sqinfo.put("Name", seq.getName());\r
sqinfo.put("Start", new Integer(seq.getStart()));\r
sqinfo.put("End", new Integer(seq.getEnd()));\r
- sqinfo.put("SeqFeatures", seq.getSequenceFeatures());\r
+ sqinfo.put("SeqFeatures", (seq.getSequenceFeatures() !=null) ? seq.getSequenceFeatures() : new Vector());\r
sqinfo.put("PdbId",\r
(seq.getPDBId() != null) ? seq.getPDBId() : new String(""));\r
-\r
+ sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));\r
return sqinfo;\r
}\r
\r
java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(\r
"SeqFeatures");\r
String pdbid = (String) sqinfo.get("PdbId");\r
-\r
+ Sequence seqds = (Sequence) sqinfo.get("datasetSequence");\r
if (oldname == null)\r
{\r
namePresent = false;\r
sq.setEnd(end.intValue());\r
}\r
\r
- if (sfeatures != null)\r
+ if ((sfeatures != null) && (sfeatures.size()>0))\r
{\r
sq.setSequenceFeatures(sfeatures);\r
}\r
+ if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {\r
+ sq.setDatasetSequence(seqds);\r
+ }\r
\r
return namePresent;\r
}\r
{\r
// Generate a safely named sequence set and a hash to recover the sequence names\r
Hashtable map = new Hashtable();\r
- String[] un_names = new String[sequences.length];\r
+ //String[] un_names = new String[sequences.length];\r
\r
for (int i = 0; i < sequences.length; i++)\r
{\r