- int hiddenIndex = av.adjustForHiddenSeqs(i);\r
- int lastIndex = av.adjustForHiddenSeqs(i - 1);\r
- int nextIndex = av.adjustForHiddenSeqs(i + 1);\r
+ SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\r
+ //Use this method here instead of calling hiddenSeq adjust\r
+ //3 times.\r
+ int hSize = hseqs.length;\r
+\r
+ int hiddenIndex = i;\r
+ int lastIndex = i - 1;\r
+ int nextIndex = i + 1;\r