2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.rest;
23 import java.util.Locale;
25 import jalview.bin.Console;
26 import jalview.datamodel.Alignment;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.AlignmentOrder;
30 import jalview.datamodel.Annotation;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.SequenceGroup;
33 import jalview.datamodel.SequenceI;
34 import jalview.gui.AlignFrame;
35 import jalview.gui.Desktop;
36 import jalview.gui.PaintRefresher;
37 import jalview.gui.WebserviceInfo;
38 import jalview.io.NewickFile;
39 import jalview.io.packed.JalviewDataset;
40 import jalview.io.packed.JalviewDataset.AlignmentSet;
41 import jalview.util.MessageManager;
42 import jalview.ws.AWSThread;
43 import jalview.ws.AWsJob;
45 import java.awt.event.ActionEvent;
46 import java.awt.event.ActionListener;
47 import java.io.IOException;
48 import java.util.ArrayList;
49 import java.util.Hashtable;
50 import java.util.List;
51 import java.util.Map.Entry;
53 import org.apache.axis.transport.http.HTTPConstants;
54 import org.apache.http.Header;
55 import org.apache.http.HttpEntity;
56 import org.apache.http.HttpResponse;
57 import org.apache.http.client.ClientProtocolException;
58 import org.apache.http.client.methods.HttpGet;
59 import org.apache.http.client.methods.HttpPost;
60 import org.apache.http.client.methods.HttpRequestBase;
61 import org.apache.http.entity.mime.HttpMultipartMode;
62 import org.apache.http.entity.mime.MultipartEntity;
63 import org.apache.http.impl.client.DefaultHttpClient;
64 import org.apache.http.protocol.BasicHttpContext;
65 import org.apache.http.protocol.HttpContext;
66 import org.apache.http.util.EntityUtils;
68 public class RestJobThread extends AWSThread
75 protected RestClient restClient;
77 public RestJobThread(RestClient restClient)
79 super(restClient.af, null, restClient._input,
80 restClient.service.postUrl);
81 this.restClient = restClient; // may not be needed
83 // minimal job - submit given input and parse result onto alignment as
84 // annotation/whatever
86 // look for tree data, etc.
88 // for moment do following job type only
89 // input=visiblealignment,groupsindex
90 // ie one subjob using groups defined on alignment.
91 if (!restClient.service.isHseparable())
93 jobs = new RestJob[1];
94 jobs[0] = new RestJob(0, this,
95 restClient._input.getVisibleAlignment(
96 restClient.service.getGapCharacter()),
97 restClient._input.getVisibleContigs());
98 // need a function to get a range on a view/alignment and return both
99 // annotation, groups and selection subsetted to just that region.
104 int[] viscontig = restClient._input.getVisibleContigs();
105 AlignmentI[] viscontigals = restClient._input
106 .getVisibleContigAlignments(
107 restClient.service.getGapCharacter());
108 if (viscontigals != null && viscontigals.length > 0)
110 jobs = new RestJob[viscontigals.length];
111 for (int j = 0; j < jobs.length; j++)
113 int[] visc = new int[] { viscontig[j * 2], viscontig[j * 2 + 1] };
116 jobs[j] = new RestJob(j, this, viscontigals[j], visc);
120 jobs[j] = new RestJob(0, this, viscontigals[j], visc);
127 * subjob types row based: per sequence in alignment/selected region { input
128 * is one sequence or sequence ID } per alignment/selected region { input is
129 * set of sequences, alignment, one or more sets of sequence IDs,
132 if (!restClient.service.isHseparable())
135 // create a bunch of subjobs per visible contig to ensure result honours
137 // TODO: determine if a 'soft' hSeperable property is needed - e.g. if
138 // user does SS-pred on sequence with big hidden regions, its going to be
143 // create a single subjob for the visible/selected input
146 // TODO: decide if vSeperable exists: eg. column wide analysis where hidden
147 // rows do not affect output - generally no analysis that generates
148 // alignment annotation is vSeparable -
152 * create gui components for monitoring jobs
154 * @param webserviceInfo
156 public void setWebServiceInfo(WebserviceInfo webserviceInfo)
158 wsInfo = webserviceInfo;
159 for (int j = 0; j < jobs.length; j++)
162 // Copy over any per job params
165 wsInfo.setProgressName("region " + jobs[j].getJobnum(),
166 jobs[j].getJobnum());
170 wsInfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
175 private String getStage(Stage stg)
177 if (stg == Stage.SUBMIT)
179 return "submitting ";
181 if (stg == Stage.POLL)
183 return "checking status of ";
186 return (" being confused about ");
189 private void doPoll(RestJob rj) throws Exception
191 String postUrl = rj.getPollUrl();
192 doHttpReq(Stage.POLL, rj, postUrl);
196 * construct the post and handle the response.
