- String confidence = 100 * Double.valueOf(st.nextToken()) + "";
- String pid = st.nextToken();
- String alignRange = st.nextToken() + "-" + st.nextToken();
- String otherInfo = st.hasMoreTokens() ? st.nextToken() : "";
+ String confidence = !st.hasMoreTokens() ? "" : 100
+ * Double.valueOf(st.nextToken()) + "";
+ String pid = !st.hasMoreTokens() ? "" : st.nextToken();
+ String alignRange = !st.hasMoreTokens() ? "" : st.nextToken()
+ + "-" + st.nextToken();
+ String otherInfo = !st.hasMoreTokens() ? "" : st.nextToken();
- if (add_structmodel(al, refSeq, tempId, fastaMapping,
+ if (add_structmodel(al, querySeq, refSeq, tempId,
+ fastaMapping,
String modelFile, String fastaFile, String aRange,
String coverage, String confidence,
String pid, String otherInfo)
String modelFile, String fastaFile, String aRange,
String coverage, String confidence,
String pid, String otherInfo)
- String fastaMappingFile = resolveAbsolute(fastaFile);
- // System.out.println("Model File >> " + fastaMappingFile);
- // System.out.println("Fasta File >> " + structureModelFile);
+ String fastaMappingFile = resolveAbsolute(fastaFile.replaceAll(
+ ".fasta.jal", ".fasta"));
+ // System.out.println("Model File >> " + structureModelFile);
+ // System.out.println("Fasta File >> " + fastaMappingFile);
PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
structureModelFile);
String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
coverage, confidence, pid, otherInfo);
phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
structureModelFile);
String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
coverage, confidence, pid, otherInfo);
phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
- refSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ if (querySequence != null)
+ {
+ querySequence.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ }
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);