+ /**
+ * resolve a structural model and generate and add an alignment sequence for
+ * it
+ *
+ * @param refSeq2
+ * @param tempId
+ * @param urlToModel
+ * @param urlToPairwise
+ * @return true if model and sequence was added
+ */
+ private boolean add_structmodel(AlignmentI al, SequenceI refSeq2, String tempId,
+ String urlToModel, String urlToPairwise)
+ {
+ String warningMessage = null, modelPath = null, modelProt = null, aliPath = null, aliProt = null;
+ boolean added = false;
+ try {
+ // locate tempId. if it exists, will need to merge, otherwise:
+ SequenceI templateSeq = al.findName(tempId);
+ // 1. load urlToModel
+ modelPath = resolveAbsolute(urlToModel);
+ modelProt = AppletFormatAdapter.checkProtocol(modelPath);
+ // need to transfer to local temp file ?
+ PDBEntry modelpe = new PDBEntry(tempId, null, Type.FILE, modelPath);
+ PDBEntry templpe = new PDBEntry(tempId, null, Type.FILE, modelPath);
+ refSeq2.addPDBId(modelpe);
+ aliPath = resolveAbsolute(urlToPairwise);
+ aliProt = AppletFormatAdapter.checkProtocol(aliPath);
+ // 2. load urlToPairwise
+ AlignmentI pwa = new AppletFormatAdapter().readFile(aliPath, aliProt,
+ "FASTA");
+ SequenceI qPw = null, tPw = null;
+ if (pwa != null)
+ {
+ // resolve query/template sequences in provided alignment
+ qPw = pwa.findName(refSeqId);
+ tPw = pwa.findName(tempId);
+ }
+ if (false)
+ // (qPw != null && tPw != null)
+ {
+ // not yet complete
+ // refalQ vvva--addrvvvtttddd
+ // refalT ---aaaa---sss---ddd
+ // profalQ ---v-v-v-a.-.-a---dd--r--vvvtt--td--dd
+ // profalT ---.-.-.-aa-a-a---..--.--sss..--.d--dd
+ // Pragmatic solution here:
+ // Map templpe onto refalT only where refalT and refalQ are both
+ // non-gaps
+
+ // columns for start..end in refSeq2
+ int[] gapMap = refSeq2.gapMap();
+ // insert gaps in tPw
+ int curi = 0, width = refSeq2.getLength();
+ // TBC
+ }
+ else
+ {
+ // assume 1:1 - so synthesise sequences to use to construct mapping
+ StructureFile pdbf = StructureSelectionManager
+ .getStructureSelectionManager().setMapping(false,
+ new SequenceI[] { refSeq2.getDatasetSequence() },
+ null, modelPath, modelProt);
+ refSeq2.getDatasetSequence().addPDBId(modelpe);
+ if (templateSeq == null && tPw != null)
+ {
+ tPw.createDatasetSequence();
+ tPw.getDatasetSequence().addPDBId(templpe); // needs to set mapping based on model yet...
+ al.addSequence(tPw);
+ added = true;
+ }
+ }
+ // 3. pad/insert gaps in urlToPairwise according to gaps already present in
+ // refSeq2
+ // 4. add padded tempId sequence to alignment
+ // 4. associate urlToModel with refSeq2 based on position map provided by
+ // urlToPairwise
+ // 5. associate urlToModel with tempId based on position map provided by
+ // urlToPairwise
+ // start a thread to load urlToModel and process/annotate sequences.
+ } catch (IOException x)
+ {
+ warningMessage = x.toString();
+ } finally {
+ if (warningMessage !=null)
+ {
+ System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
+ }
+ return added;
+ }
+ }
+
+ private String resolveAbsolute(String relURI)
+ {
+ if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
+ || "".equals(baseUri) || relURI.startsWith(baseUri))
+ {
+ return relURI;
+ }
+ return baseUri + relURI;
+ }
+