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.ColumnSelection;
30 import jalview.datamodel.SequenceGroup;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.AlignFrame;
33 import jalview.gui.AlignmentPanel;
34 import jalview.gui.Desktop;
35 import jalview.gui.PaintRefresher;
36 import jalview.gui.WebserviceInfo;
37 import jalview.io.NewickFile;
38 import jalview.io.packed.JalviewDataset;
39 import jalview.io.packed.JalviewDataset.AlignmentSet;
40 import jalview.util.MessageManager;
41 import jalview.ws.AWSThread;
42 import jalview.ws.AWsJob;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.io.IOException;
47 import java.util.ArrayList;
48 import java.util.Hashtable;
49 import java.util.List;
50 import java.util.Map.Entry;
52 import org.apache.axis.transport.http.HTTPConstants;
53 import org.apache.http.Header;
54 import org.apache.http.HttpEntity;
55 import org.apache.http.HttpResponse;
56 import org.apache.http.client.ClientProtocolException;
57 import org.apache.http.client.methods.HttpGet;
58 import org.apache.http.client.methods.HttpPost;
59 import org.apache.http.client.methods.HttpRequestBase;
60 import org.apache.http.entity.mime.HttpMultipartMode;
61 import org.apache.http.entity.mime.MultipartEntity;
62 import org.apache.http.impl.client.DefaultHttpClient;
63 import org.apache.http.protocol.BasicHttpContext;
64 import org.apache.http.protocol.HttpContext;
65 import org.apache.http.util.EntityUtils;
67 public class RestJobThread extends AWSThread
74 protected RestClient restClient;
76 public RestJobThread(RestClient restClient)
78 super(restClient.af, null, restClient._input,
79 restClient.service.postUrl);
80 this.restClient = restClient; // may not be needed
82 // minimal job - submit given input and parse result onto alignment as
83 // annotation/whatever
85 // look for tree data, etc.
87 // for moment do following job type only
88 // input=visiblealignment,groupsindex
89 // ie one subjob using groups defined on alignment.
90 if (!restClient.service.isHseparable())
92 jobs = new RestJob[1];
93 jobs[0] = new RestJob(0, this,
94 restClient._input.getVisibleAlignment(restClient.service
96 restClient._input.getVisibleContigs());
97 // need a function to get a range on a view/alignment and return both
98 // annotation, groups and selection subsetted to just that region.
103 int[] viscontig = restClient._input.getVisibleContigs();
104 AlignmentI[] viscontigals = restClient._input
105 .getVisibleContigAlignments(restClient.service
107 if (viscontigals != null && viscontigals.length > 0)
109 jobs = new RestJob[viscontigals.length];
110 for (int j = 0; j < jobs.length; j++)
112 int[] visc = new int[]
113 { 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(), input.getValue()
239 .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 Cache.log.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 Cache.log.warn("IO Exception for REST Job " + getStage(stg)
281 + "exception for URL " + rj.rsd.postUrl);
285 switch (response.getStatusLine().getStatusCode())
289 Cache.log.debug("Processing result set.");
290 processResultSet(rj, response, request);
293 rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
303 if (!rj.isSubmitted()
305 .getHeaders(HTTPConstants.HEADER_LOCATION)) != null
311 .warn("Ignoring additional "
313 + " location(s) provided in response header ( next one is '"
314 + loc[1].getValue() + "' )");
316 rj.setJobId(loc[0].getValue());
317 rj.setSubmitted(true);
319 completeStatus(rj, response);
323 rj.setSubmitted(true);
324 rj.setAllowedServerExceptions(0);
325 rj.setSubjobComplete(true);
328 completeStatus(rj, response, "" + getStage(stg)
329 + "failed. Reason below:\n");
332 // Some other response. Probably need to pop up the content in a window.
333 // TODO: deal with all other HTTP response codes from server.
334 Cache.log.warn("Unhandled response status when " + getStage(stg)
335 + "for " + postUrl + ": " + response.getStatusLine());
337 rj.setAllowedServerExceptions(0);
338 rj.setSubjobComplete(true);
339 rj.setSubmitted(true);
347 + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
351 + "</a><br/>Filtered response content below:<br/>");
352 } catch (IOException e)
354 Cache.log.debug("IOException when consuming unhandled response",
363 * job has completed. Something valid should be available from con
368 * is a stateless request - expected to return the same data
369 * regardless of how many times its called.