200 public void doPost(RestJob rj) throws Exception
202 String postUrl = rj.getPostUrl();
203 doHttpReq(Stage.SUBMIT, rj, postUrl);
208 * do the HTTP request - and respond/set statuses appropriate to the current
213 * - provides any data needed for posting and used to record state
215 * - actual URL to post/get from
218 protected void doHttpReq(Stage stg, RestJob rj, String postUrl)
221 StringBuffer respText = new StringBuffer();
222 // con.setContentHandlerFactory(new
223 // jalview.ws.io.mime.HttpContentHandler());
224 HttpRequestBase request = null;
225 String messages = "";
226 if (stg == Stage.SUBMIT)
229 // http://evgenyg.wordpress.com/2010/05/01/uploading-files-multipart-post-apache/
231 HttpPost htpost = new HttpPost(postUrl);
232 MultipartEntity postentity = new MultipartEntity(
233 HttpMultipartMode.STRICT);
234 for (Entry<String, InputType> input : rj.getInputParams())
236 if (input.getValue().validFor(rj))
238 postentity.addPart(input.getKey(),
239 input.getValue().formatForInput(rj));
243 messages += "Skipped an input (" + input.getKey()
244 + ") - Couldn't generate it from available data.";
247 htpost.setEntity(postentity);
252 request = new HttpGet(postUrl);
256 DefaultHttpClient httpclient = new DefaultHttpClient();
258 HttpContext localContext = new BasicHttpContext();
259 HttpResponse response = null;
262 response = httpclient.execute(request);
263 } catch (ClientProtocolException he)
265 rj.statMessage = "Web Protocol Exception when " + getStage(stg)
266 + "Job. <br>Problematic url was <a href=\""
267 + request.getURI() + "\">" + request.getURI()
268 + "</a><br>See Console output for details.";
269 rj.setAllowedServerExceptions(0);// unrecoverable;
271 Console.fatal("Unexpected REST Job " + getStage(stg)
272 + "exception for URL " + rj.rsd.postUrl);
274 } catch (IOException e)
276 rj.statMessage = "IO Exception when " + getStage(stg)
277 + "Job. <br>Problematic url was <a href=\""
278 + request.getURI() + "\">" + request.getURI()
279 + "</a><br>See Console output for details.";
280 Console.warn("IO Exception for REST Job " + getStage(stg)
281 + "exception for URL " + rj.rsd.postUrl);
285 switch (response.getStatusLine().getStatusCode())
289 Console.debug("Processing result set.");
290 processResultSet(rj, response, request);
293 rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
294 + "<a href=" + rj.getJobId() + "\">" + rj.getJobId()
300 if (!rj.isSubmitted()
302 .getHeaders(HTTPConstants.HEADER_LOCATION)) != null
307 Console.warn("Ignoring additional " + (loc.length - 1)
308 + " location(s) provided in response header ( next one is '"
309 + loc[1].getValue() + "' )");
311 rj.setJobId(loc[0].getValue());
312 rj.setSubmitted(true);
314 completeStatus(rj, response);
318 rj.setSubmitted(true);
319 rj.setAllowedServerExceptions(0);
320 rj.setSubjobComplete(true);
323 completeStatus(rj, response,
324 "" + getStage(stg) + "failed. Reason below:\n");
327 // Some other response. Probably need to pop up the content in a window.
