- 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
- entry.setFile(inFile.getAbsolutePath());\r
-\r
- seq.setDatasetSequence(dataset);\r
- dataset.addPDBId(entry);\r
-\r
- getSeqs().addElement(seq);\r
- }\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(),\r
+ 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
+ }catch(OutOfMemoryError er)\r
+ {\r
+ System.out.println("OUT OF MEMORY LOADING PDB FILE");\r
+ throw new IOException("Out of memory loading PDB File");\r
+ }\r