371 private void processResultSet(RestJob rj, HttpResponse con,
374 if (rj.statMessage == null)
378 rj.statMessage += "Job Complete.\n";
381 rj.resSet = new HttpResultSet(rj, con, req);
383 } catch (IOException e)
385 rj.statMessage += "Couldn't parse results. Failed.";
387 rj.gotresult = false;
391 private void completeStatus(RestJob rj, HttpResponse con)
394 completeStatus(rj, con, null);
398 private void completeStatus(RestJob rj, HttpResponse con, String prefix)
401 StringBuffer sb = new StringBuffer();
407 if (rj.statMessage != null && rj.statMessage.length() > 0)
409 sb.append(rj.statMessage);
411 HttpEntity en = con.getEntity();
413 * Just append the content as a string.
416 StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
418 int body = f.indexOf("<body");
421 content.delete(0, f.indexOf(">", body) + 1);
423 if (body > -1 && sb.length() > 0)
426 content.insert(0, sb);
430 rj.statMessage = content.toString();
434 public void pollJob(AWsJob job) throws Exception
436 assert (job instanceof RestJob);
437 System.err.println("Debug RestJob: Polling Job");
438 doPoll((RestJob) job);
442 public void StartJob(AWsJob job)
444 assert (job instanceof RestJob);
447 System.err.println("Debug RestJob: Posting Job");
448 doPost((RestJob) job);
449 } catch (NoValidInputDataException erex)
451 job.setSubjobComplete(true);
452 job.setSubmitted(true);
453 ((RestJob) job).statMessage = "<br>It looks like there was a problem with the data sent to the service :<br>"
454 + erex.getMessage() + "\n";
455 ((RestJob) job).error = true;
457 } catch (Exception ex)
459 job.setSubjobComplete(true);
460 job.setAllowedServerExceptions(-1);
461 Cache.log.error("Exception when trying to start Rest Job.", ex);
466 public void parseResult()
468 // crazy users will see this message
469 // TODO: finish this! and remove the message below!
470 Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
472 for (RestJob rj : (RestJob[]) jobs)
474 if (rj.hasResponse() && rj.resSet != null && rj.resSet.isValid())
479 Cache.log.debug("Parsing data for job " + rj.getJobId());
485 Cache.log.debug("Finished parsing data for job " + rj.getJobId());
489 Cache.log.warn("Failed to finish parsing data for job "
491 ex.printStackTrace();
492 } catch (Exception ex)
494 Cache.log.warn("Failed to finish parsing data for job "
496 ex.printStackTrace();
500 rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
510 // add listeners and activate result display gui elements
512 * decisions based on job result content + state of alignFrame that
513 * originated the job:
516 * 1. Can/Should this job automatically open a new window for results
520 // preserver current jalview behaviour
521 wsInfo.setViewResultsImmediatly(true);
525 // realiseResults(true, true);
527 // otherwise, should automatically view results
529 // TODO: check if at least one or more contexts are valid - if so, enable
531 wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
535 public void actionPerformed(ActionEvent e)
537 realiseResults(false);
541 wsInfo.mergeResults.addActionListener(new ActionListener()
545 public void actionPerformed(ActionEvent e)
547 realiseResults(true);
552 wsInfo.setResultsReady();
556 // tell the user nothing was returned.
557 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
558 wsInfo.setFinishedNoResults();
563 * instructions for whether to create new alignment view on current alignment
564 * set, add to current set, or create new alignFrame
566 private enum AddDataTo
569 * add annotation, trees etc to current view
573 * create a new view derived from current view and add data to that
577 * create a new alignment frame for the result set and add annotation to
583 public void realiseResults(boolean merge)
586 * 2. Should the job modify the parent alignment frame/view(s) (if they
587 * still exist and the alignment hasn't been edited) in order to display new
588 * annotation/features.
591 * alignment panels derived from each alignment set returned by service.
593 ArrayList<AlignmentPanel> destPanels = new ArrayList<AlignmentPanel>();
595 * list of instructions for how to process each distinct alignment set
596 * returned by the job set
598 ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>();
600 * when false, zeroth pane is panel derived from input deta.
602 boolean newAlignment = false;
604 * gap character to be used for alignment reconstruction
606 char gapCharacter = restClient.av.getGapCharacter();
607 // Now, iterate over all alignment sets returned from all jobs:
608 // first inspect jobs and collate results data in order to count alignments
610 // then assemble results from decomposed (v followed by h-separated) jobs
611 // finally, new views and alignments will be created and displayed as
613 boolean hsepjobs = restClient.service.isHseparable();
614 boolean vsepjobs = restClient.service.isVseparable();
615 // total number of distinct alignment sets generated by job set.
