From: cmzmasek@gmail.com Date: Fri, 14 Mar 2014 23:07:33 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e893d04cff700c7c75f26e88e1d945b3c2ae5981;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index fd5ca08..3f989a0 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -34,7 +34,6 @@ import java.util.Date; import java.util.List; import java.util.SortedSet; -import org.forester.archaeopteryx.Archaeopteryx; import org.forester.evoinference.distance.NeighborJoining; import org.forester.evoinference.distance.NeighborJoiningF; import org.forester.evoinference.distance.NeighborJoiningR; @@ -70,13 +69,13 @@ public class TestPhylogenyReconstruction { } public static void main( final String[] args ) { - // System.out.println( "NJ" ); - // if ( testNeighborJoining() ) { - // System.out.println( " OK." ); - // } - // else { - // System.out.println( " failed." ); - // } + System.out.println( "NJ" ); + if ( testNeighborJoining() ) { + System.out.println( " OK." ); + } + else { + System.out.println( " failed." ); + } System.out.println( "S" ); if ( testS() ) { System.out.println( " OK." ); @@ -2192,7 +2191,7 @@ public class TestPhylogenyReconstruction { m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); - njf = NeighborJoiningF.createInstance( false, 5 ); + njf = NeighborJoiningF.createInstance( true, 5 ); final Phylogeny p2f = njf.execute( m ); p2f.reRoot( p2f.getNode( "Bovine" ) ); if ( isUnequal( p2f.getNode( "Chimp" ).getDistanceToParent(), 0.15168 ) ) { @@ -2383,143 +2382,117 @@ public class TestPhylogenyReconstruction { private static boolean testNeighborJoiningR() { try { - // final NeighborJoiningR nj0 = NeighborJoiningR.createInstance(); - // final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 ); - // m0.setIdentifier( 0, "A" ); - // m0.setIdentifier( 1, "B" ); - // m0.setIdentifier( 2, "C" ); - // m0.setIdentifier( 3, "D" ); - // m0.setRow( "5 ", 1 ); - // m0.setRow( "3 6 ", 2 ); - // m0.setRow( "7.5 10.5 5.5", 3 ); - // final Phylogeny p0 = nj0.execute( m0 ); - // p0.reRoot( p0.getNode( "D" ) ); - // // Archaeopteryx.createApplication( p0 ); - // if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) { - // return false; - // } - // if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) { - // return false; - // } - // if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { - // return false; - // } - // if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { - // return false; - // } - // if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { - // return false; - // } - // if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) { - // return false; - // } - BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 ); - // m.setRow( "5", 1 ); - // m.setRow( "4 7", 2 ); - // m.setRow( "7 10 7", 3 ); - // m.setRow( "6 9 6 5", 4 ); - // m.setRow( "8 11 8 9 8", 5 ); - // m.setIdentifier( 0, "A" ); - // m.setIdentifier( 1, "B" ); - // m.setIdentifier( 2, "C" ); - // m.setIdentifier( 3, "D" ); - // m.setIdentifier( 4, "E" ); - // m.setIdentifier( 5, "F" ); - // final NeighborJoiningR nj1 = NeighborJoiningR.createInstance(); - // final Phylogeny p1 = nj1.execute( m ); - // p1.reRoot( p1.getNode( "F" ) ); - // Archaeopteryx.createApplication( p1 ); - // if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) { - // return false; - // } - // if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) { - // return false; - // } - /////////////// - m = new BasicSymmetricalDistanceMatrix( 7 ); - m.setIdentifier( 0, "Bovine" ); - m.setIdentifier( 1, "Mouse" ); - m.setIdentifier( 2, "Gibbon" ); - m.setIdentifier( 3, "Orang" ); - m.setIdentifier( 4, "Gorilla" ); - m.setIdentifier( 5, "Chimp" ); - m.setIdentifier( 6, "Human" ); - m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 ); - m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 ); - m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 ); - m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 ); - m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); - m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); - m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); - final NeighborJoining nj = NeighborJoining.createInstance( true, 6 ); - //nj = NeighborJoining.createInstance( true, 6 ); - final Phylogeny pnj = nj.execute( m ); - pnj.reRoot( pnj.getNode( "Bovine" ) ); - Archaeopteryx.createApplication( pnj ); - // - m = new BasicSymmetricalDistanceMatrix( 7 ); - m.setIdentifier( 0, "Bovine" ); - m.setIdentifier( 