.println("MERGE WITH OLD FRAME");\r
+ // TODO: modify alignment in original frame, replacing old for new\r
+ // alignment using the commands.EditCommand model to ensure the update can\r
+ // be undone\r
+ }\r
+ }\r
+\r
+ public boolean canMergeResults()\r
+ {\r
+ return false;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff