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 jalview.bin.Cache;
24 import jalview.datamodel.Alignment;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.AlignmentOrder;
28 import jalview.datamodel.Annotation;
29 import jalview.datamodel.HiddenColumns;
30 import jalview.datamodel.SequenceGroup;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.AlignFrame;
33 import jalview.gui.Desktop;
34 import jalview.gui.PaintRefresher;
35 import jalview.gui.WebserviceInfo;
36 import jalview.io.NewickFile;
37 import jalview.io.packed.JalviewDataset;
38 import jalview.io.packed.JalviewDataset.AlignmentSet;
39 import jalview.util.MessageManager;
40 import jalview.ws.AWSThread;
41 import jalview.ws.AWsJob;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.io.IOException;
46 import java.util.ArrayList;
47 import java.util.Hashtable;
48 import java.util.List;
49 import java.util.Map.Entry;
51 import org.apache.axis.transport.http.HTTPConstants;
52 import org.apache.http.Header;
53 import org.apache.http.HttpEntity;
54 import org.apache.http.HttpResponse;
55 import org.apache.http.client.ClientProtocolException;
56 import org.apache.http.client.methods.HttpGet;
57 import org.apache.http.client.methods.HttpPost;
58 import org.apache.http.client.methods.HttpRequestBase;
59 import org.apache.http.entity.mime.HttpMultipartMode;
60 import org.apache.http.entity.mime.MultipartEntity;
61 import org.apache.http.impl.client.DefaultHttpClient;
62 import org.apache.http.protocol.BasicHttpContext;
63 import org.apache.http.protocol.HttpContext;
64 import org.apache.http.util.EntityUtils;
66 public class RestJobThread extends AWSThread
73 protected RestClient restClient;
75 public RestJobThread(RestClient restClient)
77 super(restClient.af, null, restClient._input,
78 restClient.service.postUrl);
79 this.restClient = restClient; // may not be needed
81 // minimal job - submit given input and parse result onto alignment as
82 // annotation/whatever
84 // look for tree data, etc.
86 // for moment do following job type only
87 // input=visiblealignment,groupsindex
88 // ie one subjob using groups defined on alignment.
89 if (!restClient.service.isHseparable())
91 jobs = new RestJob[1];
92 jobs[0] = new RestJob(0, this,
93 restClient._input.getVisibleAlignment(restClient.service
95 restClient._input.getVisibleContigs());
96 // need a function to get a range on a view/alignment and return both
97 // annotation, groups and selection subsetted to just that region.
102 int[] viscontig = restClient._input.getVisibleContigs();
103 AlignmentI[] viscontigals = restClient._input
104 .getVisibleContigAlignments(restClient.service
106 if (viscontigals != null && viscontigals.length > 0)
108 jobs = new RestJob[viscontigals.length];
109 for (int j = 0; j < jobs.length; j++)
111 int[] visc = new int[] { viscontig[j * 2], viscontig[j * 2 + 1] };
114 jobs[j] = new RestJob(j, this, viscontigals[j], visc);
118 jobs[j] = new RestJob(0, this, viscontigals[j], visc);
125 * subjob types row based: per sequence in alignment/selected region { input
126 * is one sequence or sequence ID } per alignment/selected region { input is
127 * set of sequences, alignment, one or more sets of sequence IDs,
130 if (!restClient.service.isHseparable())
133 // create a bunch of subjobs per visible contig to ensure result honours
135 // TODO: determine if a 'soft' hSeperable property is needed - e.g. if
136 // user does SS-pred on sequence with big hidden regions, its going to be
141 // create a single subjob for the visible/selected input
144 // TODO: decide if vSeperable exists: eg. column wide analysis where hidden
145 // rows do not affect output - generally no analysis that generates
146 // alignment annotation is vSeparable -
150 * create gui components for monitoring jobs
152 * @param webserviceInfo
154 public void setWebServiceInfo(WebserviceInfo webserviceInfo)
156 wsInfo = webserviceInfo;
157 for (int j = 0; j < jobs.length; j++)
160 // Copy over any per job params
163 wsInfo.setProgressName("region " + jobs[j].getJobnum(),
164 jobs[j].getJobnum());
168 wsInfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
173 private String getStage(Stage stg)
175 if (stg == Stage.SUBMIT)
177 return "submitting ";
179 if (stg == Stage.POLL)
181 return "checking status of ";
184 return (" being confused about ");
187 private void doPoll(RestJob rj) throws Exception
189 String postUrl = rj.getPollUrl();
190 doHttpReq(Stage.POLL, rj, postUrl);
194 * construct the post and handle the response.
