+ if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=\r
+ -1) &&\r
+ consensus[j].contains(String.valueOf(c)))\r
+ {\r
+ sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
+\r
+ if (!jalview.util.Comparison.isGap(c))\r