328 // TODO: deal with all other HTTP response codes from server.
329 Console.warn("Unhandled response status when " + getStage(stg)
330 + "for " + postUrl + ": " + response.getStatusLine());
332 rj.setAllowedServerExceptions(0);
333 rj.setSubjobComplete(true);
334 rj.setSubmitted(true);
337 completeStatus(rj, response, "" + getStage(stg)
338 + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
339 + request.getURI() + "\">" + request.getURI()
340 + "</a><br/>Filtered response content below:<br/>");
341 } catch (IOException e)
343 Console.debug("IOException when consuming unhandled response", e);
351 * job has completed. Something valid should be available from con
356 * is a stateless request - expected to return the same data
357 * regardless of how many times its called.
359 private void processResultSet(RestJob rj, HttpResponse con,
362 if (rj.statMessage == null)
366 rj.statMessage += "Job Complete.\n";
369 rj.resSet = new HttpResultSet(rj, con, req);
371 } catch (IOException e)
373 rj.statMessage += "Couldn't parse results. Failed.";
375 rj.gotresult = false;
379 private void completeStatus(RestJob rj, HttpResponse con)
382 completeStatus(rj, con, null);
386 private void completeStatus(RestJob rj, HttpResponse con, String prefix)
389 StringBuffer sb = new StringBuffer();
395 if (rj.statMessage != null && rj.statMessage.length() > 0)
397 sb.append(rj.statMessage);
399 HttpEntity en = con.getEntity();
401 * Just append the content as a string.
404 StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
405 f = f.toLowerCase(Locale.ROOT);
406 int body = f.indexOf("<body");
409 content.delete(0, f.indexOf(">", body) + 1);
411 if (body > -1 && sb.length() > 0)
414 content.insert(0, sb);
418 rj.statMessage = content.toString();
422 public void pollJob(AWsJob job) throws Exception
424 assert (job instanceof RestJob);
425 System.err.println("Debug RestJob: Polling Job");
426 doPoll((RestJob) job);
430 public void StartJob(AWsJob job)
432 assert (job instanceof RestJob);
435 System.err.println("Debug RestJob: Posting Job");
436 doPost((RestJob) job);
437 } catch (NoValidInputDataException erex)
439 job.setSubjobComplete(true);
440 job.setSubmitted(true);
441 ((RestJob) job).statMessage = "<br>It looks like there was a problem with the data sent to the service :<br>"
442 + erex.getMessage() + "\n";
443 ((RestJob) job).error = true;
445 } catch (Exception ex)
447 job.setSubjobComplete(true);
448 job.setAllowedServerExceptions(-1);
449 Console.error("Exception when trying to start Rest Job.", ex);
454 public void parseResult()
456 // crazy users will see this message
457 // TODO: finish this! and remove the message below!
458 Console.warn("Rest job result parser is currently INCOMPLETE!");
460 for (RestJob rj : (RestJob[]) jobs)
462 if (rj.hasResponse() && rj.resSet != null && rj.resSet.isValid())
467 Console.debug("Parsing data for job " + rj.getJobId());
473 Console.debug("Finished parsing data for job " + rj.getJobId());
478 "Failed to finish parsing data for job " + rj.getJobId());
479 ex.printStackTrace();
480 } catch (Exception ex)
483 "Failed to finish parsing data for job " + rj.getJobId());
484 ex.printStackTrace();
488 rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
489 + rj.resSet.getUrl() + "\">" + rj.resSet.getUrl()
496 // add listeners and activate result display gui elements
498 * decisions based on job result content + state of alignFrame that
499 * originated the job:
502 * 1. Can/Should this job automatically open a new window for results
506 // preserver current jalview behaviour
507 wsInfo.setViewResultsImmediatly(true);
511 // realiseResults(true, true);
513 // otherwise, should automatically view results
515 // TODO: check if at least one or more contexts are valid - if so, enable
517 wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
521 public void actionPerformed(ActionEvent e)
523 realiseResults(false);
527 wsInfo.mergeResults.addActionListener(new ActionListener()
531 public void actionPerformed(ActionEvent e)
533 realiseResults(true);
538 wsInfo.setResultsReady();
542 // tell the user nothing was returned.
