2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.ws.rest;
20 import jalview.bin.Cache;
21 import jalview.datamodel.Alignment;
22 import jalview.datamodel.AlignmentAnnotation;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.AlignmentOrder;
25 import jalview.datamodel.Annotation;
26 import jalview.datamodel.ColumnSelection;
27 import jalview.datamodel.SequenceGroup;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.AlignFrame;
30 import jalview.gui.Desktop;
31 import jalview.gui.PaintRefresher;
32 import jalview.gui.WebserviceInfo;
33 import jalview.io.NewickFile;
34 import jalview.io.packed.JalviewDataset;
35 import jalview.io.packed.JalviewDataset.AlignmentSet;
36 import jalview.ws.AWSThread;
37 import jalview.ws.AWsJob;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.io.IOException;
42 import java.util.ArrayList;
43 import java.util.Hashtable;
44 import java.util.List;
45 import java.util.Map.Entry;
47 import org.apache.axis.transport.http.HTTPConstants;
48 import org.apache.http.Header;
49 import org.apache.http.HttpEntity;
50 import org.apache.http.HttpResponse;
51 import org.apache.http.client.ClientProtocolException;
52 import org.apache.http.client.methods.HttpGet;
53 import org.apache.http.client.methods.HttpPost;
54 import org.apache.http.client.methods.HttpRequestBase;
55 import org.apache.http.entity.mime.HttpMultipartMode;
56 import org.apache.http.entity.mime.MultipartEntity;
57 import org.apache.http.impl.client.DefaultHttpClient;
58 import org.apache.http.protocol.BasicHttpContext;
59 import org.apache.http.protocol.HttpContext;
60 import org.apache.http.util.EntityUtils;
62 public class RestJobThread extends AWSThread
69 protected RestClient restClient;
71 public RestJobThread(RestClient restClient)
73 super(restClient.af, null, restClient._input,
74 restClient.service.postUrl);
75 this.restClient = restClient; // may not be needed
77 // minimal job - submit given input and parse result onto alignment as
78 // annotation/whatever
80 // look for tree data, etc.
82 // for moment do following job type only
83 // input=visiblealignment,groupsindex
84 // ie one subjob using groups defined on alignment.
85 if (!restClient.service.isHseparable())
87 jobs = new RestJob[1];
88 jobs[0] = new RestJob(0, this,
89 restClient._input.getVisibleAlignment(restClient.service
91 restClient._input.getVisibleContigs());
92 // need a function to get a range on a view/alignment and return both
93 // annotation, groups and selection subsetted to just that region.
98 int[] viscontig = restClient._input.getVisibleContigs();
99 AlignmentI[] viscontigals = restClient._input
100 .getVisibleContigAlignments(restClient.service
102 if (viscontigals != null && viscontigals.length > 0)
104 jobs = new RestJob[viscontigals.length];
105 for (int j = 0; j < jobs.length; j++)
107 int[] visc = new int[]
108 { viscontig[j * 2], viscontig[j * 2 + 1] };
111 jobs[j] = new RestJob(j, this, viscontigals[j], visc);
115 jobs[j] = new RestJob(0, this, viscontigals[j], visc);
122 * subjob types row based: per sequence in alignment/selected region { input
123 * is one sequence or sequence ID } per alignment/selected region { input is
124 * set of sequences, alignment, one or more sets of sequence IDs,
127 if (!restClient.service.isHseparable())
130 // create a bunch of subjobs per visible contig to ensure result honours
132 // TODO: determine if a 'soft' hSeperable property is needed - e.g. if
133 // user does SS-pred on sequence with big hidden regions, its going to be
138 // create a single subjob for the visible/selected input
141 // TODO: decide if vSeperable exists: eg. column wide analysis where hidden
142 // rows do not affect output - generally no analysis that generates
143 // alignment annotation is vSeparable -
147 * create gui components for monitoring jobs
149 * @param webserviceInfo
151 public void setWebServiceInfo(WebserviceInfo webserviceInfo)
153 wsInfo = webserviceInfo;
154 for (int j = 0; j < jobs.length; j++)
157 // Copy over any per job params
160 wsInfo.setProgressName("region " + jobs[j].getJobnum(),
161 jobs[j].getJobnum());
165 wsInfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
170 private String getStage(Stage stg)
172 if (stg == Stage.SUBMIT)
173 return "submitting ";
174 if (stg == Stage.POLL)
175 return "checking status of ";
177 return (" being confused about ");
180 private void doPoll(RestJob rj) throws Exception
182 String postUrl = rj.getPollUrl();
183 doHttpReq(Stage.POLL, rj, postUrl);
187 * construct the post and handle the response.