1, "Mouse" ); - m.setIdentifier( 2, "Gibbon" ); - m.setIdentifier( 3, "Orang" ); - m.setIdentifier( 4, "Gorilla" ); - m.setIdentifier( 5, "Chimp" ); - m.setIdentifier( 6, "Human" ); - m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 ); - m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 ); - m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 ); - m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 ); - m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); - m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); - m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); + final NeighborJoiningR nj0 = NeighborJoiningR.createInstance(); + final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 ); + m0.setIdentifier( 0, "A" ); + m0.setIdentifier( 1, "B" ); + m0.setIdentifier( 2, "C" ); + m0.setIdentifier( 3, "D" ); + m0.setRow( "5 ", 1 ); + m0.setRow( "3 6 ", 2 ); + m0.setRow( "7.5 10.5 5.5", 3 ); + final Phylogeny p0 = nj0.execute( m0 ); + p0.reRoot( p0.getNode( "D" ) ); + if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } + final BasicSymmetricalDistanceMatrix m1 = new BasicSymmetricalDistanceMatrix( 6 ); + m1.setRow( "5", 1 ); + m1.setRow( "4 7", 2 ); + m1.setRow( "7 10 7", 3 ); + m1.setRow( "6 9 6 5", 4 ); + m1.setRow( "8 11 8 9 8", 5 ); + m1.setIdentifier( 0, "A" ); + m1.setIdentifier( 1, "B" ); + m1.setIdentifier( 2, "C" ); + m1.setIdentifier( 3, "D" ); + m1.setIdentifier( 4, "E" ); + m1.setIdentifier( 5, "F" ); + final NeighborJoiningR nj1 = NeighborJoiningR.createInstance(); + final Phylogeny p1 = nj1.execute( m1 ); + p1.reRoot( p1.getNode( "F" ) ); + if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + final BasicSymmetricalDistanceMatrix m2 = new BasicSymmetricalDistanceMatrix( 7 ); + m2.setIdentifier( 0, "Bovine" ); + m2.setIdentifier( 1, "Mouse" ); + m2.setIdentifier( 2, "Gibbon" ); + m2.setIdentifier( 3, "Orang" ); + m2.setIdentifier( 4, "Gorilla" ); + m2.setIdentifier( 5, "Chimp" ); + m2.setIdentifier( 6, "Human" ); + m2.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 ); + m2.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 ); + m2.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 ); + m2.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 ); + m2.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); + m2.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); + m2.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 ); - //nj = NeighborJoining.createInstance( true, 6 ); - final Phylogeny p2 = nj2.execute( m ); + final Phylogeny p2 = nj2.execute( m2 ); p2.reRoot( p2.getNode( "Bovine" ) ); - Archaeopteryx.createApplication( p2 ); - if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.15168 ) ) { + if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) { return false; } - if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.11752 ) ) { + if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) { return false; } - if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.15393 ) ) { + if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153931 ) ) { return false; } - if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.28469 ) ) { + if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) { return false; } - if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.35793 ) ) { + if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.357931 ) ) { return false; } if ( isUnequal( p2.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) { @@ -2528,26 +2501,90 @@ public class TestPhylogenyReconstruction { if ( isUnequal( p2.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) { return false; } - if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.03982 ) ) { + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.039819 ) ) { return false; } - if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.03982 ) ) { + if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.039819 ) ) { return false; } - if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.02696 ) ) { + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.026956 ) ) { return false; } - if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.04648 ) ) { + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.046481 ) ) { return false; } if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getDistanceToParent(), - 0.42027 ) ) { + 0.420269 ) ) { return false; } if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() .getDistanceToParent(), 