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[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
a79f083
..
8061e67
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-21,6
+21,7
@@
package jalview.schemes;
import java.awt.*;
\r
\r
import jalview.datamodel.*;
\r
import java.awt.*;
\r
\r
import jalview.datamodel.*;
\r
+import jalview.analysis.AAFrequency;
\r
\r
public class PIDColourScheme
\r
extends ResidueColourScheme
\r
\r
public class PIDColourScheme
\r
extends ResidueColourScheme
\r
@@
-43,6
+44,12
@@
public class PIDColourScheme
s = String.valueOf(res -= ('a' - 'A'));
\r
}
\r
\r
s = String.valueOf(res -= ('a' - 'A'));
\r
}
\r
\r
+ if (consensus == null
\r
+ || j >= consensus.length
\r
+ || consensus[j]==null)
\r
+ {
\r
+ return Color.white;
\r
+ }
\r
\r
if ( (threshold != 0) && !aboveThreshold(s, j))
\r
{
\r
\r
if ( (threshold != 0) && !aboveThreshold(s, j))
\r
{
\r
@@
-56,7
+63,7
@@
public class PIDColourScheme
if(consensus.length<=j)
\r
return Color.white;
\r
\r
if(consensus.length<=j)
\r
return Color.white;
\r
\r
- if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
\r
+ if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
\r
consensus[j].contains(s))
\r
{
\r
sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
\r
consensus[j].contains(s))
\r
{
\r
sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
\r