+ /**
+ *
+ * @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
+ *
+ * NB this is the 'saved' viewId as in the project file XML, _not_ the
+ * 'uniquified' sviewid used to reconstruct the viewer here
+ */
+ String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
+ chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
+ "chimera", null);
+
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
+ List<PDBEntry> pdbs = new ArrayList<>();
+ List<SequenceI[]> allseqs = new ArrayList<>();
+ 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();
+
+ ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
+ af.alignPanel, pdbArray, seqsArray, colourByChimera,
+ colourBySequence, newViewId);
+ cvf.setSize(data.getWidth(), data.getHeight());
+ cvf.setLocation(data.getX(), data.getY());
+ }
+
+ /**
+ * 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<>();
+ List<SequenceI[]> seqmaps = new ArrayList<>();
+ List<String> pdbids = new ArrayList<>();
+ StringBuilder newFileLoc = new StringBuilder(64);
+ int cp = 0, ncp, ecp;
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ do
+ {
+ // look for next filename in load statement
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do
+ // filename
+ // translation differently.
+ StructureData filedat = oldFiles.get(new File(oldfilenam));
+ if (filedat == null)