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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
evoinference
/
distance
/
NeighborJoiningR.java
diff --git
a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
index
be18018
..
209b93f
100644
(file)
--- a/
forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
+++ b/
forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java
@@
-120,7
+120,7
@@
public final class NeighborJoiningR {
if ( _verbose ) {
System.out.println( "" );
System.out
if ( _verbose ) {
System.out.println( "" );
System.out
- .println( "----------------------------------------------------------------------------------" );
+ .println( "----------------------------------------------------------------------------------" );
System.out.println( "" );
}
}
System.out.println( "" );
}
}
@@
-183,12
+183,12
@@
public final class NeighborJoiningR {
}
double new_d;
if ( otu1 < mj ) {
}
double new_d;
if ( otu1 < mj ) {
- new_d = ( _d_values[ otu1 ][ mj ] + getDvalue( j, otu2 ) - d ) / 2;
+ new_d = ( ( _d_values[ otu1 ][ mj ] + getDvalue( j, otu2 ) ) - d ) / 2;
_s.addPairing( new_d, otu1, mj );
_d_values[ otu1 ][ mj ] = new_d;
}
else {
_s.addPairing( new_d, otu1, mj );
_d_values[ otu1 ][ mj ] = new_d;
}
else {
- new_d = ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) - d ) / 2;
+ new_d = ( ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) ) - d ) / 2;
_s.addPairing( new_d, mj, otu1 );
_d_values[ mj ][ otu1 ] = new_d;
}
_s.addPairing( new_d, mj, otu1 );
_d_values[ mj ][ otu1 ] = new_d;
}
@@
-259,9
+259,9
@@
public final class NeighborJoiningR {
+ " ("
+ ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
.getName() )
+ " ("
+ ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
.getName() )
- + "+"
- + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
- .getName() ) + ")";
+ + "+"
+ + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
+ .getName() ) + ")";
}
// only the values in the lower triangle are used.
}
// only the values in the lower triangle are used.