191 public void doPost(RestJob rj) throws Exception
193 String postUrl = rj.getPostUrl();
194 doHttpReq(Stage.SUBMIT, rj, postUrl);
199 * do the HTTP request - and respond/set statuses appropriate to the current
204 * - provides any data needed for posting and used to record state
206 * - actual URL to post/get from
209 protected void doHttpReq(Stage stg, RestJob rj, String postUrl)
212 StringBuffer respText = new StringBuffer();
213 // con.setContentHandlerFactory(new
214 // jalview.ws.io.mime.HttpContentHandler());
215 HttpRequestBase request = null;
216 String messages = "";
217 if (stg == Stage.SUBMIT)
220 // http://evgenyg.wordpress.com/2010/05/01/uploading-files-multipart-post-apache/
222 HttpPost htpost = new HttpPost(postUrl);
223 MultipartEntity postentity = new MultipartEntity(
224 HttpMultipartMode.STRICT);
225 for (Entry<String, InputType> input : rj.getInputParams())
227 if (input.getValue().validFor(rj))
229 postentity.addPart(input.getKey(), input.getValue()
230 .formatForInput(rj));
234 messages += "Skipped an input (" + input.getKey()
235 + ") - Couldn't generate it from available data.";
238 htpost.setEntity(postentity);
243 request = new HttpGet(postUrl);
247 DefaultHttpClient httpclient = new DefaultHttpClient();
249 HttpContext localContext = new BasicHttpContext();
250 HttpResponse response = null;
253 response = httpclient.execute(request);
254 } catch (ClientProtocolException he)
256 rj.statMessage = "Web Protocol Exception when " + getStage(stg)
257 + "Job. <br>Problematic url was <a href=\""
258 + request.getURI() + "\">" + request.getURI()
259 + "</a><br>See Console output for details.";
260 rj.setAllowedServerExceptions(0);// unrecoverable;
262 Cache.log.fatal("Unexpected REST Job " + getStage(stg)
263 + "exception for URL " + rj.rsd.postUrl);
265 } catch (IOException e)
267 rj.statMessage = "IO Exception when " + getStage(stg)
268 + "Job. <br>Problematic url was <a href=\""
269 + request.getURI() + "\">" + request.getURI()
270 + "</a><br>See Console output for details.";
271 Cache.log.warn("IO Exception for REST Job " + getStage(stg)
272 + "exception for URL " + rj.rsd.postUrl);
276 switch (response.getStatusLine().getStatusCode())
280 Cache.log.debug("Processing result set.");
281 processResultSet(rj, response, request);
284 rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
294 if (!rj.isSubmitted()
296 .getHeaders(HTTPConstants.HEADER_LOCATION)) != null
302 .warn("Ignoring additional "
304 + " location(s) provided in response header ( next one is '"
305 + loc[1].getValue() + "' )");
307 rj.setJobId(loc[0].getValue());
308 rj.setSubmitted(true);
310 completeStatus(rj, response);
314 rj.setSubmitted(true);
315 rj.setAllowedServerExceptions(0);
316 rj.setSubjobComplete(true);
319 completeStatus(rj, response, "" + getStage(stg)
320 + "failed. Reason below:\n");
323 // Some other response. Probably need to pop up the content in a window.
324 // TODO: deal with all other HTTP response codes from server.
325 Cache.log.warn("Unhandled response status when " + getStage(stg)
326 + "for " + postUrl + ": " + response.getStatusLine());
328 rj.setAllowedServerExceptions(0);
329 rj.setSubjobComplete(true);
330 rj.setSubmitted(true);
338 + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
342 + "</a><br/>Filtered response content below:<br/>");
343 } catch (IOException e)
345 Cache.log.debug("IOException when consuming unhandled response",
354 * job has completed. Something valid should be available from con
359 * is a stateless request - expected to return the same data
360 * regardless of how many times its called.
