+ }
+
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ }
+ }
+ if (vamsasSeq[i].getDBRefCount() > 0)
+ {
+ addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+ }
+ if (jseqs[i].getPdbidsCount() > 0)
+ {
+ Pdbids[] ids = jseqs[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+ entry.setId(ids[p].getId());
+ if (ids[p].getType() != null)
+ {
+ if (ids[p].getType().equalsIgnoreCase("PDB"))
+ {
+ entry.setType(PDBEntry.Type.PDB);
+ }
+ else
+ {
+ entry.setType(PDBEntry.Type.FILE);
+ }
+ }
+ if (ids[p].getFile() != null)
+ {
+ if (!pdbloaded.containsKey(ids[p].getFile()))
+ {
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ }
+ else
+ {
+ entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+ }
+ }
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(entry);
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ }
+ }
+ } // end !multipleview
+
+ // ///////////////////////////////
+ // LOAD SEQUENCE MAPPINGS
+
+ if (vamsasSet.getAlcodonFrameCount() > 0)
+ {
+ // TODO Potentially this should only be done once for all views of an
+ // alignment
+ AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
+ for (int i = 0; i < alc.length; i++)
+ {
+ AlignedCodonFrame cf = new AlignedCodonFrame();
+ if (alc[i].getAlcodMapCount() > 0)
+ {
+ AlcodMap[] maps = alc[i].getAlcodMap();
+ for (int m = 0; m < maps.length; m++)
+ {
+ SequenceI dnaseq = seqRefIds.get(maps[m].getDnasq());
+ // Load Mapping
+ jalview.datamodel.Mapping mapping = null;
+ // attach to dna sequence reference.
+ if (maps[m].getMapping() != null)
+ {
+ mapping = addMapping(maps[m].getMapping());
+ }
+ if (dnaseq != null && mapping.getTo() != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
+ mapping });
+ }
+ }
+ }
+ al.addCodonFrame(cf);
+ }
+ }
+
+ // ////////////////////////////////
+ // LOAD ANNOTATIONS
+ List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+
+ /*
+ * store any annotations which forward reference a group's ID
+ */
+ Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
+
+ if (vamsasSet.getAnnotationCount() > 0)
+ {
+ Annotation[] an = vamsasSet.getAnnotation();
+
+ for (int i = 0; i < an.length; i++)
+ {
+ Annotation annotation = an[i];
+
+ /**
+ * test if annotation is automatically calculated for this view only
+ */
+ boolean autoForView = false;
+ if (annotation.getLabel().equals("Quality")
+ || annotation.getLabel().equals("Conservation")
+ || annotation.getLabel().equals("Consensus"))
+ {
+ // Kludge for pre 2.5 projects which lacked the autocalculated flag
+ autoForView = true;
+ if (!annotation.hasAutoCalculated())
+ {
+ annotation.setAutoCalculated(true);
+ }
+ }
+ if (autoForView
+ || (annotation.hasAutoCalculated() && annotation
+ .isAutoCalculated()))
+ {
+ // remove ID - we don't recover annotation from other views for
+ // view-specific annotation
+ annotation.setId(null);
+ }
+
+ // set visiblity for other annotation in this view
+ String annotationId = annotation.getId();
+ if (annotationId != null && annotationIds.containsKey(annotationId))
+ {
+ AlignmentAnnotation jda = annotationIds.get(annotationId);
+ // in principle Visible should always be true for annotation displayed
+ // in multiple views
+ if (annotation.hasVisible())
+ {
+ jda.visible = annotation.getVisible();
+ }
+
+ al.addAnnotation(jda);
+
+ continue;
+ }
+ // Construct new annotation from model.
