From: cmzmasek@gmail.com Date: Thu, 13 Mar 2014 19:52:46 +0000 (+0000) Subject: cleanup X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c6b555fc6d0009cbdfd1dbc3df1f908ff8630dca;p=jalview.git cleanup --- diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index f6d3975..3b4ac8d 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -91,7 +91,7 @@ public class TestPhylogenyReconstruction { else { System.out.println( " failed." ); } - // timeNeighborJoining(); + // timeNeighborJoining(); } public static boolean test( final File test_dir ) { @@ -2504,7 +2504,7 @@ public class TestPhylogenyReconstruction { final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 ); //nj = NeighborJoining.createInstance( true, 6 ); final Phylogeny p2 = nj2.execute( m ); - Archaeopteryx.createApplication( p2 ); + Archaeopteryx.createApplication( p2 ); p2.reRoot( p2.getNode( "Bovine" ) ); if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) { return false; diff --git a/forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java index 692287e..2a0e6ee 100644 --- a/forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java @@ -347,7 +347,7 @@ public final class CopyOfNeighborJoiningR { } public final static CopyOfNeighborJoiningR createInstance( final boolean verbose, - final int maximum_fraction_digits_for_distances ) { + final int maximum_fraction_digits_for_distances ) { return new CopyOfNeighborJoiningR( verbose, maximum_fraction_digits_for_distances ); } } diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java index b4f42ea..7bccea2 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java @@ -138,24 +138,21 @@ public final class NeighborJoining { if ( otu1 < i ) { if ( otu2 > i ) { _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2; - System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) ); + System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) ); } else { _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2; - System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) ); - + System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) ); } } else { if ( otu2 > i ) { _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2; - System.out.print( DF.format( _d_values[ m_i ][ m_otu1 ] ) ); - + System.out.print( DF.format( _d_values[ m_i ][ m_otu1 ] ) ); } else { _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2; - System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) ); - + System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) ); } } System.out.print( " " ); diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java index 384b6e9..db146ed 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -87,7 +87,7 @@ public final class NeighborJoiningR { final PhylogenyNode node = new PhylogenyNode(); //final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] ); final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ]; - final double d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) ); + final double d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) ); final double d2 = d - d1; if ( _df == null ) { _external_nodes[ otu1 ].setDistanceToParent( d1 ); @@ -149,7 +149,7 @@ public final class NeighborJoiningR { if ( j == otu2 ) { continue; } - if ( otu1 < _mappings[ j ] ) { + if ( otu1 < _mappings[ j ] ) { updateDvalue( otu1, otu2, j, d ); } } @@ -159,28 +159,22 @@ public final class NeighborJoiningR { private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) { final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2; System.out.print( DF.format( new_d ) + " " ); - // System.out.println( "going to remove: " + getDvalueUnmapped( otu1, _mappings[ j ] ) + ", " + otu1 + ", " - // + _mappings[ j ] ); - - if ( otu1< _mappings[ j ] ) { + // System.out.println( "going to remove: " + getDvalueUnmapped( otu1, _mappings[ j ] ) + ", " + otu1 + ", " + // + _mappings[ j ] ); + if ( otu1 < _mappings[ j ] ) { _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), otu1, _mappings[ j ] ); } else { - _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ] , otu1 ); + _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ], otu1 ); } - - - // System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " +_mappings[ otu2 ] + ", " - // + _mappings[ j ] ); - - if ( _mappings[ otu2 ] < _mappings[ j ] ) { - _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ] , _mappings[ j ] ); + // System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " +_mappings[ otu2 ] + ", " + // + _mappings[ j ] ); + if ( _mappings[ otu2 ] < _mappings[ j ] ) { + _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], _mappings[ j ] ); } else { - _s.removePairing( getDvalue( j, otu2 ) , _mappings[ j ], _mappings[ otu2 ] ); - + _s.removePairing( getDvalue( j, otu2 ), _mappings[ j ], _mappings[ otu2 ] ); } - _s.addPairing( new_d, otu1, _mappings[ j ] ); setDvalueU( otu1, j, new_d ); } @@ -189,7 +183,7 @@ public final class NeighborJoiningR { if ( i < _mappings[ j ] ) { _d_values[ i ][ _mappings[ j ] ] = d; } - _d_values[_mappings[ j] ][ i ] = d; + _d_values[ _mappings[ j ] ][ i ] = d; } private double getDvalue( final int i, final int j ) {