/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
boolean includeAllConsSymbols, char[] alphabet)
{
float tval, value;
+ if (consensus==null || consensus.annotations==null || consensus.annotations.length<width)
+ {
+ // called with a bad alignment annotation row - wait for it to be initialised properly
+ return;
+ }
for (int i = iStart; i < width; i++)
{
+ if (i>=hconsensus.length) {
+ // happens if sequences calculated over were shorter than alignment width
+ consensus.annotations[i]=null;
+ continue;
+ }
value = 0;
if (ignoreGapsInConsensusCalculation)
{