+ AnnotationElement[] ae = annotation.getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = null;
+ java.awt.Color firstColour = null;
+ int anpos;
+ if (!annotation.getScoreOnly())
+ {
+ anot = new jalview.datamodel.Annotation[al.getWidth()];
+ for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ {
+ anpos = ae[aa].getPosition();
+
+ if (anpos >= anot.length)
+ {
+ continue;
+ }
+
+ anot[anpos] = new jalview.datamodel.Annotation(
+
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+ (ae[aa].getSecondaryStructure() == null || ae[aa]
+ .getSecondaryStructure().length() == 0) ? ' '
+ : ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue()
+
+ );
+ // JBPNote: Consider verifying dataflow for IO of secondary
+ // structure annotation read from Stockholm files
+ // this was added to try to ensure that
+ // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
+ // {
+ // anot[ae[aa].getPosition()].displayCharacter = "";
+ // }
+ anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+ if (firstColour == null)
+ {
+ firstColour = anot[anpos].colour;
+ }
+ }
+ }
+ jalview.datamodel.AlignmentAnnotation jaa = null;
+
+ if (annotation.getGraph())
+ {
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
+ jaa = new jalview.datamodel.AlignmentAnnotation(
+ annotation.getLabel(), annotation.getDescription(), anot,
+ llim, hlim, annotation.getGraphType());
+
+ jaa.graphGroup = annotation.getGraphGroup();
+ jaa._linecolour = firstColour;
+ if (annotation.getThresholdLine() != null)
+ {
+ jaa.setThreshold(new jalview.datamodel.GraphLine(annotation
+ .getThresholdLine().getValue(), annotation
+ .getThresholdLine().getLabel(), new java.awt.Color(
+ annotation.getThresholdLine().getColour())));
+
+ }
+ if (autoForView || annotation.isAutoCalculated())
+ {
+ // Hardwire the symbol display line to ensure that labels for
+ // histograms are displayed
+ jaa.hasText = true;
+ }
+ }
+ else
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot);
+ jaa._linecolour = firstColour;
+ }
+ // register new annotation
+ if (an[i].getId() != null)
+ {
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
+ // recover sequence association
+ String sequenceRef = an[i].getSequenceRef();
+ if (sequenceRef != null)
+ {
+ // from 2.9 sequenceRef is to sequence id (JAL-1781)
+ SequenceI sequence = seqRefIds.get(sequenceRef);
+ if (sequence == null)
+ {
+ // in pre-2.9 projects sequence ref is to sequence name
+ sequence = al.findName(sequenceRef);
+ }
+ if (sequence != null)
+ {
+ jaa.createSequenceMapping(sequence, 1, true);
+ sequence.addAlignmentAnnotation(jaa);
+ }
+ }
+ // and make a note of any group association
+ if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
+ {
+ List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+ .get(an[i].getGroupRef());
+ if (aal == null)
+ {
+ aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+ groupAnnotRefs.put(an[i].getGroupRef(), aal);
+ }
+ aal.add(jaa);
+ }
+
+ if (an[i].hasScore())
+ {
+ jaa.setScore(an[i].getScore());
+ }
+ if (an[i].hasVisible())
+ {
+ jaa.visible = an[i].getVisible();
+ }
+
+ if (an[i].hasCentreColLabels())
+ {
+ jaa.centreColLabels = an[i].getCentreColLabels();
+ }
+
+ if (an[i].hasScaleColLabels())
+ {
+ jaa.scaleColLabel = an[i].getScaleColLabels();
+ }
+ if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
+ {
+ // newer files have an 'autoCalculated' flag and store calculation
+ // state in viewport properties
+ jaa.autoCalculated = true; // means annotation will be marked for
+ // update at end of load.
+ }
+ if (an[i].hasGraphHeight())
+ {
+ jaa.graphHeight = an[i].getGraphHeight();
+ }
+ if (an[i].hasBelowAlignment())
+ {
+ jaa.belowAlignment = an[i].isBelowAlignment();
+ }
+ jaa.setCalcId(an[i].getCalcId());
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
+ if (jaa.autoCalculated)
+ {
+ autoAlan.add(new JvAnnotRow(i, jaa));
+ }
+ else
+ // if (!autoForView)
+ {
+ // add autocalculated group annotation and any user created annotation
+ // for the view
+ al.addAnnotation(jaa);
+ }
+ }
+ }
+ // ///////////////////////
+ // LOAD GROUPS
+ // Create alignment markup and styles for this view
+ if (jms.getJGroupCount() > 0)
+ {
+ JGroup[] groups = jms.getJGroup();
+ boolean addAnnotSchemeGroup = false;
+ for (int i = 0; i < groups.length; i++)
+ {
+ JGroup jGroup = groups[i];
+ ColourSchemeI cs = null;
+ if (jGroup.getColour() != null)
+ {
+ if (jGroup.getColour().startsWith("ucs"))
+ {
+ cs = getUserColourScheme(jms, jGroup.getColour());
+ }
+ else if (jGroup.getColour().equals("AnnotationColourGradient")
+ && jGroup.getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ cs = null;
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
+ }
+
+ if (cs != null)
+ {
+ cs.setThreshold(jGroup.getPidThreshold(), true);
+ }
+ }
+
+ Vector<SequenceI> seqs = new Vector<SequenceI>();