+ * alignment panels derived from each alignment set returned by service.
+ */
+ ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
+ /**
+ * list of instructions for how to process each distinct alignment set
+ * returned by the job set
+ */
+ ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>();
+ /**
+ * when false, zeroth pane is panel derived from input deta.
+ */
+ boolean newAlignment = false;
+ /**
+ * gap character to be used for alignment reconstruction
+ */
+ char gapCharacter = restClient.av.getGapCharacter();
+ // Now, iterate over all alignment sets returned from all jobs:
+ // first inspect jobs and collate results data in order to count alignments
+ // and other results
+ // then assemble results from decomposed (v followed by h-separated) jobs
+ // finally, new views and alignments will be created and displayed as
+ // necessary.
+ boolean hsepjobs = restClient.service.isHseparable();
+ boolean vsepjobs = restClient.service.isVseparable();
+ // total number of distinct alignment sets generated by job set.
+ int numAlSets = 0, als = 0;
+ List<AlignmentI> destAls = new ArrayList<AlignmentI>();
+ List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<jalview.datamodel.HiddenColumns>();
+ List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
+
+ do
+ {
+ // Step 1.
+ // iterate over each alignment set returned from each subjob. Treating
+ // each one returned in parallel with others.
+ // Result collation arrays
+
+ /**
+ * mapping between index of sequence in alignment that was submitted to
+ * server and index of sequence in the input alignment
+ */
+ int[][] ordermap = new int[jobs.length][];
+ SequenceI[][] rseqs = new SequenceI[jobs.length][];
+ AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
+ AlignmentAnnotation[][] alan = new AlignmentAnnotation[jobs.length][];
+ SequenceGroup[][] sgrp = new SequenceGroup[jobs.length][];
+ // Now collect all data for alignment Set als from job array
+ for (int j = 0; j < jobs.length; j++)
+ {
+ RestJob rj = (RestJob) jobs[j];
+ if (rj.hasResults())
+ {
+ JalviewDataset rset = rj.context;
+ if (rset.hasAlignments())
+ {
+ if (numAlSets < rset.getAl().size())
+ {
+ numAlSets = rset.getAl().size();
+ }
+ if (als < rset.getAl().size()
+ && rset.getAl().get(als).isModified())
+ {
+ // Collate result data
+ // TODO: decide if all alignmentI should be collected rather than
+ // specific alignment data containers
+ // for moment, we just extract content, but this means any
+ // alignment properties may be lost.
+ AlignmentSet alset = rset.getAl().get(als);
+ alan[j] = alset.al.getAlignmentAnnotation();
+ if (alset.al.getGroups() != null)
+ {
+ sgrp[j] = new SequenceGroup[alset.al.getGroups().size()];
+ alset.al.getGroups().toArray(sgrp[j]);
+ }
+ else
+ {
+ sgrp[j] = null;
+ }
+ orders[j] = new AlignmentOrder(alset.al);
+ rseqs[j] = alset.al.getSequencesArray();
+ ordermap[j] = rj.getOrderMap();
+ // if (rj.isInputUniquified()) {
+ // jalview.analysis.AlignmentSorter.recoverOrder(rseqs[als]);
+ // }
+
+ if (alset.trees != null)
+ {
+ trees.add(new ArrayList<NewickFile>(alset.trees));
+ }
+ else
+ {
+ trees.add(new ArrayList<NewickFile>());
+ }
+ }
+ }
+ }
+ }
+ // Now aggregate and present results from this frame of alignment data.
+ int nvertsep = 0, nvertseps = 1;
+ if (vsepjobs)
+ {
+ // Jobs relate to different rows of input alignment.
+ // Jobs are subdivided by rows before columns,
+ // so there will now be a number of subjobs according tohsep for each
+ // vertsep
+ // TODO: get vertical separation intervals for each job and set
+ // nvertseps
+ // TODO: merge data from each group/sequence onto whole
+ // alignment
+ }
+ /**
+ * index into rest jobs subdivided vertically
+ */
+ int vrestjob = 0;
+ // Destination alignments for all result data.
+ ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>();
+ Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>();
+ ArrayList<AlignmentAnnotation> visAlAn = null;
+ for (nvertsep = 0; nvertsep < nvertseps; nvertsep++)
+ {
+ // TODO: set scope w.r.t. original alignment view for vertical
+ // separation.