362 private void processResultSet(RestJob rj, HttpResponse con,
365 if (rj.statMessage == null)
369 rj.statMessage += "Job Complete.\n";
372 rj.resSet = new HttpResultSet(rj, con, req);
374 } catch (IOException e)
376 rj.statMessage += "Couldn't parse results. Failed.";
378 rj.gotresult = false;
382 private void completeStatus(RestJob rj, HttpResponse con)
385 completeStatus(rj, con, null);
389 private void completeStatus(RestJob rj, HttpResponse con, String prefix)
392 StringBuffer sb = new StringBuffer();
398 if (rj.statMessage != null && rj.statMessage.length() > 0)
400 sb.append(rj.statMessage);
402 HttpEntity en = con.getEntity();
404 * Just append the content as a string.
407 StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
409 int body = f.indexOf("<body");
412 content.delete(0, f.indexOf(">", body) + 1);
414 if (body > -1 && sb.length() > 0)
417 content.insert(0, sb);
421 rj.statMessage = content.toString();
425 public void pollJob(AWsJob job) throws Exception
427 assert (job instanceof RestJob);
428 System.err.println("Debug RestJob: Polling Job");
429 doPoll((RestJob) job);
433 public void StartJob(AWsJob job)
435 assert (job instanceof RestJob);
438 System.err.println("Debug RestJob: Posting Job");
439 doPost((RestJob) job);
440 } catch (NoValidInputDataException erex)
442 job.setSubjobComplete(true);
443 job.setSubmitted(true);
444 ((RestJob) job).statMessage = "<br>It looks like there was a problem with the data sent to the service :<br>"
445 + erex.getMessage() + "\n";
446 ((RestJob) job).error = true;
448 } catch (Exception ex)
450 job.setSubjobComplete(true);
451 job.setAllowedServerExceptions(-1);
452 Cache.log.error("Exception when trying to start Rest Job.", ex);
457 public void parseResult()
459 // crazy users will see this message
460 // TODO: finish this! and remove the message below!
461 Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
463 for (RestJob rj : (RestJob[]) jobs)
465 if (rj.hasResponse() && rj.resSet != null && rj.resSet.isValid())
470 Cache.log.debug("Parsing data for job " + rj.getJobId());
476 Cache.log.debug("Finished parsing data for job " + rj.getJobId());
480 Cache.log.warn("Failed to finish parsing data for job "
482 ex.printStackTrace();
483 } catch (Exception ex)
485 Cache.log.warn("Failed to finish parsing data for job "
487 ex.printStackTrace();
491 rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
501 // add listeners and activate result display gui elements
503 * decisions based on job result content + state of alignFrame that
504 * originated the job:
507 * 1. Can/Should this job automatically open a new window for results
511 // preserver current jalview behaviour
512 wsInfo.setViewResultsImmediatly(true);
516 // realiseResults(true, true);
518 // otherwise, should automatically view results
520 // TODO: check if at least one or more contexts are valid - if so, enable
522 wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 realiseResults(false);
532 wsInfo.mergeResults.addActionListener(new ActionListener()
536 public void actionPerformed(ActionEvent e)
538 realiseResults(true);
543 wsInfo.setResultsReady();
547 // tell the user nothing was returned.
548 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
549 wsInfo.setFinishedNoResults();
554 * instructions for whether to create new alignment view on current alignment
555 * set, add to current set, or create new alignFrame
557 private enum AddDataTo
560 * add annotation, trees etc to current view
564 * create a new view derived from current view and add data to that
568 * create a new alignment frame for the result set and add annotation to
574 public void realiseResults(boolean merge)
577 * 2. Should the job modify the parent alignment frame/view(s) (if they
578 * still exist and the alignment hasn't been edited) in order to display new
579 * annotation/features.
582 * alignment panels derived from each alignment set returned by service.
584 ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
586 * list of instructions for how to process each distinct alignment set
587 * returned by the job set
589 ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>();
591 * when false, zeroth pane is panel derived from input deta.
593 boolean newAlignment = false;
595 * gap character to be used for alignment reconstruction
597 char gapCharacter = restClient.av.getGapCharacter();
598 // Now, iterate over all alignment sets returned from all jobs:
599 // first inspect jobs and collate results data in order to count alignments
601 // then assemble results from decomposed (v followed by h-separated) jobs
602 // finally, new views and alignments will be created and displayed as
604 boolean hsepjobs = restClient.service.isHseparable();
605 boolean vsepjobs = restClient.service.isVseparable();
606 // total number of distinct alignment sets generated by job set.