543 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
544 wsInfo.setFinishedNoResults();
549 * instructions for whether to create new alignment view on current alignment
550 * set, add to current set, or create new alignFrame
552 private enum AddDataTo
555 * add annotation, trees etc to current view
559 * create a new view derived from current view and add data to that
563 * create a new alignment frame for the result set and add annotation to
569 public void realiseResults(boolean merge)
572 * 2. Should the job modify the parent alignment frame/view(s) (if they
573 * still exist and the alignment hasn't been edited) in order to display new
574 * annotation/features.
577 * alignment panels derived from each alignment set returned by service.
579 ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
581 * list of instructions for how to process each distinct alignment set
582 * returned by the job set
584 ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>();
586 * when false, zeroth pane is panel derived from input deta.
588 boolean newAlignment = false;
590 * gap character to be used for alignment reconstruction
592 char gapCharacter = restClient.av.getGapCharacter();
593 // Now, iterate over all alignment sets returned from all jobs:
594 // first inspect jobs and collate results data in order to count alignments
596 // then assemble results from decomposed (v followed by h-separated) jobs
597 // finally, new views and alignments will be created and displayed as
599 boolean hsepjobs = restClient.service.isHseparable();
600 boolean vsepjobs = restClient.service.isVseparable();
601 // total number of distinct alignment sets generated by job set.
602 int numAlSets = 0, als = 0;
603 List<AlignmentI> destAls = new ArrayList<AlignmentI>();
604 List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<jalview.datamodel.HiddenColumns>();
605 List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
610 // iterate over each alignment set returned from each subjob. Treating
611 // each one returned in parallel with others.
612 // Result collation arrays
615 * mapping between index of sequence in alignment that was submitted to
616 * server and index of sequence in the input alignment
618 int[][] ordermap = new int[jobs.length][];
619 SequenceI[][] rseqs = new SequenceI[jobs.length][];
620 AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
621 AlignmentAnnotation[][] alan = new AlignmentAnnotation[jobs.length][];
622 SequenceGroup[][] sgrp = new SequenceGroup[jobs.length][];
623 // Now collect all data for alignment Set als from job array
624 for (int j = 0; j < jobs.length; j++)
626 RestJob rj = (RestJob) jobs[j];
629 JalviewDataset rset = rj.context;
630 if (rset.hasAlignments())
632 if (numAlSets < rset.getAl().size())
634 numAlSets = rset.getAl().size();
636 if (als < rset.getAl().size()
637 && rset.getAl().get(als).isModified())
639 // Collate result data
640 // TODO: decide if all alignmentI should be collected rather than
641 // specific alignment data containers
642 // for moment, we just extract content, but this means any
643 // alignment properties may be lost.
644 AlignmentSet alset = rset.getAl().get(als);
645 alan[j] = alset.al.getAlignmentAnnotation();
646 if (alset.al.getGroups() != null)
648 sgrp[j] = new SequenceGroup[alset.al.getGroups().size()];
649 alset.al.getGroups().toArray(sgrp[j]);
655 orders[j] = new AlignmentOrder(alset.al);
656 rseqs[j] = alset.al.getSequencesArray();
657 ordermap[j] = rj.getOrderMap();
658 // if (rj.isInputUniquified()) {
659 // jalview.analysis.AlignmentSorter.recoverOrder(rseqs[als]);
662 if (alset.trees != null)
664 trees.add(new ArrayList<NewickFile>(alset.trees));
668 trees.add(new ArrayList<NewickFile>());
674 // Now aggregate and present results from this frame of alignment data.
