/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
\r
for (int i = 0; i < JSEQ.length; i++)\r
{\r
- af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),\r
+ af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),\r
new java.awt.Color(JSEQ[i].getColour()));\r
}\r
\r
if (cs != null)\r
{\r
cs.setThreshold(view.getPidThreshold(), true);\r
- cs.setConsensus(af.viewport.hconsensus);\r
+ cs.setConsensus(af.viewport.getSequenceConsensusHash());\r
}\r
}\r
\r