616 int numAlSets = 0, als = 0;
617 List<AlignmentI> destAls = new ArrayList<AlignmentI>();
618 List<ColumnSelection> destColsel = new ArrayList<ColumnSelection>();
619 List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
624 // iterate over each alignment set returned from each subjob. Treating
625 // each one returned in parallel with others.
626 // Result collation arrays
629 * mapping between index of sequence in alignment that was submitted to
630 * server and index of sequence in the input alignment
632 int[][] ordermap = new int[jobs.length][];
633 SequenceI[][] rseqs = new SequenceI[jobs.length][];
634 AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
635 AlignmentAnnotation[][] alan = new AlignmentAnnotation[jobs.length][];
636 SequenceGroup[][] sgrp = new SequenceGroup[jobs.length][];
637 // Now collect all data for alignment Set als from job array
638 for (int j = 0; j < jobs.length; j++)
640 RestJob rj = (RestJob) jobs[j];
643 JalviewDataset rset = rj.context;
644 if (rset.hasAlignments())
646 if (numAlSets < rset.getAl().size())
648 numAlSets = rset.getAl().size();
650 if (als < rset.getAl().size()
651 && rset.getAl().get(als).isModified())
653 // Collate result data
654 // TODO: decide if all alignmentI should be collected rather than
655 // specific alignment data containers
656 // for moment, we just extract content, but this means any
657 // alignment properties may be lost.
658 AlignmentSet alset = rset.getAl().get(als);
659 alan[j] = alset.al.getAlignmentAnnotation();
660 if (alset.al.getGroups() != null)
662 sgrp[j] = new SequenceGroup[alset.al.getGroups().size()];
663 alset.al.getGroups().toArray(sgrp[j]);
669 orders[j] = new AlignmentOrder(alset.al);
670 rseqs[j] = alset.al.getSequencesArray();
671 ordermap[j] = rj.getOrderMap();
672 // if (rj.isInputUniquified()) {
673 // jalview.analysis.AlignmentSorter.recoverOrder(rseqs[als]);
676 if (alset.trees != null)
678 trees.add(new ArrayList<NewickFile>(alset.trees));
682 trees.add(new ArrayList<NewickFile>());
688 // Now aggregate and present results from this frame of alignment data.
689 int nvertsep = 0, nvertseps = 1;
692 // Jobs relate to different rows of input alignment.
693 // Jobs are subdivided by rows before columns,
694 // so there will now be a number of subjobs according tohsep for each
696 // TODO: get vertical separation intervals for each job and set
698 // TODO: merge data from each group/sequence onto whole
702 * index into rest jobs subdivided vertically
705 // Destination alignments for all result data.
706 ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>();
707 Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>();
708 ArrayList<AlignmentAnnotation> visAlAn = null;
709 for (nvertsep = 0; nvertsep < nvertseps; nvertsep++)
711 // TODO: set scope w.r.t. original alignment view for vertical
714 // results for a job exclude hidden columns of input data, so map
715 // back on to all visible regions
717 * rest job result we are working with
721 RestJob rj = (RestJob) jobs[nrj];
722 int contigs[] = input.getVisibleContigs();
723 AlignmentI destAl = null;
724 ColumnSelection destCs = null;
725 // Resolve destAl for this data.
726 if (als == 0 && rj.isInputContextModified())
728 // special case: transfer features, annotation, groups, etc,
730 // context to align panel derived from input data
731 if (destAls.size() > als)
733 destAl = destAls.get(als);
737 if (!restClient.isAlignmentModified() && merge)
739 destAl = restClient.av.getAlignment();
740 destCs = restClient.av.getColumnSelection();
742 .add(restClient.isShowResultsInNewView() ? AddDataTo.newView
743 : AddDataTo.currentView);
744 destPanels.add(restClient.recoverAlignPanelForView());
749 // recreate the input alignment data
750 Object[] idat = input
751 .getAlignmentAndColumnSelection(gapCharacter);
752 destAl = new Alignment((SequenceI[]) idat[0]);
753 destCs = (ColumnSelection) idat[1];
754 resultDest.add(AddDataTo.newAlignment);
755 // but do not add to the alignment panel list - since we need to
756 // create a whole new alignFrame set.