675 int nvertsep = 0, nvertseps = 1;
678 // Jobs relate to different rows of input alignment.
679 // Jobs are subdivided by rows before columns,
680 // so there will now be a number of subjobs according tohsep for each
682 // TODO: get vertical separation intervals for each job and set
684 // TODO: merge data from each group/sequence onto whole
688 * index into rest jobs subdivided vertically
691 // Destination alignments for all result data.
692 ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>();
693 Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>();
694 ArrayList<AlignmentAnnotation> visAlAn = null;
695 for (nvertsep = 0; nvertsep < nvertseps; nvertsep++)
697 // TODO: set scope w.r.t. original alignment view for vertical
700 // results for a job exclude hidden columns of input data, so map
701 // back on to all visible regions
703 * rest job result we are working with
707 RestJob rj = (RestJob) jobs[nrj];
708 int contigs[] = input.getVisibleContigs();
709 AlignmentI destAl = null;
710 jalview.datamodel.HiddenColumns destHCs = null;
711 // Resolve destAl for this data.
712 if (als == 0 && rj.isInputContextModified())
714 // special case: transfer features, annotation, groups, etc,
716 // context to align panel derived from input data
717 if (destAls.size() > als)
719 destAl = destAls.get(als);
723 if (!restClient.isAlignmentModified() && merge)
725 destAl = restClient.av.getAlignment();
726 destHCs = restClient.av.getAlignment().getHiddenColumns();
727 resultDest.add(restClient.isShowResultsInNewView()
729 : AddDataTo.currentView);
730 destPanels.add(restClient.recoverAlignPanelForView());
735 // recreate the input alignment data
736 Object[] idat = input
737 .getAlignmentAndHiddenColumns(gapCharacter);
738 destAl = new Alignment((SequenceI[]) idat[0]);
739 destHCs = (HiddenColumns) idat[1];
740 resultDest.add(AddDataTo.newAlignment);
741 // but do not add to the alignment panel list - since we need to
742 // create a whole new alignFrame set.
745 destColsel.add(destHCs);
750 // alignment(s) returned by service is to be re-integrated and
752 if (destAls.size() > als)
756 // TODO: decide if multiple multiple alignments returned by
757 // non-vseparable services are allowed.
759 "dealing with multiple alignment products returned by non-vertically separable service.");
761 // recover reference to last alignment created for this rest frame
762 // ready for extension
763 destAl = destAls.get(als);
764 destHCs = destColsel.get(als);
772 // single alignment for any job that gets mapped back on to
773 // input data. Reconstruct by interleaving parts of returned
774 // alignment with hidden parts of input data.
775 SequenceI[][] nsq = splitSeqsOnVisibleContigs(rseqs[nrj],
776 contigs, gapCharacter);
777 AlignmentOrder alo[] = new AlignmentOrder[nsq.length];
778 for (int no = 0; no < alo.length; no++)
780 alo[no] = new AlignmentOrder(orders[nrj].getOrder());
782 newview = input.getUpdatedView(nsq, orders, gapCharacter);
786 // each job maps to a single visible contig, and all need to be
787 // stitched back together.
788 // reconstruct using sub-region based MSA alignment construction
790 newview = input.getUpdatedView(rseqs, orders, gapCharacter);
792 destAl = new Alignment((SequenceI[]) newview[0]);
793 destHCs = (HiddenColumns) newview[1];
795 // TODO create alignment from result data with propagated
798 destColsel.add(destHCs);
799 resultDest.add(AddDataTo.newAlignment);
801 MessageManager.getString("error.implementation_error")
806 * save initial job in this set in case alignment is h-separable
810 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
814 // single alignment for any job that gets mapped back on to input
819 // each job maps to a single visible contig, and all need to be
820 // stitched back together.
