+\r
+ if(id==null)\r
+ {\r
+ id = inFile.getName();\r
+ }\r
+ for (int i = 0; i < chains.size(); i++)\r
+ {\r
+ SequenceI seq = ( (PDBChain) chains.elementAt(i)).\r
+ sequence;\r
+ seq.setName(id + "|" + seq.getName());\r
+ Sequence dataset = new Sequence(seq.\r
+ getName(),\r
+ seq.getSequence().toString(), seq.getStart(), seq.getEnd());\r
+\r
+ PDBEntry entry = new PDBEntry();\r
+ entry.setId(id);\r
+ if(inFile!=null)\r
+ entry.setFile(inFile.getAbsolutePath());\r
+\r
+ seq.setDatasetSequence(dataset);\r
+ dataset.addPDBId(entry);\r
+\r
+ getSeqs().addElement(seq);\r
+ }\r