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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
evoinference
/
distance
/
PairwiseDistanceCalculator.java
diff --git
a/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
b/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
index
0dc6c6e
..
67d4b53
100644
(file)
--- a/
forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
+++ b/
forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
@@
-27,12
+27,10
@@
package org.forester.evoinference.distance;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.msa.Msa;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.msa.Msa;
-import org.forester.sequence.Sequence;
public final class PairwiseDistanceCalculator {
public final class PairwiseDistanceCalculator {
- public static final double DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA = 10; // Felsenstein uses -1
- private static final char GAP = Sequence.GAP;
+ public static final double DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA = 10; // Felsenstein uses -1
private final Msa _msa;
private final double _value_for_too_large_distance_for_kimura_formula;
private final Msa _msa;
private final double _value_for_too_large_distance_for_kimura_formula;
@@
-44,23
+42,12
@@
public final class PairwiseDistanceCalculator {
private double calcFractionalDissimilarity( final int row_1, final int row_2 ) {
final int length = _msa.getLength();
int nd = 0;
private double calcFractionalDissimilarity( final int row_1, final int row_2 ) {
final int length = _msa.getLength();
int nd = 0;
- int n = 0;
- char aa_1;
- char aa_2;
for( int col = 0; col < length; ++col ) {
for( int col = 0; col < length; ++col ) {
- aa_1 = _msa.getResidueAt( row_1, col );
- aa_2 = _msa.getResidueAt( row_2, col );
- if ( ( aa_1 != GAP ) && ( aa_2 != GAP ) ) {
- if ( aa_1 != aa_2 ) {
- nd++;
- }
- n++;
+ if ( _msa.getResidueAt( row_1, col ) != _msa.getResidueAt( row_2, col ) ) {
+ ++nd;
}
}
}
}
- if ( n == 0 ) {
- return 1;
- }
- return ( double ) nd / n;
+ return ( double ) nd / length;
}
/**
}
/**