198 public void doPost(RestJob rj) throws Exception
200 String postUrl = rj.getPostUrl();
201 doHttpReq(Stage.SUBMIT, rj, postUrl);
206 * do the HTTP request - and respond/set statuses appropriate to the current
211 * - provides any data needed for posting and used to record state
213 * - actual URL to post/get from
216 protected void doHttpReq(Stage stg, RestJob rj, String postUrl)
219 StringBuffer respText = new StringBuffer();
220 // con.setContentHandlerFactory(new
221 // jalview.ws.io.mime.HttpContentHandler());
222 HttpRequestBase request = null;
223 String messages = "";
224 if (stg == Stage.SUBMIT)
227 // http://evgenyg.wordpress.com/2010/05/01/uploading-files-multipart-post-apache/
229 HttpPost htpost = new HttpPost(postUrl);
230 MultipartEntity postentity = new MultipartEntity(
231 HttpMultipartMode.STRICT);
232 for (Entry<String, InputType> input : rj.getInputParams())
234 if (input.getValue().validFor(rj))
236 postentity.addPart(input.getKey(), input.getValue()
237 .formatForInput(rj));
241 messages += "Skipped an input (" + input.getKey()
242 + ") - Couldn't generate it from available data.";
245 htpost.setEntity(postentity);
250 request = new HttpGet(postUrl);
254 DefaultHttpClient httpclient = new DefaultHttpClient();
256 HttpContext localContext = new BasicHttpContext();
257 HttpResponse response = null;
260 response = httpclient.execute(request);
261 } catch (ClientProtocolException he)
263 rj.statMessage = "Web Protocol Exception when " + getStage(stg)
264 + "Job. <br>Problematic url was <a href=\""
265 + request.getURI() + "\">" + request.getURI()
266 + "</a><br>See Console output for details.";
267 rj.setAllowedServerExceptions(0);// unrecoverable;
269 Cache.log.fatal("Unexpected REST Job " + getStage(stg)
270 + "exception for URL " + rj.rsd.postUrl);
272 } catch (IOException e)
274 rj.statMessage = "IO Exception when " + getStage(stg)
275 + "Job. <br>Problematic url was <a href=\""
276 + request.getURI() + "\">" + request.getURI()
277 + "</a><br>See Console output for details.";
278 Cache.log.warn("IO Exception for REST Job " + getStage(stg)
279 + "exception for URL " + rj.rsd.postUrl);
283 switch (response.getStatusLine().getStatusCode())
287 Cache.log.debug("Processing result set.");
288 processResultSet(rj, response, request);
291 rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
301 if (!rj.isSubmitted()
303 .getHeaders(HTTPConstants.HEADER_LOCATION)) != null
309 .warn("Ignoring additional "
311 + " location(s) provided in response header ( next one is '"
312 + loc[1].getValue() + "' )");
314 rj.setJobId(loc[0].getValue());
315 rj.setSubmitted(true);
317 completeStatus(rj, response);
321 rj.setSubmitted(true);
322 rj.setAllowedServerExceptions(0);
323 rj.setSubjobComplete(true);
326 completeStatus(rj, response, "" + getStage(stg)
327 + "failed. Reason below:\n");
330 // Some other response. Probably need to pop up the content in a window.
331 // TODO: deal with all other HTTP response codes from server.
332 Cache.log.warn("Unhandled response status when " + getStage(stg)
333 + "for " + postUrl + ": " + response.getStatusLine());
335 rj.setAllowedServerExceptions(0);
336 rj.setSubjobComplete(true);
337 rj.setSubmitted(true);
345 + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
349 + "</a><br/>Filtered response content below:<br/>");
350 } catch (IOException e)
352 Cache.log.debug("IOException when consuming unhandled response",
361 * job has completed. Something valid should be available from con
366 * is a stateless request - expected to return the same data
367 * regardless of how many times its called.