759 destColsel.add(destCs);
764 // alignment(s) returned by service is to be re-integrated and
766 if (destAls.size() > als)
770 // TODO: decide if multiple multiple alignments returned by
771 // non-vseparable services are allowed.
773 .warn("dealing with multiple alignment products returned by non-vertically separable service.");
775 // recover reference to last alignment created for this rest frame
776 // ready for extension
777 destAl = destAls.get(als);
778 destCs = destColsel.get(als);
786 // single alignment for any job that gets mapped back on to
787 // input data. Reconstruct by interleaving parts of returned
788 // alignment with hidden parts of input data.
789 SequenceI[][] nsq = splitSeqsOnVisibleContigs(rseqs[nrj],
790 contigs, gapCharacter);
791 AlignmentOrder alo[] = new AlignmentOrder[nsq.length];
792 for (int no = 0; no < alo.length; no++)
794 alo[no] = new AlignmentOrder(orders[nrj].getOrder());
796 newview = input.getUpdatedView(nsq, orders, gapCharacter);
800 // each job maps to a single visible contig, and all need to be
801 // stitched back together.
802 // reconstruct using sub-region based MSA alignment construction
804 newview = input.getUpdatedView(rseqs, orders, gapCharacter);
806 destAl = new Alignment((SequenceI[]) newview[0]);
807 destCs = (ColumnSelection) newview[1];
809 // TODO create alignment from result data with propagated
812 destColsel.add(destCs);
813 resultDest.add(AddDataTo.newAlignment);
814 throw new Error(MessageManager.getString("error.implementation_error")+"TODO: ");
818 * save initial job in this set in case alignment is h-separable
822 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
826 // single alignment for any job that gets mapped back on to input
831 // each job maps to a single visible contig, and all need to be
832 // stitched back together.
837 // TODO: apply options for group merging and annotation merging.
838 // If merging not supported, then either clear hashtables now or
839 // use them to rename the new annotation/groups for each contig if
840 // a conflict occurs.
842 if (sgrp[nrj] != null)
844 for (SequenceGroup sg : sgrp[nrj])
846 boolean recovered = false;
847 SequenceGroup exsg = null;
848 if (sg.getName() != null)
850 exsg = groupNames.get(sg.getName());
854 exsg = new SequenceGroup(sg);
855 groupNames.put(exsg.getName(), exsg);
857 exsg.setStartRes(sg.getStartRes() + contigs[ncnt]);
858 exsg.setEndRes(sg.getEndRes() + contigs[ncnt]);
864 // now replace any references from the result set with
865 // corresponding refs from alignment input set.
867 // TODO: cope with recovering hidden sequences from
870 for (SequenceI oseq : sg.getSequences(null))
872 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
873 ordermap[nrj], destAl);
878 exsg.deleteSequence(oseq, false);
880 exsg.addSequence(nseq, false);
885 .warn("Couldn't resolve original sequence for new sequence.");
890 if (exsg.getSeqrep() == sg.getSeqrep())
892 // lift over sequence rep reference too
893 SequenceI oseq = sg.getSeqrep();
894 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
895 ordermap[nrj], destAl);
898 exsg.setSeqrep(nseq);
905 // adjust boundaries of recovered group w.r.t. new group being
906 // merged on to original alignment.
907 int start = sg.getStartRes() + contigs[ncnt], end = sg
908 .getEndRes() + contigs[ncnt];
909 if (start < exsg.getStartRes())
911 exsg.setStartRes(start);
913 if (end > exsg.getEndRes())
923 // and finally add in annotation and any trees for each job
924 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
928 // single alignment for any job that gets mapped back on to input
933 // each job maps to a single visible contig, and all need to be
934 // stitched back together.
941 // merge alignmentAnnotation into one row
942 if (alan[nrj] != null)
944 for (int an = 0; an < alan[nrj].length; an++)
946 SequenceI sqass = null;
947 SequenceGroup grass = null;
948 if (alan[nrj][an].sequenceRef != null)
950 // TODO: ensure this relocates sequence reference to local
952 sqass = getNewSeq(alan[nrj][an].sequenceRef, rseqs[nrj],
953 ordermap[nrj], destAl);
955 if (alan[nrj][an].groupRef != null)
957 // TODO: verify relocate group reference to local context
959 grass = groupNames.get(alan[nrj][an].groupRef.getName());
963 .error("Couldn't relocate group referemce for group "
964 + alan[nrj][an].groupRef.getName());
969 visAlAn = new ArrayList<AlignmentAnnotation>();
971 AlignmentAnnotation visan = null;
972 for (AlignmentAnnotation v : visAlAn)
975 && v.label.equals(alan[nrj][an].label))
982 visan = new AlignmentAnnotation(alan[nrj][an]);
983 // copy annotations, and wipe out/update refs.