+ {
+ // results for a job exclude hidden columns of input data, so map
+ // back on to all visible regions
+ /**
+ * rest job result we are working with
+ */
+ int nrj = vrestjob;
+
+ RestJob rj = (RestJob) jobs[nrj];
+ int contigs[] = input.getVisibleContigs();
+ AlignmentI destAl = null;
+ jalview.datamodel.HiddenColumns destHCs = null;
+ // Resolve destAl for this data.
+ if (als == 0 && rj.isInputContextModified())
+ {
+ // special case: transfer features, annotation, groups, etc,
+ // from input
+ // context to align panel derived from input data
+ if (destAls.size() > als)
+ {
+ destAl = destAls.get(als);
+ }
+ else
+ {
+ if (!restClient.isAlignmentModified() && merge)
+ {
+ destAl = restClient.av.getAlignment();
+ destHCs = restClient.av.getAlignment().getHiddenColumns();
+ resultDest.add(restClient.isShowResultsInNewView()
+ ? AddDataTo.newView
+ : AddDataTo.currentView);
+ destPanels.add(restClient.recoverAlignPanelForView());
+ }
+ else
+ {
+ newAlignment = true;
+ // recreate the input alignment data
+ Object[] idat = input
+ .getAlignmentAndHiddenColumns(gapCharacter);
+ destAl = new Alignment((SequenceI[]) idat[0]);
+ destHCs = (HiddenColumns) idat[1];
+ resultDest.add(AddDataTo.newAlignment);
+ // but do not add to the alignment panel list - since we need to
+ // create a whole new alignFrame set.
+ }
+ destAls.add(destAl);
+ destColsel.add(destHCs);
+ }
+ }
+ else
+ {
+ // alignment(s) returned by service is to be re-integrated and
+ // displayed
+ if (destAls.size() > als)
+ {
+ if (!vsepjobs)
+ {
+ // TODO: decide if multiple multiple alignments returned by
+ // non-vseparable services are allowed.
+ Cache.log.warn(
+ "dealing with multiple alignment products returned by non-vertically separable service.");
+ }
+ // recover reference to last alignment created for this rest frame
+ // ready for extension
+ destAl = destAls.get(als);
+ destHCs = destColsel.get(als);
+ }
+ else
+ {
+ Object[] newview;
+
+ if (!hsepjobs)
+ {
+ // single alignment for any job that gets mapped back on to
+ // input data. Reconstruct by interleaving parts of returned
+ // alignment with hidden parts of input data.
+ SequenceI[][] nsq = splitSeqsOnVisibleContigs(rseqs[nrj],
+ contigs, gapCharacter);
+ AlignmentOrder alo[] = new AlignmentOrder[nsq.length];
+ for (int no = 0; no < alo.length; no++)
+ {
+ alo[no] = new AlignmentOrder(orders[nrj].getOrder());
+ }
+ newview = input.getUpdatedView(nsq, orders, gapCharacter);
+ }
+ else
+ {
+ // each job maps to a single visible contig, and all need to be
+ // stitched back together.
+ // reconstruct using sub-region based MSA alignment construction
+ // mechanism
+ newview = input.getUpdatedView(rseqs, orders, gapCharacter);
+ }
+ destAl = new Alignment((SequenceI[]) newview[0]);
+ destHCs = (HiddenColumns) newview[1];
+ newAlignment = true;
+ // TODO create alignment from result data with propagated
+ // references.
+ destAls.add(destAl);
+ destColsel.add(destHCs);
+ resultDest.add(AddDataTo.newAlignment);
+ throw new Error(
+ MessageManager.getString("error.implementation_error")
+ + "TODO: ");
+ }
+ }
+ /**
+ * save initial job in this set in case alignment is h-separable
+ */
+ int initnrj = nrj;
+ // Now add in groups
+ for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
+ {
+ if (!hsepjobs)
+ {
+ // single alignment for any job that gets mapped back on to input
+ // data.
+ }
+ else
+ {
+ // each job maps to a single visible contig, and all need to be
+ // stitched back together.
+ if (ncnt > 0)
+ {
+ nrj++;
+ }
+ // TODO: apply options for group merging and annotation merging.
+ // If merging not supported, then either clear hashtables now or
+ // use them to rename the new annotation/groups for each contig if
+ // a conflict occurs.