0.458845 ) ) { return false; } + // + final BasicSymmetricalDistanceMatrix m3 = new BasicSymmetricalDistanceMatrix( 20 ); + m3.setIdentifier( 0, "F_MOUSE" ); + m3.setIdentifier( 1, "11_RAT" ); + m3.setIdentifier( 2, "A_CAVPO" ); + m3.setIdentifier( 3, "D_HUMAN" ); + m3.setIdentifier( 4, "E_HUMAN" ); + m3.setIdentifier( 5, "F_HUMAN" ); + m3.setIdentifier( 6, "C_HUMAN" ); + m3.setIdentifier( 7, "6_FELCA" ); + m3.setIdentifier( 8, "D_MOUSE" ); + m3.setIdentifier( 9, "E_MOUSE" ); + m3.setIdentifier( 10, "E_RAT " ); + m3.setIdentifier( 11, "C_MOUSE" ); + m3.setIdentifier( 12, "10_RAT" ); + m3.setIdentifier( 13, "3_TAEGU" ); + m3.setIdentifier( 14, "2_SACKO" ); + m3.setIdentifier( 15, "2_PANTR" ); + m3.setIdentifier( 16, "3_CANFA" ); + m3.setIdentifier( 17, "9_HUMAN" ); + m3.setIdentifier( 18, "A_HUMAN" ); + m3.setIdentifier( 19, "B_HUMAN" ); + m3.setRow( "0.000000 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376 ", + 0 ); + m3.setRow( "0.000010 0.000000 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 1 ); + m3.setRow( "0.020875 0.020875 0.000000 0.031503 0.031503 0.031503 0.031503 0.031477 0.020875 0.020875 0.020875 0.020875 0.020875 0.096983 0.768150 0.031503 0.031503 0.031503 0.031503 0.031503", + 2 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000000 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 3 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000000 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 4 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000000 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 5 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000000 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 6 ); + m3.setRow( "0.010368 0.010368 0.031477 0.010375 0.010375 0.010375 0.010375 0.000000 0.010368 0.010368 0.010368 0.010368 0.010368 0.098591 0.745047 0.010375 0.010375 0.010375 0.010375 0.010375", + 7 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000000 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 8 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000000 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 9 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000000 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 10 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000000 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 11 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000000 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 12 ); + m3.setRow( "0.087165 0.087165 0.096983 0.098678 0.098678 0.098678 0.098678 0.098591 0.087165 0.087165 0.087165 0.087165 0.087165 0.000000 0.720387 0.098678 0.098678 0.098678 0.098678 0.098678", + 13 ); + m3.setRow( "0.743570 0.743570 0.768150 0.741282 0.741282 0.741282 0.741282 0.745047 0.743570 0.743570 0.743570 0.743570 0.743570 0.720387 0.000000 0.741282 0.741282 0.741282 0.741282 0.741282", + 14 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000000 0.000010 0.000010 0.000010 0.000010", + 15 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000000 0.000010 0.000010 0.000010", + 16 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000000 0.000010 0.000010", + 17 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000000 0.000010", + 18 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000000", + 19 ); + final NeighborJoiningR nj3 = NeighborJoiningR.createInstance( true, 6 ); + final Phylogeny p3 = nj3.execute( m3 ); } catch ( final Exception e ) { e.printStackTrace( System.out ); diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java index 7bccea2..156d72e 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java @@ -73,7 +73,7 @@ public final class NeighborJoining { updateM(); final int otu1 = _min_i; final int otu2 = _min_j; - System.out.println( _min_i + " " + _min_j ); + //System.out.println( _min_i + " " + _min_j ); // It is a condition that otu1 < otu2. final PhylogenyNode node = new PhylogenyNode(); final double d = _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ]; @@ -138,24 +138,24 @@ 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( " " ); + //System.out.print( " " ); } } @@ -248,28 +248,23 @@ public final class NeighborJoining { } } } - for( int j = 1; j < _n; ++j ) { - final double r_j = _r[ j ]; - final int m_j = _mappings[ j ]; - for( int i = 0; i < j; ++i ) { - System.out.print( i ); - System.out.print( "->" ); - System.out.print( DF.format( _r[ i ] ) ); - System.out.print( " " ); - } - System.out.println(); - } + // for( int