- if(graphLines!=null && index<graphLines.size())\r
- return (GraphLine)graphLines.elementAt(index);\r
+ if(seqRef == null)\r
+ return;\r
+\r
+ sequenceMapping = new java.util.Hashtable();\r
+\r
+ sequenceRef = seqRef;\r
+\r
+ if(startRes < sequenceRef.getStart())\r
+ startRes = sequenceRef.getStart();\r
+\r
+ int seqPos;\r
+\r
+ int fileOffset = 0;\r
+ if(startRes > sequenceRef.getStart())\r
+ {\r
+ fileOffset = startRes - sequenceRef.getStart();\r
+ }\r
+\r
+ for(int i = 0; i < annotations.length; i++)\r
+ {\r
+ seqPos = sequenceRef.findPosition(i + fileOffset);\r
+ if(seqPos<annotations.length)\r
+ {\r
+ if (annotations[i] != null)\r
+ {\r
+ sequenceMapping.put(new Integer(seqPos),\r
+ annotations[i]);\r
+ }\r
+ }\r
+ }\r
+\r
+ adjustForAlignment();\r