607 int numAlSets = 0, als = 0;
608 List<AlignmentI> destAls = new ArrayList<AlignmentI>();
609 List<jalview.datamodel.ColumnSelection> destColsel = new ArrayList<jalview.datamodel.ColumnSelection>();
610 List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
615 // iterate over each alignment set returned from each subjob. Treating
616 // each one returned in parallel with others.
617 // Result collation arrays
620 * mapping between index of sequence in alignment that was submitted to
621 * server and index of sequence in the input alignment
623 int[][] ordermap = new int[jobs.length][];
624 SequenceI[][] rseqs = new SequenceI[jobs.length][];
625 AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
626 AlignmentAnnotation[][] alan = new AlignmentAnnotation[jobs.length][];
627 SequenceGroup[][] sgrp = new SequenceGroup[jobs.length][];
628 // Now collect all data for alignment Set als from job array
629 for (int j = 0; j < jobs.length; j++)
631 RestJob rj = (RestJob) jobs[j];
634 JalviewDataset rset = rj.context;
635 if (rset.hasAlignments())
637 if (numAlSets < rset.getAl().size())
639 numAlSets = rset.getAl().size();
641 if (als < rset.getAl().size()
642 && rset.getAl().get(als).isModified())
644 // Collate result data
645 // TODO: decide if all alignmentI should be collected rather than
646 // specific alignment data containers
647 // for moment, we just extract content, but this means any
648 // alignment properties may be lost.
649 AlignmentSet alset = rset.getAl().get(als);
650 alan[j] = alset.al.getAlignmentAnnotation();
651 if (alset.al.getGroups() != null)
653 sgrp[j] = new SequenceGroup[alset.al.getGroups().size()];
654 alset.al.getGroups().toArray(sgrp[j]);
660 orders[j] = new AlignmentOrder(alset.al);
661 rseqs[j] = alset.al.getSequencesArray();
662 ordermap[j] = rj.getOrderMap();
663 // if (rj.isInputUniquified()) {
664 // jalview.analysis.AlignmentSorter.recoverOrder(rseqs[als]);
667 if (alset.trees != null)
669 trees.add(new ArrayList<NewickFile>(alset.trees));
673 trees.add(new ArrayList<NewickFile>());
679 // Now aggregate and present results from this frame of alignment data.
680 int nvertsep = 0, nvertseps = 1;
683 // Jobs relate to different rows of input alignment.
684 // Jobs are subdivided by rows before columns,
685 // so there will now be a number of subjobs according tohsep for each
687 // TODO: get vertical separation intervals for each job and set
689 // TODO: merge data from each group/sequence onto whole
693 * index into rest jobs subdivided vertically
696 // Destination alignments for all result data.
697 ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>();
698 Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>();
699 ArrayList<AlignmentAnnotation> visAlAn = null;
700 for (nvertsep = 0; nvertsep < nvertseps; nvertsep++)
702 // TODO: set scope w.r.t. original alignment view for vertical
705 // results for a job exclude hidden columns of input data, so map
706 // back on to all visible regions
708 * rest job result we are working with
712 RestJob rj = (RestJob) jobs[nrj];
713 int contigs[] = input.getVisibleContigs();
714 AlignmentI destAl = null;
715 jalview.datamodel.ColumnSelection destCs = null;
716 // Resolve destAl for this data.
717 if (als == 0 && rj.isInputContextModified())
719 // special case: transfer features, annotation, groups, etc,
721 // context to align panel derived from input data
722 if (destAls.size() > als)
724 destAl = destAls.get(als);
728 if (!restClient.isAlignmentModified() && merge)
730 destAl = restClient.av.getAlignment();
731 destCs = restClient.av.getColumnSelection();
733 .add(restClient.isShowResultsInNewView() ? AddDataTo.newView
734 : AddDataTo.currentView);
735 destPanels.add(restClient.recoverAlignPanelForView());
740 // recreate the input alignment data
741 Object[] idat = input
742 .getAlignmentAndColumnSelection(gapCharacter);
743 destAl = new Alignment((SequenceI[]) idat[0]);
744 destCs = (ColumnSelection) idat[1];
745 resultDest.add(AddDataTo.newAlignment);
746 // but do not add to the alignment panel list - since we need to
747 // create a whole new alignFrame set.
750 destColsel.add(destCs);
755 // alignment(s) returned by service is to be re-integrated and
757 if (destAls.size() > als)
761 // TODO: decide if multiple multiple alignments returned by
762 // non-vseparable services are allowed.
