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Add pdb ref
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
3d1c18b
..
1575a6a
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-49,31
+49,35
@@
public class PIDColourScheme
return Color.white;
\r
}
\r
\r
return Color.white;
\r
}
\r
\r
-
\r
-
\r
- Color c = Color.white;
\r
+ currentColour = Color.white;
\r
\r
double sc = 0;
\r
\r
\r
double sc = 0;
\r
\r
- if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
\r
- consensus[j].contains(s))
\r
- {
\r
- sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
\r
+ if(consensus.length<=j)
\r
+ return Color.white;
\r
\r
\r
- if (!jalview.util.Comparison.isGap( res ))
\r
+ if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
\r
+ consensus[j].contains(s))
\r
{
\r
{
\r
- for (int i = 0; i < thresholds.length; i++)
\r
+ sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
\r
+
\r
+ if (!jalview.util.Comparison.isGap(res))
\r
{
\r
{
\r
- if (sc > thresholds[i])
\r
+ for (int i = 0; i < thresholds.length; i++)
\r
{
\r
{
\r
- c = pidColours[i];
\r
+ if (sc > thresholds[i])
\r
+ {
\r
+ currentColour = pidColours[i];
\r
\r
\r
- break;
\r
+ break;
\r
+ }
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
- }
\r
\r
\r
- return c;
\r
+ if(conservationColouring)
\r
+ applyConservation(j);
\r
+
\r
+ return currentColour;
\r
}
\r
}
\r
}
\r
}
\r