+ }
+ if (sgrp[nrj] != null)
+ {
+ for (SequenceGroup sg : sgrp[nrj])
+ {
+ boolean recovered = false;
+ SequenceGroup exsg = null;
+ if (sg.getName() != null)
+ {
+ exsg = groupNames.get(sg.getName());
+ }
+ if (exsg == null)
+ {
+ exsg = new SequenceGroup(sg);
+ groupNames.put(exsg.getName(), exsg);
+ visgrps.add(exsg);
+ exsg.setStartRes(sg.getStartRes() + contigs[ncnt]);
+ exsg.setEndRes(sg.getEndRes() + contigs[ncnt]);
+ }
+ else
+ {
+ recovered = true;
+ }
+ // now replace any references from the result set with
+ // corresponding refs from alignment input set.
+
+ // TODO: cope with recovering hidden sequences from
+ // resultContext
+ {
+ for (SequenceI oseq : sg.getSequences(null))
+ {
+ SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
+ ordermap[nrj], destAl);
+ if (nseq != null)
+ {
+ if (!recovered)
+ {
+ exsg.deleteSequence(oseq, false);
+ }
+ exsg.addSequence(nseq, false);
+ }
+ else
+ {
+ Cache.log.warn(
+ "Couldn't resolve original sequence for new sequence.");
+ }
+ }
+ if (sg.hasSeqrep())
+ {
+ if (exsg.getSeqrep() == sg.getSeqrep())
+ {
+ // lift over sequence rep reference too
+ SequenceI oseq = sg.getSeqrep();
+ SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
+ ordermap[nrj], destAl);
+ if (nseq != null)
+ {
+ exsg.setSeqrep(nseq);
+ }
+ }
+ }
+ }
+ if (recovered)
+ {
+ // adjust boundaries of recovered group w.r.t. new group being
+ // merged on to original alignment.
+ int start = sg.getStartRes() + contigs[ncnt],
+ end = sg.getEndRes() + contigs[ncnt];
+ if (start < exsg.getStartRes())
+ {
+ exsg.setStartRes(start);
+ }
+ if (end > exsg.getEndRes())
+ {
+ exsg.setEndRes(end);
+ }
+ }
+ }
+ }
+ }
+ // reset job counter
+ nrj = initnrj;
+ // and finally add in annotation and any trees for each job
+ for (int ncnt = 0; ncnt < contigs.length; ncnt += 2)
+ {
+ if (!hsepjobs)
+ {
+ // single alignment for any job that gets mapped back on to input
+ // data.
+ }
+ else
+ {
+ // each job maps to a single visible contig, and all need to be
+ // stitched back together.
+ if (ncnt > 0)
+ {
+ nrj++;
+ }
+ }
+
+ // merge alignmentAnnotation into one row
+ if (alan[nrj] != null)
+ {
+ for (int an = 0; an < alan[nrj].length; an++)
+ {
+ SequenceI sqass = null;
+ SequenceGroup grass = null;
+ if (alan[nrj][an].sequenceRef != null)
+ {
+ // TODO: ensure this relocates sequence reference to local
+ // context.
+ sqass = getNewSeq(alan[nrj][an].sequenceRef, rseqs[nrj],
+ ordermap[nrj], destAl);
+ }
+ if (alan[nrj][an].groupRef != null)
+ {
+ // TODO: verify relocate group reference to local context
+ // works correctly
+ grass = groupNames.get(alan[nrj][an].groupRef.getName());
+ if (grass == null)
+ {
+ Cache.log.error(
+ "Couldn't relocate group referemce for group "
+ + alan[nrj][an].groupRef.getName());
+ }
+ }
+ if (visAlAn == null)
+ {
+ visAlAn = new ArrayList<AlignmentAnnotation>();
+ }
+ AlignmentAnnotation visan = null;
+ for (AlignmentAnnotation v : visAlAn)
+ {
+ if (v.label != null
+ && v.label.equals(alan[nrj][an].label))
+ {
+ visan = v;
+ }
+ }
+ if (visan == null)
+ {
+ visan = new AlignmentAnnotation(alan[nrj][an]);
+ // copy annotations, and wipe out/update refs.