764 .warn("dealing with multiple alignment products returned by non-vertically separable service.");
766 // recover reference to last alignment created for this rest frame
767 // ready for extension
768 destAl = destAls.get(als);
769 destCs = destColsel.get(als);
777 // single alignment for any job that gets mapped back on to
778 // input data. Reconstruct by interleaving parts of returned
779 // alignment with hidden parts of input data.
780 SequenceI[][] nsq = splitSeqsOnVisibleContigs(rseqs[nrj],
781 contigs, gapCharacter);
782 AlignmentOrder alo[] = new AlignmentOrder[nsq.length];
783 for (int no = 0; no < alo.length; no++)
785 alo[no] = new AlignmentOrder(orders[nrj].getOrder());
787 newview = input.getUpdatedView(nsq, orders, gapCharacter);
791 // each job maps to a single visible contig, and all need to be
792 // stitched back together.
793 // reconstruct using sub-region based MSA alignment construction
795 newview = input.getUpdatedView(rseqs, orders, gapCharacter);
797 destAl = new Alignment((SequenceI[]) newview[0]);
798 destCs = (ColumnSelection) newview[1];
800 // TODO create alignment from result data with propagated
803 destColsel.add(destCs);
804 resultDest.add(AddDataTo.newAlignment);
805 throw new Error("Impl. Error! TODO: ");
809 * save initial job in this set in case alignment is h-separable
813 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
817 // single alignment for any job that gets mapped back on to input
822 // each job maps to a single visible contig, and all need to be
823 // stitched back together.
828 // TODO: apply options for group merging and annotation merging.
829 // If merging not supported, then either clear hashtables now or
830 // use them to rename the new annotation/groups for each contig if
831 // a conflict occurs.
833 if (sgrp[nrj] != null)
835 for (SequenceGroup sg : sgrp[nrj])
837 boolean recovered = false;
838 SequenceGroup exsg = null;
839 if (sg.getName() != null)
841 exsg = groupNames.get(sg.getName());
845 exsg = new SequenceGroup(sg);
846 groupNames.put(exsg.getName(), exsg);
848 exsg.setStartRes(sg.getStartRes() + contigs[ncnt]);
849 exsg.setEndRes(sg.getEndRes() + contigs[ncnt]);
855 // now replace any references from the result set with
856 // corresponding refs from alignment input set.
858 // TODO: cope with recovering hidden sequences from
861 for (SequenceI oseq : sg.getSequences(null))
863 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
864 ordermap[nrj], destAl);
869 exsg.deleteSequence(oseq, false);
871 exsg.addSequence(nseq, false);
876 .warn("Couldn't resolve original sequence for new sequence.");
881 if (exsg.getSeqrep() == sg.getSeqrep())
883 // lift over sequence rep reference too
884 SequenceI oseq = sg.getSeqrep();
885 SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
886 ordermap[nrj], destAl);
889 exsg.setSeqrep(nseq);
896 // adjust boundaries of recovered group w.r.t. new group being
897 // merged on to original alignment.
898 int start = sg.getStartRes() + contigs[ncnt], end = sg
899 .getEndRes() + contigs[ncnt];
900 if (start < exsg.getStartRes())
902 exsg.setStartRes(start);
904 if (end > exsg.getEndRes())
914 // and finally add in annotation and any trees for each job
915 for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
919 // single alignment for any job that gets mapped back on to input
924 // each job maps to a single visible contig, and all need to be
925 // stitched back together.
932 // merge alignmentAnnotation into one row
933 if (alan[nrj] != null)
935 for (int an = 0; an < alan[nrj].length; an++)
937 SequenceI sqass = null;
938 SequenceGroup grass = null;
939 if (alan[nrj][an].sequenceRef != null)
941 // TODO: ensure this relocates sequence reference to local
943 sqass = getNewSeq(alan[nrj][an].sequenceRef, rseqs[nrj],
944 ordermap[nrj], destAl);
946 if (alan[nrj][an].groupRef != null)
948 // TODO: verify relocate group reference to local context
950 grass = groupNames.get(alan[nrj][an].groupRef.getName());
954 .error("Couldn't relocate group referemce for group "
955 + alan[nrj][an].groupRef.getName());
960 visAlAn = new ArrayList<AlignmentAnnotation>();
962 AlignmentAnnotation visan = null;
963 for (AlignmentAnnotation v : visAlAn)
966 && v.label.equals(alan[nrj][an].label))
973 visan = new AlignmentAnnotation(alan[nrj][an]);
974 // copy annotations, and wipe out/update refs.
