/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
}\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
if (x.search(annContent))\r
{\r
// parse out and create alignment annotation directly.\r
- parseAnnotationRow(annotations, x.stringMatched(1), x\r
- .stringMatched(2));\r
+ parseAnnotationRow(annotations, x.stringMatched(1),\r
+ x.stringMatched(2));\r
}\r
}\r
else if (annType.equals("GR"))\r