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more tests for isDuplication() and isSpecation() added
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
msa
/
MsaMethods.java
diff --git
a/forester/java/src/org/forester/msa/MsaMethods.java
b/forester/java/src/org/forester/msa/MsaMethods.java
index
881e622
..
2b47020
100644
(file)
--- a/
forester/java/src/org/forester/msa/MsaMethods.java
+++ b/
forester/java/src/org/forester/msa/MsaMethods.java
@@
-107,12
+107,11
@@
public final class MsaMethods {
_ignored_seqs_ids = new ArrayList<String>();
}
_ignored_seqs_ids = new ArrayList<String>();
}
- public static final DescriptiveStatistics calcNumberOfGapsPer100Stats( final Msa msa ) {
+ public static final DescriptiveStatistics calcNumberOfGapsStats( final Msa msa ) {
final int[] gaps = calcNumberOfGapsInMsa( msa );
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
final int[] gaps = calcNumberOfGapsInMsa( msa );
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- final double n = 100.0 / msa.getLength();
for( final int gap : gaps ) {
for( final int gap : gaps ) {
- stats.addValue( n * gap );
+ stats.addValue( gap );
}
return stats;
}
}
return stats;
}