}\r
\r
// We define some Regexes here that will be used regularily later\r
- rend = new Regex("\\/\\/"); // Find the end of an alignment\r
+ rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
// id/from/to\r
s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r