j = 1; j < _n; ++j ) { + // final double r_j = _r[ j ]; + // final int m_j = _mappings[ j ]; + // for( int i = 0; i < j; ++i ) { + // System.out.print( i ); + // System.out.print( "->" ); + // System.out.print( DF.format( _r[ i ] ) ); + // System.out.print( " " ); + // } + // System.out.println(); + // } } // otu2 will, in effect, be "deleted" from the matrix. private final void updateMappings( final int otu2 ) { for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) { - System.out.print( _mappings[ i ] ); _mappings[ i ] = _mappings[ i + 1 ]; - System.out.println( "----->" + _mappings[ i ] ); - } - for( int i = 0; i < _mappings.length; ++i ) { - System.out.println( i + "-->" + _mappings[ i ] ); } } diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java index bf2a59f..c8f9b2a 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -155,25 +155,25 @@ public final class NeighborJoiningR { private final void updateDvalue( final int otu1, final int otu2, final int j, final float d ) { final float new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2; - System.out.println( "\nnew d value: " + DF.format( new_d ) ); + // System.out.println( "\nnew d value: " + DF.format( new_d ) ); if ( otu1 < _mappings[ j ] ) { - System.out.println( " otu1=" + otu1 ); - System.out.println( " otu2=" + otu2 ); - System.out.println( "motu1=" + _mappings[ otu1 ] ); - System.out.println( "motu2=" + _mappings[ otu2 ] ); - System.out.println( " j=" + j ); - System.out.println( "mj=" + _mappings[ j ] ); - System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) ); + // System.out.println( " otu1=" + otu1 ); + // System.out.println( " otu2=" + otu2 ); + // System.out.println( "motu1=" + _mappings[ otu1 ] ); + // System.out.println( "motu2=" + _mappings[ otu2 ] ); + // System.out.println( " j=" + j ); + // System.out.println( "mj=" + _mappings[ j ] ); + // System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) ); _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), otu1, _mappings[ j ] ); } else { - System.out.println( " otu1=" + otu1 ); - System.out.println( " otu2=" + otu2 ); - System.out.println( "motu1=" + _mappings[ otu1 ] ); - System.out.println( "motu2=" + _mappings[ otu2 ] ); - System.out.println( " j=" + j ); - System.out.println( "mj=" + _mappings[ j ] ); - System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) ); + // System.out.println( " otu1=" + otu1 ); + // System.out.println( " otu2=" + otu2 ); + // System.out.println( "motu1=" + _mappings[ otu1 ] ); + // System.out.println( "motu2=" + _mappings[ otu2 ] ); + // System.out.println( " j=" + j ); + // System.out.println( "mj=" + _mappings[ j ] ); + // System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) ); _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ], otu1 ); } if ( _mappings[ otu2 ] < _mappings[ j ] ) { @@ -364,16 +364,6 @@ public final class NeighborJoiningR { } } System.out.println(); - /* - for( int i = 0; i < j; ++i ) { - final double m = getDvalue( i, j ) - ( ( _r[ i ] + r_j ) / n_minus_2 ); - if ( m < min ) { - min = m; - _d_min = getDvalue( i, j ); - _min_i = i; - _min_j = j; - } - }*/ } System.out.println(); return min_m; @@ -382,13 +372,13 @@ public final class NeighborJoiningR { // otu2 will, in effect, be "deleted" from the matrix. private final void updateMappings( final int otu2 ) { for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) { - System.out.print( _mappings[ i ] ); + //System.out.print( _mappings[ i ] ); _mappings[ i ] = _mappings[ i + 1 ]; - System.out.println( "----->" + _mappings[ i ] ); - } - for( int i = 0; i < _mappings.length; ++i ) { - System.out.println( i + "-->" + _mappings[ i ] ); + //System.out.println( "----->" + _mappings[ i ] ); } + // for( int i = 0; i < _mappings.length; ++i ) { + // System.out.println( i + "-->" + _mappings[ i ] ); + // } for( int i = 0; i < _n; ++i ) { _rev_mappings[ _mappings[ i ] ] = i; } diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java index ef32273..621b42b 100644 --- a/forester/java/src/org/forester/evoinference/distance/S.java +++ b/forester/java/src/org/forester/evoinference/distance/S.java @@ -114,7 +114,7 @@ public final class S { @Override final public String toString() { - final DecimalFormat df = new DecimalFormat( "0.0000" ); + final DecimalFormat df = new DecimalFormat( "0.000000" ); final StringBuilder sb = new StringBuilder(); for( int j = 0; j < size(); ++j ) { sb.append( j );