369 private void processResultSet(RestJob rj, HttpResponse con,
372 if (rj.statMessage == null)
376 rj.statMessage += "Job Complete.\n";
379 rj.resSet = new HttpResultSet(rj, con, req);
381 } catch (IOException e)
383 rj.statMessage += "Couldn't parse results. Failed.";
385 rj.gotresult = false;
389 private void completeStatus(RestJob rj, HttpResponse con)
392 completeStatus(rj, con, null);
396 private void completeStatus(RestJob rj, HttpResponse con, String prefix)
399 StringBuffer sb = new StringBuffer();
405 if (rj.statMessage != null && rj.statMessage.length() > 0)
407 sb.append(rj.statMessage);
409 HttpEntity en = con.getEntity();
411 * Just append the content as a string.
414 StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
416 int body = f.indexOf("<body");
419 content.delete(0, f.indexOf(">", body) + 1);
421 if (body > -1 && sb.length() > 0)
424 content.insert(0, sb);
428 rj.statMessage = content.toString();
432 public void pollJob(AWsJob job) throws Exception
434 assert (job instanceof RestJob);
435 System.err.println("Debug RestJob: Polling Job");
436 doPoll((RestJob) job);
440 public void StartJob(AWsJob job)
442 assert (job instanceof RestJob);
445 System.err.println("Debug RestJob: Posting Job");
446 doPost((RestJob) job);
447 } catch (NoValidInputDataException erex)
449 job.setSubjobComplete(true);
450 job.setSubmitted(true);
451 ((RestJob) job).statMessage = "<br>It looks like there was a problem with the data sent to the service :<br>"
452 + erex.getMessage() + "\n";
453 ((RestJob) job).error = true;
455 } catch (Exception ex)
457 job.setSubjobComplete(true);
458 job.setAllowedServerExceptions(-1);
459 Cache.log.error("Exception when trying to start Rest Job.", ex);
464 public void parseResult()
466 // crazy users will see this message
467 // TODO: finish this! and remove the message below!
468 Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
470 for (RestJob rj : (RestJob[]) jobs)
472 if (rj.hasResponse() && rj.resSet != null && rj.resSet.isValid())
477 Cache.log.debug("Parsing data for job " + rj.getJobId());
483 Cache.log.debug("Finished parsing data for job " + rj.getJobId());
487 Cache.log.warn("Failed to finish parsing data for job "
489 ex.printStackTrace();
490 } catch (Exception ex)
492 Cache.log.warn("Failed to finish parsing data for job "
494 ex.printStackTrace();
498 rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
508 // add listeners and activate result display gui elements
510 * decisions based on job result content + state of alignFrame that
511 * originated the job:
514 * 1. Can/Should this job automatically open a new window for results
518 // preserver current jalview behaviour
519 wsInfo.setViewResultsImmediatly(true);
523 // realiseResults(true, true);
525 // otherwise, should automatically view results
527 // TODO: check if at least one or more contexts are valid - if so, enable
529 wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
533 public void actionPerformed(ActionEvent e)
535 realiseResults(false);
539 wsInfo.mergeResults.addActionListener(new ActionListener()
543 public void actionPerformed(ActionEvent e)
545 realiseResults(true);
550 wsInfo.setResultsReady();
554 // tell the user nothing was returned.
555 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
556 wsInfo.setFinishedNoResults();
561 * instructions for whether to create new alignment view on current alignment
562 * set, add to current set, or create new alignFrame
564 private enum AddDataTo
567 * add annotation, trees etc to current view
571 * create a new view derived from current view and add data to that
575 * create a new alignment frame for the result set and add annotation to
581 public void realiseResults(boolean merge)
584 * 2. Should the job modify the parent alignment frame/view(s) (if they
585 * still exist and the alignment hasn't been edited) in order to display new
586 * annotation/features.
589 * alignment panels derived from each alignment set returned by service.
591 ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
593 * list of instructions for how to process each distinct alignment set
594 * returned by the job set
596 ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>();
598 * when false, zeroth pane is panel derived from input deta.
600 boolean newAlignment = false;
602 * gap character to be used for alignment reconstruction
604 char gapCharacter = restClient.av.getGapCharacter();
605 // Now, iterate over all alignment sets returned from all jobs:
606 // first inspect jobs and collate results data in order to count alignments
608 // then assemble results from decomposed (v followed by h-separated) jobs
609 // finally, new views and alignments will be created and displayed as
611 boolean hsepjobs = restClient.service.isHseparable();
612 boolean vsepjobs = restClient.service.isVseparable();
613 // total number of distinct alignment sets generated by job set.