975 visan.annotations = new Annotation[input.getWidth()];
976 visan.groupRef = grass;
977 visan.sequenceRef = sqass;
980 if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
982 // increase width of annotation row
983 Annotation[] newannv = new Annotation[contigs[ncnt]
984 + alan[nrj][an].annotations.length];
985 System.arraycopy(visan.annotations, 0, newannv, 0,
986 visan.annotations.length);
987 visan.annotations = newannv;
989 // now copy local annotation data into correct position
990 System.arraycopy(alan[nrj][an].annotations, 0,
991 visan.annotations, contigs[ncnt],
992 alan[nrj][an].annotations.length);
997 if (trees.get(nrj).size() > 0)
999 for (NewickFile nf : trees.get(nrj))
1001 // TODO: process each newick file, lifting over sequence refs to
1002 // current alignment, if necessary.
1004 .error("Tree recovery from restjob not yet implemented.");
1009 } // end of vseps loops.
1010 if (visAlAn != null)
1012 for (AlignmentAnnotation v : visAlAn)
1014 destAls.get(als).addAnnotation(v);
1017 if (visgrps != null)
1019 for (SequenceGroup sg : visgrps)
1021 destAls.get(als).addGroup(sg);
1024 } while (++als < numAlSets);
1025 // Finally, assemble each new alignment, and create new gui components to
1028 * current AlignFrame where results will go.
1030 AlignFrame destaf = restClient.recoverAlignFrameForView();
1032 * current pane being worked with
1034 jalview.gui.AlignmentPanel destPanel = restClient
1035 .recoverAlignPanelForView();
1037 for (AddDataTo action : resultDest)
1040 ColumnSelection destcs;
1041 String alTitle = restClient.service.details.Action + " using "
1042 + restClient.service.details.Name + " on "
1043 + restClient.viewTitle;
1047 destal = destAls.get(als);
1048 destcs = destColsel.get(als);
1049 destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
1050 AlignFrame.DEFAULT_HEIGHT);
1051 PaintRefresher.Refresh(destaf, destaf.getViewport()
1052 .getSequenceSetId());
1053 // todo transfer any feature settings and colouring
1055 * destaf.getFeatureRenderer().transferSettings(this.featureSettings);
1056 * // update orders if (alorders.size() > 0) { if (alorders.size() == 1)
1057 * { af.addSortByOrderMenuItem(WebServiceName + " Ordering",
1058 * (AlignmentOrder) alorders.get(0)); } else { // construct a
1059 * non-redundant ordering set Vector names = new Vector(); for (int i =
1060 * 0, l = alorders.size(); i < l; i++) { String orderName = new
1061 * String(" Region " + i); int j = i + 1;
1063 * while (j < l) { if (((AlignmentOrder) alorders.get(i))
1064 * .equals(((AlignmentOrder) alorders.get(j)))) { alorders.remove(j);
1065 * l--; orderName += "," + j; } else { j++; } }
1067 * if (i == 0 && j == 1) { names.add(new String("")); } else {
1068 * names.add(orderName); } } for (int i = 0, l = alorders.size(); i < l;
1069 * i++) { af.addSortByOrderMenuItem( WebServiceName + ((String)
1070 * names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } }
1072 // TODO: modify this and previous alignment's title if many alignments
1073 // have been returned.
1074 Desktop.addInternalFrame(destaf, alTitle, AlignFrame.DEFAULT_WIDTH,
1075 AlignFrame.DEFAULT_HEIGHT);
1079 // TODO: determine title for view
1087 if (restClient.isShowResultsInNewView())
1089 // destPanel = destPanel.alignFrame.newView(false);
1097 * if (als) // add the destination panel to frame zero of result panel set }
1098 * } if (destPanels.size()==0) { AlignFrame af = new AlignFrame((AlignmentI)
1099 * idat[0], (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
1100 * AlignFrame.DEFAULT_HEIGHT);
1102 * jalview.gui.Desktop.addInternalFrame(af, "Results for " +
1103 * restClient.service.details.Name + " " + restClient.service.details.Action
1104 * + " on " + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH,
1105 * AlignFrame.DEFAULT_HEIGHT); destPanel = af.alignPanel; // create totally
1106 * new alignment from stashed data/results
1113 * alignments. New alignments are added to dataset, and subsequently
1114 * annotated/visualised accordingly. 1. New alignment frame created for new
1115 * alignment. Decide if any vis settings should be inherited from old
1116 * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
1117 * alignment as below:
1120 * annotation update to original/newly created context alignment: 1.
