- for (int i = 0; i < sequences.size();i++) {\r
- String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);\r
- if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {\r
+ for (int i = 0; i < sequences.size();i++)\r
+ {\r
+ if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())\r
+ { count++; continue;}\r
+\r
+ char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);\r
+ if (jalview.util.Comparison.isGap((c)))\r