614 int numAlSets = 0, als = 0;
615 List<AlignmentI> destAls = new ArrayList<AlignmentI>();
616 List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<jalview.datamodel.HiddenColumns>();
617 List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
622 // iterate over each alignment set returned from each subjob. Treating
623 // each one returned in parallel with others.
624 // Result collation arrays
627 * mapping between index of sequence in alignment that was submitted to
628 * server and index of sequence in the input alignment
630 int[][] ordermap = new int[jobs.length][];
631 SequenceI[][] rseqs = new SequenceI[jobs.length][];
632 AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
633 AlignmentAnnotation[][] alan = new AlignmentAnnotation[jobs.length][];
634 SequenceGroup[][] sgrp = new SequenceGroup[jobs.length][];
635 // Now collect all data for alignment Set als from job array
636 for (int j = 0; j < jobs.length; j++)
638 RestJob rj = (RestJob) jobs[j];
641 JalviewDataset rset = rj.context;
642 if (rset.hasAlignments())
644 if (numAlSets < rset.getAl().size())
646 numAlSets = rset.getAl().size();
648 if (als < rset.getAl().size()
649 && rset.getAl().get(als).isModified())
651 // Collate result data
652 // TODO: decide if all alignmentI should be collected rather than
653 // specific alignment data containers
654 // for moment, we just extract content, but this means any
655 // alignment properties may be lost.
656 AlignmentSet alset = rset.getAl().get(als);
657 alan[j] = alset.al.getAlignmentAnnotation();
658 if (alset.al.getGroups() != null)
660 sgrp[j] = new SequenceGroup[alset.al.getGroups().size()];
661 alset.al.getGroups().toArray(sgrp[j]);
667 orders[j] = new AlignmentOrder(alset.al);
668 rseqs[j] = alset.al.getSequencesArray();
669 ordermap[j] = rj.getOrderMap();
670 // if (rj.isInputUniquified()) {
671 // jalview.analysis.AlignmentSorter.recoverOrder(rseqs[als]);
674 if (alset.trees != null)
676 trees.add(new ArrayList<NewickFile>(alset.trees));
680 trees.add(new ArrayList<NewickFile>());
686 // Now aggregate and present results from this frame of alignment data.
687 int nvertsep = 0, nvertseps = 1;
690 // Jobs relate to different rows of input alignment.
691 // Jobs are subdivided by rows before columns,
692 // so there will now be a number of subjobs according tohsep for each
694 // TODO: get vertical separation intervals for each job and set
696 // TODO: merge data from each group/sequence onto whole
700 * index into rest jobs subdivided vertically
703 // Destination alignments for all result data.
704 ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>();
705 Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>();
706 ArrayList<AlignmentAnnotation> visAlAn = null;
707 for (nvertsep = 0; nvertsep < nvertseps; nvertsep++)
709 // TODO: set scope w.r.t. original alignment view for vertical
712 // results for a job exclude hidden columns of input data, so map
713 // back on to all visible regions
715 * rest job result we are working with
719 RestJob rj = (RestJob) jobs[nrj];
720 int contigs[] = input.getVisibleContigs();
721 AlignmentI destAl = null;
722 jalview.datamodel.HiddenColumns destHCs = null;
723 // Resolve destAl for this data.
724 if (als == 0 && rj.isInputContextModified())
726 // special case: transfer features, annotation, groups, etc,
728 // context to align panel derived from input data
729 if (destAls.size() > als)
731 destAl = destAls.get(als);
735 if (!restClient.isAlignmentModified() && merge)
737 destAl = restClient.av.getAlignment();
738 destHCs = restClient.av.getAlignment().getHiddenColumns();
740 .add(restClient.isShowResultsInNewView() ? AddDataTo.newView
741 : AddDataTo.currentView);
742 destPanels.add(restClient.recoverAlignPanelForView());
747 // recreate the input alignment data
748 Object[] idat = input
749 .getAlignmentAndHiddenColumns(gapCharacter);
750 destAl = new Alignment((SequenceI[]) idat[0]);
751 destHCs = (HiddenColumns) idat[1];
752 resultDest.add(AddDataTo.newAlignment);
753 // but do not add to the alignment panel list - since we need to
754 // create a whole new alignFrame set.
757 destColsel.add(destHCs);
762 // alignment(s) returned by service is to be re-integrated and
764 if (destAls.size() > als)
768 // TODO: decide if multiple multiple alignments returned by
769 // non-vseparable services are allowed.
