+ // Make sure we save none displayed feature settings
+ Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ .keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ if (settingsAdded.contains(key))
+ {
+ continue;
+ }
+
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(key).getRGB());
+
+ setting.setDisplay(false);
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
+ key);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(key);
+ }
+ en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
+ Vector groupsAdded = new Vector();
+ while (en.hasMoreElements())
+ {
+ String grp = en.nextElement().toString();
+ if (groupsAdded.contains(grp))
+ {
+ continue;
+ }
+ Group g = new Group();
+ g.setName(grp);
+ g
+ .setDisplay(((Boolean) ap.seqPanel.seqCanvas
+ .getFeatureRenderer().featureGroups.get(grp))
+ .booleanValue());
+ fs.addGroup(g);
+ groupsAdded.addElement(grp);
+ }
+ jms.setFeatureSettings(fs);
+
+ }
+
+ if (av.hasHiddenColumns)
+ {
+ for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
+ {
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
+ }
+
+ jms.addViewport(view);
+
+ object.setJalviewModelSequence(jms);
+ object.getVamsasModel().addSequenceSet(vamsasSet);
+
+ if (jout != null && fileName != null)
+ {
+ // We may not want to write the object to disk,
+ // eg we can copy the alignViewport to a new view object
+ // using save and then load
+ try
+ {
+ JarEntry entry = new JarEntry(fileName);
+ jout.putNextEntry(entry);
+ PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
+ org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
+ pout);
+ marshaller.marshal(object);
+ pout.flush();
+ jout.closeEntry();
+ } catch (Exception ex)
+ {
+ // TODO: raise error in GUI if marshalling failed.
+ ex.printStackTrace();
+ }
+ }
+ return object;
+ }
+
+ private Sequence createVamsasSequence(String id, SequenceI jds)
+ {
+ return createVamsasSequence(true, id, jds, null);
+ }
+
+ private Sequence createVamsasSequence(boolean recurse, String id,
+ SequenceI jds, SequenceI parentseq)
+ {
+ Sequence vamsasSeq = new Sequence();
+ vamsasSeq.setId(id);
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+ jalview.datamodel.DBRefEntry[] dbrefs = null;
+ if (jds.getDatasetSequence() != null)
+ {
+ vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
+ if (jds.getDatasetSequence().getDBRef() != null)
+ {
+ dbrefs = jds.getDatasetSequence().getDBRef();
+ }
+ }
+ else
+ {
+ vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+ // dataset sequences only
+ dbrefs = jds.getDBRef();
+ }
+ if (dbrefs != null)
+ {
+ for (int d = 0; d < dbrefs.length; d++)
+ {
+ DBRef dbref = new DBRef();
+ dbref.setSource(dbrefs[d].getSource());
+ dbref.setVersion(dbrefs[d].getVersion());
+ dbref.setAccessionId(dbrefs[d].getAccessionId());
+ if (dbrefs[d].hasMap())
+ {
+ Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ jds, recurse);
+ dbref.setMapping(mp);
+ }
+ vamsasSeq.addDBRef(dbref);
+ }
+ }
+ return vamsasSeq;
+ }
+
+ private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
+ SequenceI parentseq, SequenceI jds, boolean recurse)
+ {
+ Mapping mp = null;
+ if (jmp.getMap() != null)
+ {
+ mp = new Mapping();
+
+ jalview.util.MapList mlst = jmp.getMap();
+ int r[] = mlst.getFromRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(r[s]);
+ mfrom.setEnd(r[s + 1]);
+ mp.addMapListFrom(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(r[s]);
+ mto.setEnd(r[s + 1]);
+ mp.addMapListTo(mto);
+ }
+ mp.setMapFromUnit(mlst.getFromRatio());
+ mp.setMapToUnit(mlst.getToRatio());
+ if (jmp.getTo() != null)
+ {
+ MappingChoice mpc = new MappingChoice();
+ if (recurse
+ && (parentseq != jmp.getTo() || parentseq
+ .getDatasetSequence() != jmp.getTo()))
+ {
+ mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
+ jmp.getTo(), jds));
+ }
+ else
+ {
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
+ {
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
+ }
+ else
+ {
+ jmpid = seqHash(ps = parentseq);
+ }
+ mpc.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(mpc.getDseqFor()))
+ {
+ jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ seqRefIds.put(mpc.getDseqFor(), ps);
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ }
+ }
+ mp.setMappingChoice(mpc);
+ }
+ }
+ return mp;
+ }
+
+ String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ Vector userColours, JalviewModelSequence jms)
+ {
+ String id = null;
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+
+ if (!userColours.contains(ucs))
+ {
+ userColours.add(ucs);
+
+ java.awt.Color[] colours = ucs.getColours();
+ jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+ jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
+
+ for (int i = 0; i < colours.length; i++)
+ {
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ col.setName(ResidueProperties.aa[i]);
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ jbucs.addColour(col);
+ }
+ if (ucs.getLowerCaseColours() != null)
+ {
+ colours = ucs.getLowerCaseColours();
+ for (int i = 0; i < colours.length; i++)
+ {
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+ col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ jbucs.addColour(col);
+ }
+ }
+
+ id = "ucs" + userColours.indexOf(ucs);
+ uc.setId(id);
+ uc.setUserColourScheme(jbucs);
+ jms.addUserColours(uc);
+ }
+
+ return id;
+ }
+
+ jalview.schemes.UserColourScheme GetUserColourScheme(
+ JalviewModelSequence jms, String id)
+ {
+ UserColours[] uc = jms.getUserColours();
+ UserColours colours = null;
+
+ for (int i = 0; i < uc.length; i++)
+ {
+ if (uc[i].getId().equals(id))
+ {
+ colours = uc[i];
+
+ break;
+ }
+ }
+
+ java.awt.Color[] newColours = new java.awt.Color[24];
+
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours
+ .getUserColourScheme().getColour(i).getRGB(), 16));
+ }
+
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ newColours);
+
+ if (colours.getUserColourScheme().getColourCount() > 24)
+ {
+ newColours = new java.awt.Color[23];
+ for (int i = 0; i < 23; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(colours
+ .getUserColourScheme().getColour(i + 24).getRGB(), 16));
+ }
+ ucs.setLowerCaseColours(newColours);
+ }