984 visan.annotations = new Annotation[input.getWidth()];
985 visan.groupRef = grass;
986 visan.sequenceRef = sqass;
989 if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
991 // increase width of annotation row
992 Annotation[] newannv = new Annotation[contigs[ncnt]
993 + alan[nrj][an].annotations.length];
994 System.arraycopy(visan.annotations, 0, newannv, 0,
995 visan.annotations.length);
996 visan.annotations = newannv;
998 // now copy local annotation data into correct position
999 System.arraycopy(alan[nrj][an].annotations, 0,
1000 visan.annotations, contigs[ncnt],
1001 alan[nrj][an].annotations.length);
1006 if (trees.get(nrj).size() > 0)
1008 for (NewickFile nf : trees.get(nrj))
1010 // TODO: process each newick file, lifting over sequence refs to
1011 // current alignment, if necessary.
1013 .error("Tree recovery from restjob not yet implemented.");
1018 } // end of vseps loops.
1019 if (visAlAn != null)
1021 for (AlignmentAnnotation v : visAlAn)
1023 destAls.get(als).addAnnotation(v);
1026 if (visgrps != null)
1028 for (SequenceGroup sg : visgrps)
1030 destAls.get(als).addGroup(sg);
1033 } while (++als < numAlSets);
1034 // Finally, assemble each new alignment, and create new gui components to
1037 * current AlignFrame where results will go.
1039 AlignFrame destaf = restClient.recoverAlignFrameForView();
1041 * current pane being worked with
1043 AlignmentPanel destPanel = restClient.recoverAlignPanelForView();
1045 for (AddDataTo action : resultDest)
1048 ColumnSelection destcs;
1049 String alTitle = MessageManager.formatMessage("label.webservice_job_title_on", new String[]{restClient.service.details.Action,restClient.service.details.Name,restClient.viewTitle});
1053 destal = destAls.get(als);
1054 destcs = destColsel.get(als);
1055 destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
1056 AlignFrame.DEFAULT_HEIGHT);
1057 PaintRefresher.Refresh(destaf, destaf.getViewport()
1058 .getSequenceSetId());
1059 // todo transfer any feature settings and colouring
1061 * destaf.getFeatureRenderer().transferSettings(this.featureSettings);
1062 * // update orders if (alorders.size() > 0) { if (alorders.size() == 1)
1063 * { af.addSortByOrderMenuItem(WebServiceName + " Ordering",
1064 * (AlignmentOrder) alorders.get(0)); } else { // construct a
1065 * non-redundant ordering set Vector names = new Vector(); for (int i =
1066 * 0, l = alorders.size(); i < l; i++) { String orderName = new
1067 * String(" Region " + i); int j = i + 1;
1069 * while (j < l) { if (((AlignmentOrder) alorders.get(i))
1070 * .equals(((AlignmentOrder) alorders.get(j)))) { alorders.remove(j);
1071 * l--; orderName += "," + j; } else { j++; } }
1073 * if (i == 0 && j == 1) { names.add(new String("")); } else {
1074 * names.add(orderName); } } for (int i = 0, l = alorders.size(); i < l;
1075 * i++) { af.addSortByOrderMenuItem( WebServiceName + ((String)
1076 * names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } }
1078 // TODO: modify this and previous alignment's title if many alignments
1079 // have been returned.
1080 Desktop.addInternalFrame(destaf, alTitle, AlignFrame.DEFAULT_WIDTH,
1081 AlignFrame.DEFAULT_HEIGHT);
1085 // TODO: determine title for view
1093 if (restClient.isShowResultsInNewView())
1095 // destPanel = destPanel.alignFrame.newView(false);
1103 * if (als) // add the destination panel to frame zero of result panel set }
1104 * } if (destPanels.size()==0) { AlignFrame af = new AlignFrame((AlignmentI)
1105 * idat[0], (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
1106 * AlignFrame.DEFAULT_HEIGHT);
1108 * jalview.gui.Desktop.addInternalFrame(af, "Results for " +
1109 * restClient.service.details.Name + " " + restClient.service.details.Action
1110 * + " on " + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH,
1111 * AlignFrame.DEFAULT_HEIGHT); destPanel = af.alignPanel; // create totally
1112 * new alignment from stashed data/results
1119 * alignments. New alignments are added to dataset, and subsequently
1120 * annotated/visualised accordingly. 1. New alignment frame created for new
1121 * alignment. Decide if any vis settings should be inherited from old
1122 * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
1123 * alignment as below:
1126 * annotation update to original/newly created context alignment: 1.