771 .warn("dealing with multiple alignment products returned by non-vertically separable service.");
773 // recover reference to last alignment created for this rest frame
774 // ready for extension
775 destAl = destAls.get(als);
776 destHCs = destColsel.get(als);
784 // single alignment for any job that gets mapped back on to
785 // input data. Reconstruct by interleaving parts of returned
786 // alignment with hidden parts of input data.
787 SequenceI[][] nsq = splitSeqsOnVisibleContigs(rseqs[nrj],
788 contigs, gapCharacter);
789 AlignmentOrder alo[] = new AlignmentOrder[nsq.length];
790 for (int no = 0; no < alo.length; no++)
792 alo[no] = new AlignmentOrder(orders[nrj].getOrder());
794 newview = input.getUpdatedView(nsq, orders, gapCharacter);
798 // each job maps to a single visible contig, and all need to be
799 // stitched back together.
800 // reconstruct using sub-region based MSA alignment construction
802 newview = input.getUpdatedView(rseqs, orders, gapCharacter);
804 destAl = new Alignment((SequenceI[]) newview[0]);
805 destHCs = (HiddenColumns) newview[1];
807 // TODO create alignment from result data with propagated
810 destColsel.add(destHCs);
811 resultDest.add(AddDataTo.newAlignment);
814 .getString("error.implementation_error")
819 * save initial job in this set in case alignment is h-separable
823 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
827 // single alignment for any job that gets mapped back on to input
832 // each job maps to a single visible contig, and all need to be
833 // stitched back together.
838 // TODO: apply options for group merging and annotation merging.
839 // If merging not supported, then either clear hashtables now or
840 // use them to rename the new annotation/groups for each contig if
841 // a conflict occurs.
843 if (sgrp[nrj] != null)
845 for (SequenceGroup sg : sgrp[nrj])
847 boolean recovered = false;
848 SequenceGroup exsg = null;
849 if (sg.getName() != null)
851 exsg = groupNames.get(sg.getName());
855 exsg = new SequenceGroup(sg);
856 groupNames.put(exsg.getName(), exsg);
858 exsg.setStartRes(sg.getStartRes() + contigs[ncnt]);
859 exsg.setEndRes(sg.getEndRes() + contigs[ncnt]);
865 // now replace any references from the result set with
866 // corresponding refs from alignment input set.
868 // TODO: cope with recovering hidden sequences from
871 for (SequenceI oseq : sg.getSequences(null))
873 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
874 ordermap[nrj], destAl);
879 exsg.deleteSequence(oseq, false);
881 exsg.addSequence(nseq, false);
886 .warn("Couldn't resolve original sequence for new sequence.");
891 if (exsg.getSeqrep() == sg.getSeqrep())
893 // lift over sequence rep reference too
894 SequenceI oseq = sg.getSeqrep();
895 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
896 ordermap[nrj], destAl);
899 exsg.setSeqrep(nseq);
906 // adjust boundaries of recovered group w.r.t. new group being
907 // merged on to original alignment.
908 int start = sg.getStartRes() + contigs[ncnt], end = sg
909 .getEndRes() + contigs[ncnt];
910 if (start < exsg.getStartRes())
912 exsg.setStartRes(start);
914 if (end > exsg.getEndRes())
924 // and finally add in annotation and any trees for each job
925 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
929 // single alignment for any job that gets mapped back on to input
934 // each job maps to a single visible contig, and all need to be
935 // stitched back together.
942 // merge alignmentAnnotation into one row
943 if (alan[nrj] != null)
945 for (int an = 0; an < alan[nrj].length; an++)
947 SequenceI sqass = null;
948 SequenceGroup grass = null;
949 if (alan[nrj][an].sequenceRef != null)
951 // TODO: ensure this relocates sequence reference to local
953 sqass = getNewSeq(alan[nrj][an].sequenceRef, rseqs[nrj],
954 ordermap[nrj], destAl);
956 if (alan[nrj][an].groupRef != null)
958 // TODO: verify relocate group reference to local context
960 grass = groupNames.get(alan[nrj][an].groupRef.getName());
964 .error("Couldn't relocate group referemce for group "
965 + alan[nrj][an].groupRef.getName());
970 visAlAn = new ArrayList<AlignmentAnnotation>();
972 AlignmentAnnotation visan = null;
973 for (AlignmentAnnotation v : visAlAn)
976 && v.label.equals(alan[nrj][an].label))
983 visan = new AlignmentAnnotation(alan[nrj][an]);
984 // copy annotations, and wipe out/update refs.
