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6905363
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check conservation length
author
amwaterhouse
<Andrew Waterhouse>
Tue, 27 Feb 2007 13:38:40 +0000
(13:38 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 27 Feb 2007 13:38:40 +0000
(13:38 +0000)
src/jalview/schemes/ResidueColourScheme.java
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diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
67828ce
..
f43aa02
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-47,6
+47,7
@@
public class ResidueColourScheme
\r
/** Conservation string as a char array */
\r
char[] conservation;
\r
\r
/** Conservation string as a char array */
\r
char[] conservation;
\r
+ int conservationLength=0;
\r
\r
/** DOCUMENT ME!! */
\r
int inc = 30;
\r
\r
/** DOCUMENT ME!! */
\r
int inc = 30;
\r
@@
-144,7
+145,7
@@
public class ResidueColourScheme
c -= ('a' - 'A');
\r
}
\r
\r
c -= ('a' - 'A');
\r
}
\r
\r
- if (consensus == null || consensus[j] == null)
\r
+ if (consensus == null || consensus.length<j || consensus[j] == null)
\r
{
\r
return false;
\r
}
\r
{
\r
return false;
\r
}
\r
@@
-207,6
+208,7
@@
public class ResidueColourScheme
{
\r
conservation[i] = cons.getConsSequence().getCharAt(i);
\r
}
\r
{
\r
conservation[i] = cons.getConsSequence().getCharAt(i);
\r
}
\r
+ conservationLength = conservation.length;
\r
}
\r
\r
}
\r
}
\r
\r
}
\r
@@
-223,9
+225,9
@@
public class ResidueColourScheme
Color applyConservation(Color currentColour, int i)
\r
{
\r
\r
Color applyConservation(Color currentColour, int i)
\r
{
\r
\r
- if ( (conservation[i] != '*') && (conservation[i] != '+'))
\r
+ if ((conservationLength>i) && (conservation[i] != '*') && (conservation[i] != '+'))
\r
{
\r
{
\r
- if (jalview.util.Comparison.isGap(conservation[i]))
\r
+ if ( jalview.util.Comparison.isGap(conservation[i]))
\r
{
\r
currentColour = Color.white;
\r
}
\r
{
\r
currentColour = Color.white;
\r
}
\r