+ visan.annotations = new Annotation[input.getWidth()];
+ visan.groupRef = grass;
+ visan.sequenceRef = sqass;
+ visAlAn.add(visan);
+ }
+ if (contigs[ncnt]
+ + alan[nrj][an].annotations.length > visan.annotations.length)
+ {
+ // increase width of annotation row
+ Annotation[] newannv = new Annotation[contigs[ncnt]
+ + alan[nrj][an].annotations.length];
+ System.arraycopy(visan.annotations, 0, newannv, 0,
+ visan.annotations.length);
+ visan.annotations = newannv;
+ }
+ // now copy local annotation data into correct position
+ System.arraycopy(alan[nrj][an].annotations, 0,
+ visan.annotations, contigs[ncnt],
+ alan[nrj][an].annotations.length);
+
+ }
+ }
+ // Trees
+ if (trees.get(nrj).size() > 0)
+ {
+ for (NewickFile nf : trees.get(nrj))
+ {
+ // TODO: process each newick file, lifting over sequence refs to
+ // current alignment, if necessary.
+ Cache.log.error(
+ "Tree recovery from restjob not yet implemented.");
+ }
+ }
+ }
+ }
+ } // end of vseps loops.
+ if (visAlAn != null)
+ {
+ for (AlignmentAnnotation v : visAlAn)
+ {
+ destAls.get(als).addAnnotation(v);
+ }
+ }
+ if (visgrps != null)
+ {
+ for (SequenceGroup sg : visgrps)
+ {
+ destAls.get(als).addGroup(sg);
+ }
+ }
+ } while (++als < numAlSets);
+ // Finally, assemble each new alignment, and create new gui components to
+ // present it.
+ /**
+ * current AlignFrame where results will go.
+ */
+ AlignFrame destaf = restClient.recoverAlignFrameForView();
+ /**
+ * current pane being worked with
+ */
+ jalview.gui.AlignmentPanel destPanel = restClient
+ .recoverAlignPanelForView();
+ als = 0;
+ for (AddDataTo action : resultDest)
+ {
+ AlignmentI destal;
+ HiddenColumns destcs;
+ String alTitle = MessageManager
+ .formatMessage("label.webservice_job_title_on", new String[]
+ { restClient.service.details.Action,
+ restClient.service.details.Name, restClient.viewTitle });
+ switch (action)
+ {
+ case newAlignment:
+ destal = destAls.get(als);
+ destcs = destColsel.get(als);
+ destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ PaintRefresher.Refresh(destaf,
+ destaf.getViewport().getSequenceSetId());
+ // todo transfer any feature settings and colouring
+ /*
+ * destaf.getFeatureRenderer().transferSettings(this.featureSettings);
+ * // update orders if (alorders.size() > 0) { if (alorders.size() == 1)
+ * { af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+ * (AlignmentOrder) alorders.get(0)); } else { // construct a
+ * non-redundant ordering set Vector names = new Vector(); for (int i =
+ * 0, l = alorders.size(); i < l; i++) { String orderName = new
+ * String(" Region " + i); int j = i + 1;
+ *
+ * while (j < l) { if (((AlignmentOrder) alorders.get(i))
+ * .equals(((AlignmentOrder) alorders.get(j)))) { alorders.remove(j);
+ * l--; orderName += "," + j; } else { j++; } }
+ *
+ * if (i == 0 && j == 1) { names.add(new String("")); } else {
+ * names.add(orderName); } } for (int i = 0, l = alorders.size(); i < l;
+ * i++) { af.addSortByOrderMenuItem( WebServiceName + ((String)
+ * names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } }
+ */
+ // TODO: modify this and previous alignment's title if many alignments
+ // have been returned.
+ Desktop.addInternalFrame(destaf, alTitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ break;
+ case newView:
+ // TODO: determine title for view
+ break;
+ case currentView:
+ break;
+ }
+ }
+ if (!newAlignment)
+ {
+ if (restClient.isShowResultsInNewView())
+ {
+ // destPanel = destPanel.alignFrame.newView(false);
+ }
+ }
+ else
+ {
+
+ }
+ /*
+ * if (als) // add the destination panel to frame zero of result panel set }
+ * } if (destPanels.size()==0) { AlignFrame af = new AlignFrame((AlignmentI)
+ * idat[0], (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
+ * AlignFrame.DEFAULT_HEIGHT);
+ *
+ * jalview.gui.Desktop.addInternalFrame(af, "Results for " +
+ * restClient.service.details.Name + " " + restClient.service.details.Action
+ * + " on " + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ * AlignFrame.DEFAULT_HEIGHT); destPanel = af.alignPanel; // create totally
+ * new alignment from stashed data/results
+ */
+
+ /*
+ */
+
+ /**