+ }\r
+\r
+ static void validateSequences(AlignmentI source, AlignmentI comp)\r
+ {\r
+ SequenceI[] a1;\r
+ if(source.getHiddenSequences().getSize()>0)\r
+ a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a1 = source.getSequencesArray();\r
+\r
+ SequenceI[] a2;\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a2 = comp.getSequencesArray();\r
+\r
+ int i, iSize=a1.length, j, jSize=a2.length;\r
+ boolean exists = false;\r
+ for(i=0; i<iSize; i++)\r