1127 * identify alignment where annotation is to be loaded onto. 2. Add
1128 * annotation, excluding any duplicates. 3. Ensure annotation is visible on
1129 * alignment - honouring ordering given by file.
1132 * features updated to original or newly created context alignment: 1.
1133 * Features are(or were already) added to dataset. 2. Feature settings
1134 * modified to ensure all features are displayed - honouring any ordering
1135 * given by result file. Consider merging action with the code used by the
1136 * DAS fetcher to update alignment views with new info.
1139 * Seq associated data files (PDB files). 1. locate seq association in
1140 * current dataset/alignment context and add file as normal - keep handle of
1141 * any created ref objects. 2. decide if new data should be displayed : PDB
1142 * display: if alignment has PDB display already, should new pdb files be
1146 // destPanel.adjustAnnotationHeight();
1151 * split the given array of sequences into blocks of subsequences
1152 * corresponding to each visible contig
1157 * padding character for ragged ends of visible contig region.
1160 private SequenceI[][] splitSeqsOnVisibleContigs(SequenceI[] sequenceIs,
1161 int[] contigs, char gapChar)
1163 int nvc = contigs == null ? 1 : contigs.length / 2;
1164 SequenceI[][] blocks = new SequenceI[nvc][];
1165 if (contigs == null)
1167 blocks[0] = new SequenceI[sequenceIs.length];
1168 System.arraycopy(sequenceIs, 0, blocks[0], 0, sequenceIs.length);
1172 // deja vu - have I written this before ?? propagateGaps does this in a
1174 char[] gapset = null;
1175 int start = 0, width = 0;
1176 for (int c = 0; c < nvc; c++)
1178 width = contigs[c * 2 + 1] - contigs[c * 2] + 1;
1179 for (int s = 0; s < sequenceIs.length; s++)
1181 int end = sequenceIs[s].getLength();
1184 if (start + width < end)
1186 blocks[c][s] = sequenceIs[s].getSubSequence(start, start
1191 blocks[c][s] = sequenceIs[s].getSubSequence(start, end);
1192 String sq = blocks[c][s].getSequenceAsString();
1193 for (int n = start + width; n > end; n--)
1201 if (gapset == null || gapset.length < width)
1203 char ng[] = new char[width];
1207 System.arraycopy(gapset, 0, ng, 0, gs = gapset.length);
1209 while (gs < ng.length)
1214 blocks[c][s] = sequenceIs[s].getSubSequence(end, end);
1215 blocks[c][s].setSequence(gapset.toString().substring(0, width));
1220 // adjust window for next visible segnment
1221 start += contigs[c * 2 + 1] - contigs[c * 2];
1229 * recover corresponding sequence from original input data corresponding to
1230 * sequence in a specific job's input data.
1238 private SequenceI getNewSeq(SequenceI oseq, SequenceI[] sequenceIs,
1239 int[] is, AlignmentI destAl)
1242 while (p < sequenceIs.length && sequenceIs[p] != oseq)
1246 if (p < sequenceIs.length && p < destAl.getHeight())
1248 return destAl.getSequenceAt(is[p]);
1255 * @return true if the run method is safe to call
1257 public boolean isValid()
1259 ArrayList<String> _warnings = new ArrayList<String>();
1260 boolean validt = true;
1263 for (RestJob rj : (RestJob[]) jobs)
1265 if (!rj.hasValidInput())
1267 // invalid input for this job
1268 System.err.println("Job " + rj.getJobnum()
1269 + " has invalid input. ( " + rj.getStatus() + ")");
1270 if (rj.hasStatus() && !_warnings.contains(rj.getStatus()))
1272 _warnings.add(rj.getStatus());
1281 for (String st : _warnings)
1283 if (warnings.length() > 0)
1294 protected String warnings;
1296 public boolean hasWarnings()
1298 // TODO Auto-generated method stub
1299 return warnings != null && warnings.length() > 0;
1303 * get any informative messages about why the job thread couldn't start.
1307 public String getWarnings()
1309 return isValid() ? "Job can be started. No warnings."
1310 : hasWarnings() ? warnings : "";