From: cmzmasek@gmail.com Date: Thu, 24 May 2012 02:24:59 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=99fc1a4a87f0753845f497a73e2ac98ad05c1cc6;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java index ef7fe92..18182e5 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java @@ -67,7 +67,8 @@ public final class NeighborJoining { for( int i = 0; i < _n; ++i ) { d = 0; for( int n = 0; n < _n; ++n ) { - d += getValueFromD( i, n ); + // d += getValueFromD( i, n ); + d += _d._values[ _mappings[ i ] ][ _mappings[ n ] ]; } _r[ i ] = d; } @@ -78,7 +79,6 @@ public final class NeighborJoining { final Phylogeny phylogeny = new Phylogeny(); while ( _n > 2 ) { updateM(); - //final int[] s = findMinimalDistance(); // Calculates the minimal distance. // If more than one minimal distances, always the first found is used // could randomize this, so that any would be returned in a randomized fashion... @@ -96,9 +96,6 @@ public final class NeighborJoining { } } } - // - // final int otu1 = s[ 0 ]; - // final int otu2 = s[ 1 ]; // It is a condition that otu1 < otu2. if ( DEBUG ) { if ( otu1 > otu2 ) { @@ -217,7 +214,9 @@ public final class NeighborJoining { for( int i = 0; i < j; ++i ) { //_m.setValue( i, j, calculateM( i, j ) ); //_m.setValue( i, j, getValueFromD( i, j ) - ( _r[ i ] + _r[ j ] ) / ( _n - 2 ) ); - _m._values[ i ][ j ] = getValueFromD( i, j ) - ( _r[ i ] + _r[ j ] ) / ( _n - 2 ); + //_m._values[ i ][ j ] = getValueFromD( i, j ) - ( _r[ i ] + _r[ j ] ) / ( _n - 2 ); + _m._values[ i ][ j ] = _d._values[ _mappings[ i ] ][ _mappings[ j ] ] - ( _r[ i ] + _r[ j ] ) + / ( _n - 2 ); } } }