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add partial button fix to annotation and statistics output
[jalview.git]
/
src
/
jalview
/
schemes
/
HMMERColourScheme.java
diff --git
a/src/jalview/schemes/HMMERColourScheme.java
b/src/jalview/schemes/HMMERColourScheme.java
index
a7fc8b8
..
f545fe6
100644
(file)
--- a/
src/jalview/schemes/HMMERColourScheme.java
+++ b/
src/jalview/schemes/HMMERColourScheme.java
@@
-51,19
+51,22
@@
public class HMMERColourScheme extends ResidueColourScheme
}
Double prob;
prob = hmm.getMatchEmissionProbability(position, symbol);
}
Double prob;
prob = hmm.getMatchEmissionProbability(position, symbol);
+ if (prob == 0)
+ {
+ return Color.red;
+ }
double freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
double freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
- Double value = prob - freq;
-
+ Double value = Math.log(prob / freq);
Color colour = null;
Color colour = null;
- if (value >= 0)
+ if (value > 0)
{
colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
{
colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
- Color.WHITE, 1f, Color.green);
+ Color.WHITE, 3f, Color.blue);
}
else if (value < 0)
{
}
else if (value < 0)
{
- return Color.YELLOW;
+ return Color.ORANGE;
}
return colour;
}
return colour;