+ }
+ // Instantiate the associated structure views
+ for (Entry<String, StructureViewerModel> entry : structureViewers
+ .entrySet())
+ {
+ try
+ {
+ createOrLinkStructureViewer(entry, af, ap, jprovider);
+ } catch (Exception e)
+ {
+ System.err.println("Error loading structure viewer: "
+ + e.getMessage());
+ // failed - try the next one
+ }
+ }
+ }
+
+ /**
+ *
+ * @param viewerData
+ * @param af
+ * @param ap
+ * @param jprovider
+ */
+ protected void createOrLinkStructureViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
+ AlignmentPanel ap, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel stateData = viewerData.getValue();
+
+ /*
+ * Search for any viewer windows already open from other alignment views
+ * that exactly match the stored structure state
+ */
+ StructureViewerBase comp = findMatchingViewer(viewerData);
+
+ if (comp != null)
+ {
+ linkStructureViewer(ap, comp, stateData);
+ return;
+ }
+
+ /*
+ * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
+ * "viewer_"+stateData.viewId
+ */
+ if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
+ {
+ createChimeraViewer(viewerData, af, jprovider);
+ }
+ else
+ {
+ /*
+ * else Jmol (if pre-2.9, stateData contains JMOL state string)
+ */
+ createJmolViewer(viewerData, af, jprovider);
+ }
+ }
+
+ /**
+ * Create a new Chimera viewer.
+ *
+ * @param data
+ * @param af
+ * @param jprovider
+ */
+ protected void createChimeraViewer(Entry<String, StructureViewerModel> viewerData,
+ AlignFrame af,
+ jarInputStreamProvider jprovider)
+ {
+ StructureViewerModel data = viewerData.getValue();
+ String chimeraSessionFile = data.getStateData();
+
+ /*
+ * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
+ *
+ * Note this is the 'saved' viewId as in the project file XML, _not_ the
+ * 'uniquified' sviewid used to reconstruct the viewer here
+ */
+ chimeraSessionFile = copyJarEntry(jprovider,
+ getViewerJarEntryName(data.getViewId()), "chimera");
+
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
+ List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
+ List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
+ for (Entry<File, StructureData> pdb : fileData)
+ {
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ // pdbs.add(new PDBEntry(filePath, pdbId));
+ pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
+ final List<SequenceI> seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
+ allseqs.add(seqs);
+ }
+
+ boolean colourByChimera = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
+
+ // TODO use StructureViewer as a factory here, see JAL-1761
+ final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
+ final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
+ .size()][]);
+ String newViewId = viewerData.getKey();
+ new ChimeraViewFrame(chimeraSessionFile, af.alignPanel, pdbArray,
+ seqsArray, colourByChimera, colourBySequence, newViewId);
+ }
+
+ /**
+ * Create a new Jmol window. First parse the Jmol state to translate filenames
+ * loaded into the view, and record the order in which files are shown in the
+ * Jmol view, so we can add the sequence mappings in same order.
+ *
+ * @param viewerData
+ * @param af
+ * @param jprovider
+ */
+ protected void createJmolViewer(
+ final Entry<String, StructureViewerModel> viewerData,
+ AlignFrame af, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel svattrib = viewerData.getValue();
+ String state = svattrib.getStateData();
+
+ /*
+ * Pre-2.9: state element value is the Jmol state string
+ *
+ * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
+ * + viewId
+ */
+ if (ViewerType.JMOL.toString().equals(svattrib.getType()))
+ {
+ state = readJarEntry(jprovider,
+ getViewerJarEntryName(svattrib.getViewId()));
+ }
+
+ List<String> pdbfilenames = new ArrayList<String>();
+ List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
+ List<String> pdbids = new ArrayList<String>();
+ StringBuilder newFileLoc = new StringBuilder(64);
+ int cp = 0, ncp, ecp;
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ do