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JAL-1013 - rename nucleotide and ensure current calculation score model reflected...
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
bc178df
..
aadd8f0
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-105,6
+105,11
@@
public class AAFrequency
for (j = 0; j < jSize; j++)
{
for (j = 0; j < jSize; j++)
{
+ if (sequences[j]==null)
+ {
+ System.err.println("WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
+ }
seq = sequences[j].getSequence();
if (seq.length > i)
{
seq = sequences[j].getSequence();
if (seq.length > i)
{
@@
-204,8
+209,22
@@
public class AAFrequency
boolean includeAllConsSymbols, char[] alphabet)
{
float tval, value;
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++)
{
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)
{
value = 0;
if (ignoreGapsInConsensusCalculation)
{