825 // TODO: apply options for group merging and annotation merging.
826 // If merging not supported, then either clear hashtables now or
827 // use them to rename the new annotation/groups for each contig if
828 // a conflict occurs.
830 if (sgrp[nrj] != null)
832 for (SequenceGroup sg : sgrp[nrj])
834 boolean recovered = false;
835 SequenceGroup exsg = null;
836 if (sg.getName() != null)
838 exsg = groupNames.get(sg.getName());
842 exsg = new SequenceGroup(sg);
843 groupNames.put(exsg.getName(), exsg);
845 exsg.setStartRes(sg.getStartRes() + contigs[ncnt]);
846 exsg.setEndRes(sg.getEndRes() + contigs[ncnt]);
852 // now replace any references from the result set with
853 // corresponding refs from alignment input set.
855 // TODO: cope with recovering hidden sequences from
858 for (SequenceI oseq : sg.getSequences(null))
860 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
861 ordermap[nrj], destAl);
866 exsg.deleteSequence(oseq, false);
868 exsg.addSequence(nseq, false);
873 "Couldn't resolve original sequence for new sequence.");
878 if (exsg.getSeqrep() == sg.getSeqrep())
880 // lift over sequence rep reference too
881 SequenceI oseq = sg.getSeqrep();
882 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
883 ordermap[nrj], destAl);
886 exsg.setSeqrep(nseq);
893 // adjust boundaries of recovered group w.r.t. new group being
894 // merged on to original alignment.
895 int start = sg.getStartRes() + contigs[ncnt],
896 end = sg.getEndRes() + contigs[ncnt];
897 if (start < exsg.getStartRes())
899 exsg.setStartRes(start);
901 if (end > exsg.getEndRes())
911 // and finally add in annotation and any trees for each job
912 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
916 // single alignment for any job that gets mapped back on to input
921 // each job maps to a single visible contig, and all need to be
922 // stitched back together.
929 // merge alignmentAnnotation into one row
930 if (alan[nrj] != null)
932 for (int an = 0; an < alan[nrj].length; an++)
934 SequenceI sqass = null;
935 SequenceGroup grass = null;
936 if (alan[nrj][an].sequenceRef != null)
938 // TODO: ensure this relocates sequence reference to local
940 sqass = getNewSeq(alan[nrj][an].sequenceRef, rseqs[nrj],
941 ordermap[nrj], destAl);
943 if (alan[nrj][an].groupRef != null)
945 // TODO: verify relocate group reference to local context
947 grass = groupNames.get(alan[nrj][an].groupRef.getName());
951 "Couldn't relocate group referemce for group "
952 + alan[nrj][an].groupRef.getName());
957 visAlAn = new ArrayList<AlignmentAnnotation>();
959 AlignmentAnnotation visan = null;
960 for (AlignmentAnnotation v : visAlAn)
963 && v.label.equals(alan[nrj][an].label))
970 visan = new AlignmentAnnotation(alan[nrj][an]);
971 // copy annotations, and wipe out/update refs.
972 visan.annotations = new Annotation[input.getWidth()];
973 visan.groupRef = grass;
974 visan.sequenceRef = sqass;
978 + alan[nrj][an].annotations.length > visan.annotations.length)
980 // increase width of annotation row
981 Annotation[] newannv = new Annotation[contigs[ncnt]
982 + alan[nrj][an].annotations.length];
983 System.arraycopy(visan.annotations, 0, newannv, 0,
984 visan.annotations.length);
985 visan.annotations = newannv;
987 // now copy local annotation data into correct position
988 System.arraycopy(alan[nrj][an].annotations, 0,
989 visan.annotations, contigs[ncnt],
990 alan[nrj][an].annotations.length);
995 if (trees.get(nrj).size() > 0)
997 for (NewickFile nf : trees.get(nrj))
999 // TODO: process each newick file, lifting over sequence refs to
1000 // current alignment, if necessary.
