X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2FTestPhylogenyReconstruction.java;h=3f989a0eee17c95e98328bbabad7ac5eb437c021;hb=e893d04cff700c7c75f26e88e1d945b3c2ae5981;hp=3b4ac8d51dec0ca0ed4c7fbc96d863bbc223fd71;hpb=c6b555fc6d0009cbdfd1dbc3df1f908ff8630dca;p=jalview.git diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 3b4ac8d..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." ); @@ -91,7 +90,7 @@ public class TestPhylogenyReconstruction { else { System.out.println( " failed." ); } - // timeNeighborJoining(); + //timeNeighborJoining(); } public static boolean test( final File test_dir ) { @@ -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 ) ) { @@ -2383,128 +2382,103 @@ 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 ); - 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 ); - Archaeopteryx.createApplication( p2 ); + final Phylogeny p2 = nj2.execute( m2 ); p2.reRoot( p2.getNode( "Bovine" ) ); if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) { return false; @@ -2512,7 +2486,7 @@ public class TestPhylogenyReconstruction { if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) { return false; } - if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153932 ) ) { + if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153931 ) ) { return false; } if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) { @@ -2547,6 +2521,70 @@ public class TestPhylogenyReconstruction { .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 );