985 visan.annotations = new Annotation[input.getWidth()];
986 visan.groupRef = grass;
987 visan.sequenceRef = sqass;
990 if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
992 // increase width of annotation row
993 Annotation[] newannv = new Annotation[contigs[ncnt]
994 + alan[nrj][an].annotations.length];
995 System.arraycopy(visan.annotations, 0, newannv, 0,
996 visan.annotations.length);
997 visan.annotations = newannv;
999 // now copy local annotation data into correct position
1000 System.arraycopy(alan[nrj][an].annotations, 0,
1001 visan.annotations, contigs[ncnt],
1002 alan[nrj][an].annotations.length);
1007 if (trees.get(nrj).size() > 0)
1009 for (NewickFile nf : trees.get(nrj))
1011 // TODO: process each newick file, lifting over sequence refs to
1012 // current alignment, if necessary.
1014 .error("Tree recovery from restjob not yet implemented.");
1019 } // end of vseps loops.
1020 if (visAlAn != null)
1022 for (AlignmentAnnotation v : visAlAn)
1024 destAls.get(als).addAnnotation(v);
1027 if (visgrps != null)
1029 for (SequenceGroup sg : visgrps)
1031 destAls.get(als).addGroup(sg);
1034 } while (++als < numAlSets);
1035 // Finally, assemble each new alignment, and create new gui components to
1038 * current AlignFrame where results will go.
1040 AlignFrame destaf = restClient.recoverAlignFrameForView();
1042 * current pane being worked with
1044 jalview.gui.AlignmentPanel destPanel = restClient
1045 .recoverAlignPanelForView();
1047 for (AddDataTo action : resultDest)
1050 HiddenColumns destcs;
1051 String alTitle = MessageManager.formatMessage(
1052 "label.webservice_job_title_on", new String[] {
1053 restClient.service.details.Action,
1054 restClient.service.details.Name, restClient.viewTitle });
1058 destal = destAls.get(als);
1059 destcs = destColsel.get(als);
1060 destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
1061 AlignFrame.DEFAULT_HEIGHT);
1062 PaintRefresher.Refresh(destaf, destaf.getViewport()
1063 .getSequenceSetId());
1064 // todo transfer any feature settings and colouring
1066 * destaf.getFeatureRenderer().transferSettings(this.featureSettings);
1067 * // update orders if (alorders.size() > 0) { if (alorders.size() == 1)
1068 * { af.addSortByOrderMenuItem(WebServiceName + " Ordering",
1069 * (AlignmentOrder) alorders.get(0)); } else { // construct a
1070 * non-redundant ordering set Vector names = new Vector(); for (int i =
1071 * 0, l = alorders.size(); i < l; i++) { String orderName = new
1072 * String(" Region " + i); int j = i + 1;
1074 * while (j < l) { if (((AlignmentOrder) alorders.get(i))
1075 * .equals(((AlignmentOrder) alorders.get(j)))) { alorders.remove(j);
1076 * l--; orderName += "," + j; } else { j++; } }
1078 * if (i == 0 && j == 1) { names.add(new String("")); } else {
1079 * names.add(orderName); } } for (int i = 0, l = alorders.size(); i < l;
1080 * i++) { af.addSortByOrderMenuItem( WebServiceName + ((String)
1081 * names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } }
1083 // TODO: modify this and previous alignment's title if many alignments
1084 // have been returned.
1085 Desktop.addInternalFrame(destaf, alTitle, AlignFrame.DEFAULT_WIDTH,
1086 AlignFrame.DEFAULT_HEIGHT);
1090 // TODO: determine title for view
1098 if (restClient.isShowResultsInNewView())
1100 // destPanel = destPanel.alignFrame.newView(false);
1108 * if (als) // add the destination panel to frame zero of result panel set }
1109 * } if (destPanels.size()==0) { AlignFrame af = new AlignFrame((AlignmentI)
1110 * idat[0], (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
1111 * AlignFrame.DEFAULT_HEIGHT);
1113 * jalview.gui.Desktop.addInternalFrame(af, "Results for " +
1114 * restClient.service.details.Name + " " + restClient.service.details.Action
1115 * + " on " + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH,
1116 * AlignFrame.DEFAULT_HEIGHT); destPanel = af.alignPanel; // create totally
1117 * new alignment from stashed data/results
1124 * alignments. New alignments are added to dataset, and subsequently
1125 * annotated/visualised accordingly. 1. New alignment frame created for new
1126 * alignment. Decide if any vis settings should be inherited from old
1127 * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
1128 * alignment as below:
1131 * annotation update to original/newly created context alignment: 1.
