- tree = new NJTree(seq, type, pwtype, start, end);\r
+ {\r
+ int start, end;\r
+ SequenceI [] seqs;\r
+ String [] seqStrings = null;\r
+ // if (av.hasHiddenColumns)\r
+ {\r
+ // seqStrings = av.getSelectionAsString();\r
+ }\r
+\r
+ if(av.getSelectionGroup()==null)\r
+ {\r
+ start = 0;\r
+ end = av.alignment.getWidth();\r
+ seqs = av.alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ start = av.getSelectionGroup().getStartRes();\r
+ end = av.getSelectionGroup().getEndRes()+1;\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+\r
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+ }\r