1002 "Tree recovery from restjob not yet implemented.");
1007 } // end of vseps loops.
1008 if (visAlAn != null)
1010 for (AlignmentAnnotation v : visAlAn)
1012 destAls.get(als).addAnnotation(v);
1015 if (visgrps != null)
1017 for (SequenceGroup sg : visgrps)
1019 destAls.get(als).addGroup(sg);
1022 } while (++als < numAlSets);
1023 // Finally, assemble each new alignment, and create new gui components to
1026 * current AlignFrame where results will go.
1028 AlignFrame destaf = restClient.recoverAlignFrameForView();
1030 * current pane being worked with
1032 jalview.gui.AlignmentPanel destPanel = restClient
1033 .recoverAlignPanelForView();
1035 for (AddDataTo action : resultDest)
1038 HiddenColumns destcs;
1039 String alTitle = MessageManager
1040 .formatMessage("label.webservice_job_title_on", new String[]
1041 { restClient.service.details.Action,
1042 restClient.service.details.Name, restClient.viewTitle });
1046 destal = destAls.get(als);
1047 destcs = destColsel.get(als);
1048 destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
1049 AlignFrame.DEFAULT_HEIGHT);
1050 PaintRefresher.Refresh(destaf,
1051 destaf.getViewport().getSequenceSetId());
1052 // todo transfer any feature settings and colouring
1054 * destaf.getFeatureRenderer().transferSettings(this.featureSettings);
1055 * // update orders if (alorders.size() > 0) { if (alorders.size() == 1)
1056 * { af.addSortByOrderMenuItem(WebServiceName + " Ordering",
1057 * (AlignmentOrder) alorders.get(0)); } else { // construct a
1058 * non-redundant ordering set Vector names = new Vector(); for (int i =
1059 * 0, l = alorders.size(); i < l; i++) { String orderName = new
1060 * String(" Region " + i); int j = i + 1;
1062 * while (j < l) { if (((AlignmentOrder) alorders.get(i))
1063 * .equals(((AlignmentOrder) alorders.get(j)))) { alorders.remove(j);
1064 * l--; orderName += "," + j; } else { j++; } }
1066 * if (i == 0 && j == 1) { names.add(new String("")); } else {
1067 * names.add(orderName); } } for (int i = 0, l = alorders.size(); i < l;
1068 * i++) { af.addSortByOrderMenuItem( WebServiceName + ((String)
1069 * names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } }
1071 // TODO: modify this and previous alignment's title if many alignments
1072 // have been returned.
1073 Desktop.addInternalFrame(destaf, alTitle, AlignFrame.DEFAULT_WIDTH,
1074 AlignFrame.DEFAULT_HEIGHT);
1078 // TODO: determine title for view
1086 if (restClient.isShowResultsInNewView())
1088 // destPanel = destPanel.alignFrame.newView(false);
1096 * if (als) // add the destination panel to frame zero of result panel set }
1097 * } if (destPanels.size()==0) { AlignFrame af = new AlignFrame((AlignmentI)
1098 * idat[0], (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
1099 * AlignFrame.DEFAULT_HEIGHT);
1101 * jalview.gui.Desktop.addInternalFrame(af, "Results for " +
1102 * restClient.service.details.Name + " " + restClient.service.details.Action
1103 * + " on " + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH,
1104 * AlignFrame.DEFAULT_HEIGHT); destPanel = af.alignPanel; // create totally
1105 * new alignment from stashed data/results
1112 * alignments. New alignments are added to dataset, and subsequently
1113 * annotated/visualised accordingly. 1. New alignment frame created for new
1114 * alignment. Decide if any vis settings should be inherited from old
1115 * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
1116 * alignment as below:
1119 * annotation update to original/newly created context alignment: 1.
1120 * identify alignment where annotation is to be loaded onto. 2. Add
1121 * annotation, excluding any duplicates. 3. Ensure annotation is visible on
1122 * alignment - honouring ordering given by file.
