+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
+ } catch (NumberFormatException ex)
+ {
+ if (line != null)
+ {
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
+ }
+ }
+ markCalcIds();
+ }
+
+ private static String calcIdPrefix = "JalviewPDB:";
+
+ public static boolean isCalcIdHandled(String calcId)
+ {
+ return calcId != null
+ && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
+ calcIdPrefix,
+ calcIdPrefix.length() + 1) > -1);
+ }
+ public static boolean isCalcIdForFile(String calcId, String pdbFile)
+ {
+ return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
+ + ":" + calcIdPrefix));
+ }
+
+ public static String relocateCalcId(String calcId,
+ Hashtable<String, String> alreadyLoadedPDB) throws Exception
+ {
+ int s = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s);
+ String between = calcId.substring(s, end - 1);
+ return calcIdPrefix + alreadyLoadedPDB.get(between) + ":"
+ + calcId.substring(end);
+ }
+
+ private void markCalcIds()
+ {
+ for (SequenceI sq : seqs)
+ {
+ for (AlignmentAnnotation aa : sq.getAnnotation())
+ {
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+ }
+ }
+ }
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
+ throws Exception
+ {
+ try
+ {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl != null)
+ {
+ Object jmf = cl.getConstructor(new Class[]
+ { FileParse.class }).newInstance(new Object[]
+ { new FileParse(getDataName(), type) });
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+ "getSeqsAsArray", new Class[]
+ {}).invoke(jmf));
+ cl.getMethod("addAnnotations", new Class[]
+ { Alignment.class }).invoke(jmf, al);
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
+ else
+ {
+ sq.getPDBId().clear();
+ }
+ }
+ AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+ }
+ } catch (ClassNotFoundException q)
+ {
+ }
+ }
+
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
+ throws Exception
+ {
+ // System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run
+ // without the HTTPClient bits and pieces needed for accessing Annotate3D
+ // web service
+ try
+ {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl != null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save
+ // bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[]
+ {}).newInstance(new Object[]
+ {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
+ new Class[]
+ { FileParse.class }).invoke(annotate3d, new Object[]
+ { new FileParse(getDataName(), type) }));
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
+ else
+ {
+ sq.getPDBId().clear();
+ }
+ }
+ AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ // ignore classnotfounds - occurs in applet