1132 * identify alignment where annotation is to be loaded onto. 2. Add
1133 * annotation, excluding any duplicates. 3. Ensure annotation is visible on
1134 * alignment - honouring ordering given by file.
1137 * features updated to original or newly created context alignment: 1.
1138 * Features are(or were already) added to dataset. 2. Feature settings
1139 * modified to ensure all features are displayed - honouring any ordering
1140 * given by result file. Consider merging action with the code used by the
1141 * DAS fetcher to update alignment views with new info.
1144 * Seq associated data files (PDB files). 1. locate seq association in
1145 * current dataset/alignment context and add file as normal - keep handle of
1146 * any created ref objects. 2. decide if new data should be displayed : PDB
1147 * display: if alignment has PDB display already, should new pdb files be
1151 // destPanel.adjustAnnotationHeight();
1156 * split the given array of sequences into blocks of subsequences
1157 * corresponding to each visible contig
1162 * padding character for ragged ends of visible contig region.
1165 private SequenceI[][] splitSeqsOnVisibleContigs(SequenceI[] sequenceIs,
1166 int[] contigs, char gapChar)
1168 int nvc = contigs == null ? 1 : contigs.length / 2;
1169 SequenceI[][] blocks = new SequenceI[nvc][];
1170 if (contigs == null)
1172 blocks[0] = new SequenceI[sequenceIs.length];
1173 System.arraycopy(sequenceIs, 0, blocks[0], 0, sequenceIs.length);
1177 // deja vu - have I written this before ?? propagateGaps does this in a
1179 char[] gapset = null;
1180 int start = 0, width = 0;
1181 for (int c = 0; c < nvc; c++)
1183 width = contigs[c * 2 + 1] - contigs[c * 2] + 1;
1184 for (int s = 0; s < sequenceIs.length; s++)
1186 int end = sequenceIs[s].getLength();
1189 if (start + width < end)
1191 blocks[c][s] = sequenceIs[s].getSubSequence(start, start
1196 blocks[c][s] = sequenceIs[s].getSubSequence(start, end);
1197 String sq = blocks[c][s].getSequenceAsString();
1198 for (int n = start + width; n > end; n--)
1206 if (gapset == null || gapset.length < width)
1208 char ng[] = new char[width];
1212 System.arraycopy(gapset, 0, ng, 0, gs = gapset.length);
1214 while (gs < ng.length)
1219 blocks[c][s] = sequenceIs[s].getSubSequence(end, end);
1220 blocks[c][s].setSequence(gapset.toString().substring(0, width));
1225 // adjust window for next visible segnment
1226 start += contigs[c * 2 + 1] - contigs[c * 2];
1234 * recover corresponding sequence from original input data corresponding to
1235 * sequence in a specific job's input data.
1243 private SequenceI getNewSeq(SequenceI oseq, SequenceI[] sequenceIs,
1244 int[] is, AlignmentI destAl)
1247 while (p < sequenceIs.length && sequenceIs[p] != oseq)
1251 if (p < sequenceIs.length && p < destAl.getHeight())
1253 return destAl.getSequenceAt(is[p]);
1260 * @return true if the run method is safe to call
1262 public boolean isValid()
1264 ArrayList<String> _warnings = new ArrayList<String>();
1265 boolean validt = true;
1268 for (RestJob rj : (RestJob[]) jobs)
1270 if (!rj.hasValidInput())
1272 // invalid input for this job
1273 System.err.println("Job " + rj.getJobnum()
1274 + " has invalid input. ( " + rj.getStatus() + ")");
1275 if (rj.hasStatus() && !_warnings.contains(rj.getStatus()))
1277 _warnings.add(rj.getStatus());
1286 for (String st : _warnings)
1288 if (warnings.length() > 0)
1299 protected String warnings;
1301 public boolean hasWarnings()
1303 // TODO Auto-generated method stub
1304 return warnings != null && warnings.length() > 0;
1308 * get any informative messages about why the job thread couldn't start.
1312 public String getWarnings()
1314 return isValid() ? "Job can be started. No warnings."
1315 : hasWarnings() ? warnings : "";