1125 * features updated to original or newly created context alignment: 1.
1126 * Features are(or were already) added to dataset. 2. Feature settings
1127 * modified to ensure all features are displayed - honouring any ordering
1128 * given by result file. Consider merging action with the code used by the
1129 * DAS fetcher to update alignment views with new info.
1132 * Seq associated data files (PDB files). 1. locate seq association in
1133 * current dataset/alignment context and add file as normal - keep handle of
1134 * any created ref objects. 2. decide if new data should be displayed : PDB
1135 * display: if alignment has PDB display already, should new pdb files be
1139 // destPanel.adjustAnnotationHeight();
1144 * split the given array of sequences into blocks of subsequences
1145 * corresponding to each visible contig
1150 * padding character for ragged ends of visible contig region.
1153 private SequenceI[][] splitSeqsOnVisibleContigs(SequenceI[] sequenceIs,
1154 int[] contigs, char gapChar)
1156 int nvc = contigs == null ? 1 : contigs.length / 2;
1157 SequenceI[][] blocks = new SequenceI[nvc][];
1158 if (contigs == null)
1160 blocks[0] = new SequenceI[sequenceIs.length];
1161 System.arraycopy(sequenceIs, 0, blocks[0], 0, sequenceIs.length);
1165 // deja vu - have I written this before ?? propagateGaps does this in a
1167 char[] gapset = null;
1168 int start = 0, width = 0;
1169 for (int c = 0; c < nvc; c++)
1171 width = contigs[c * 2 + 1] - contigs[c * 2] + 1;
1172 for (int s = 0; s < sequenceIs.length; s++)
1174 int end = sequenceIs[s].getLength();
1177 if (start + width < end)
1179 blocks[c][s] = sequenceIs[s].getSubSequence(start,
1184 blocks[c][s] = sequenceIs[s].getSubSequence(start, end);
1185 String sq = blocks[c][s].getSequenceAsString();
1186 for (int n = start + width; n > end; n--)
1194 if (gapset == null || gapset.length < width)
1196 char ng[] = new char[width];
1200 System.arraycopy(gapset, 0, ng, 0, gs = gapset.length);
1202 while (gs < ng.length)
1207 blocks[c][s] = sequenceIs[s].getSubSequence(end, end);
1208 blocks[c][s].setSequence(gapset.toString().substring(0, width));
1213 // adjust window for next visible segnment
1214 start += contigs[c * 2 + 1] - contigs[c * 2];
1222 * recover corresponding sequence from original input data corresponding to
1223 * sequence in a specific job's input data.
1231 private SequenceI getNewSeq(SequenceI oseq, SequenceI[] sequenceIs,
1232 int[] is, AlignmentI destAl)
1235 while (p < sequenceIs.length && sequenceIs[p] != oseq)
1239 if (p < sequenceIs.length && p < destAl.getHeight())
1241 return destAl.getSequenceAt(is[p]);
1248 * @return true if the run method is safe to call
1250 public boolean isValid()
1252 ArrayList<String> _warnings = new ArrayList<String>();
1253 boolean validt = true;
1256 for (RestJob rj : (RestJob[]) jobs)
1258 if (!rj.hasValidInput())
1260 // invalid input for this job
1261 System.err.println("Job " + rj.getJobnum()
1262 + " has invalid input. ( " + rj.getStatus() + ")");
1263 if (rj.hasStatus() && !_warnings.contains(rj.getStatus()))
1265 _warnings.add(rj.getStatus());
1274 for (String st : _warnings)
1276 if (warnings.length() > 0)
1287 protected String warnings;
1289 public boolean hasWarnings()
1291 // TODO Auto-generated method stub
1292 return warnings != null && warnings.length() > 0;
1296 * get any informative messages about why the job thread couldn't start.
1300 public String getWarnings()
1302 return isValid() ? "Job can be started. No warnings."
1303 : hasWarnings() ? warnings : "";