1121 * identify alignment where annotation is to be loaded onto. 2. Add
1122 * annotation, excluding any duplicates. 3. Ensure annotation is visible on
1123 * alignment - honouring ordering given by file.
1126 * features updated to original or newly created context alignment: 1.
1127 * Features are(or were already) added to dataset. 2. Feature settings
1128 * modified to ensure all features are displayed - honouring any ordering
1129 * given by result file. Consider merging action with the code used by the
1130 * DAS fetcher to update alignment views with new info.
1133 * Seq associated data files (PDB files). 1. locate seq association in
1134 * current dataset/alignment context and add file as normal - keep handle of
1135 * any created ref objects. 2. decide if new data should be displayed : PDB
1136 * display: if alignment has PDB display already, should new pdb files be
1140 // destPanel.adjustAnnotationHeight();
1145 * split the given array of sequences into blocks of subsequences
1146 * corresponding to each visible contig
1151 * padding character for ragged ends of visible contig region.
1154 private SequenceI[][] splitSeqsOnVisibleContigs(SequenceI[] sequenceIs,
1155 int[] contigs, char gapChar)
1157 int nvc = contigs == null ? 1 : contigs.length / 2;
1158 SequenceI[][] blocks = new SequenceI[nvc][];
1159 if (contigs == null)
1161 blocks[0] = new SequenceI[sequenceIs.length];
1162 System.arraycopy(sequenceIs, 0, blocks[0], 0, sequenceIs.length);
1166 // deja vu - have I written this before ?? propagateGaps does this in a
1168 char[] gapset = null;
1169 int start = 0, width = 0;
1170 for (int c = 0; c < nvc; c++)
1172 width = contigs[c * 2 + 1] - contigs[c * 2] + 1;
1173 for (int s = 0; s < sequenceIs.length; s++)
1175 int end = sequenceIs[s].getLength();
1178 if (start + width < end)
1180 blocks[c][s] = sequenceIs[s].getSubSequence(start, start
1185 blocks[c][s] = sequenceIs[s].getSubSequence(start, end);
1186 String sq = blocks[c][s].getSequenceAsString();
1187 for (int n = start + width; n > end; n--)
1195 if (gapset == null || gapset.length < width)
1197 char ng[] = new char[width];
1201 System.arraycopy(gapset, 0, ng, 0, gs = gapset.length);
1203 while (gs < ng.length)
1208 blocks[c][s] = sequenceIs[s].getSubSequence(end, end);
1209 blocks[c][s].setSequence(gapset.toString().substring(0, width));
1214 // adjust window for next visible segnment
1215 start += contigs[c * 2 + 1] - contigs[c * 2];
1223 * recover corresponding sequence from original input data corresponding to
1224 * sequence in a specific job's input data.
1232 private SequenceI getNewSeq(SequenceI oseq, SequenceI[] sequenceIs,
1233 int[] is, AlignmentI destAl)
1236 while (p < sequenceIs.length && sequenceIs[p] != oseq)
1240 if (p < sequenceIs.length && p < destAl.getHeight())
1242 return destAl.getSequenceAt(is[p]);
1249 * @return true if the run method is safe to call
1251 public boolean isValid()
1253 ArrayList<String> _warnings = new ArrayList<String>();
1254 boolean validt = true;
1257 for (RestJob rj : (RestJob[]) jobs)
1259 if (!rj.hasValidInput())
1261 // invalid input for this job
1262 System.err.println("Job " + rj.getJobnum()
1263 + " has invalid input. ( " + rj.getStatus() + ")");
1264 if (rj.hasStatus() && !_warnings.contains(rj.getStatus()))
1266 _warnings.add(rj.getStatus());
1275 for (String st : _warnings)
1277 if (warnings.length() > 0)
1288 protected String warnings;
1290 public boolean hasWarnings()
1292 // TODO Auto-generated method stub
1293 return warnings != null && warnings.length() > 0;
1297 * get any informative messages about why the job thread couldn't start.
1301 public String getWarnings()
1303 return isValid() ? "Job can be started. No warnings."
1304 : hasWarnings() ? warnings : "";