int res = Integer.parseInt(searchString);\r
found = true;\r
\r
- if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
{\r
seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
}\r
SequenceGroup selection = av.getSelectionGroup();\r
if (selection != null)\r
{\r
- if (selection.getSize() < 1 ||\r
+ if (selection.getSize(false) < 1 ||\r
(selection.getEndRes() - selection.getStartRes() < 2))\r
{\r
selection = null;\r
\r
seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
\r
- if (selection != null && !selection.sequences.contains(seq))\r
+ if (selection != null && !selection.getSequences(false).contains(seq))\r
{\r
seqIndex++;\r
resIndex = 0;\r