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add partial button fix to annotation and statistics output
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
3cc57bf
..
57e00fe
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-107,6
+107,7
@@
public class AAFrequency
}
}
}
}
+
/**
* Calculate the consensus symbol(s) for each column in the given range.
*
/**
* Calculate the consensus symbol(s) for each column in the given range.
*
@@
-762,7
+763,7
@@
public class AAFrequency
value = hmm.getMatchEmissionProbability(column, symbol);
double freq;
value = hmm.getMatchEmissionProbability(column, symbol);
double freq;
- if (alph == AMINO && removeBelowBackground)
+ if (AMINO.equals(alph) && removeBelowBackground)
{
freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
if (value < freq)
{
freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
if (value < freq)
@@
-770,7
+771,7
@@
public class AAFrequency
value = 0d;
}
}
value = 0d;
}
}
- else if (alph == DNA && removeBelowBackground)
+ else if (DNA.equals(alph) && removeBelowBackground)
{
freq = ResidueProperties.nucleotideBackgroundFrequencies
.get(symbol);
{
freq = ResidueProperties.nucleotideBackgroundFrequencies
.get(symbol);