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mungo merge
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
5227795
..
3d61b11
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-32,7
+32,6
@@
import jalview.util.QuickSort;
import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
-import java.util.Set;
/**
* Takes in a vector or array of sequences and column start and column end and
/**
* Takes in a vector or array of sequences and column start and column end and
@@
-520,7
+519,7
@@
public class AAFrequency
Hashtable[] hconsensus)
{
final char gapCharacter = alignment.getGapCharacter();
Hashtable[] hconsensus)
{
final char gapCharacter = alignment.getGapCharacter();
- Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
if (mappings == null || mappings.isEmpty())
{
return;
if (mappings == null || mappings.isEmpty())
{
return;
@@
-541,12
+540,16
@@
public class AAFrequency
{
continue;
}
{
continue;
}
- char[] codon = MappingUtils.findCodonFor(seq, col, mappings);
- int codonEncoded = CodingUtils.encodeCodon(codon);
- if (codonEncoded >= 0)
+ List<char[]> codons = MappingUtils
+ .findCodonsFor(seq, col, mappings);
+ for (char[] codon : codons)
{
{
- codonCounts[codonEncoded + 2]++;
- ungappedCount++;
+ int codonEncoded = CodingUtils.encodeCodon(codon);
+ if (codonEncoded >= 0)
+ {
+ codonCounts[codonEncoded + 2]++;
+ ungappedCount++;
+ }
}
}
codonCounts[1] = ungappedCount;
}
}
codonCounts[1] = ungappedCount;