X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fpccx%2FTestPccx.java;h=2e36f25103ff9805ea6727d03887590f9a211ecd;hb=d4d61f9d2969283e821f650d031c169899fb3870;hp=9cb772f9e1e01a0a2b43c30a31b0d0a2a27d22d8;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git diff --git a/forester/java/src/org/forester/pccx/TestPccx.java b/forester/java/src/org/forester/pccx/TestPccx.java index 9cb772f..2e36f25 100644 --- a/forester/java/src/org/forester/pccx/TestPccx.java +++ b/forester/java/src/org/forester/pccx/TestPccx.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; @@ -65,53 +65,53 @@ public class TestPccx { final CoverageCalculator cc = CoverageCalculator.getInstance( new ExternalNodeBasedCoverageMethod(), options ); Coverage cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 / 2 + 1.0 / 3 + 1.0 / 4 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 - + 1.0 / 7 + 1.0 / 5 ) / 9 ) ) { + if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + ( 1.0 / 2 ) + ( 1.0 / 3 ) + ( 1.0 / 4 ) + ( 1.0 / 7 ) + + ( 1.0 / 7 ) + ( 1.0 / 7 ) + ( 1.0 / 7 ) + ( 1.0 / 5 ) ) / 9 ) ) { return false; } names.add( "B" ); names.add( "B" ); cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 - / 7 + 1.0 / 5 ) / 9 ) ) { + if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 + ( 1.0 / 3 ) + ( 1.0 / 4 ) + ( 1.0 / 7 ) + ( 1.0 / 7 ) + + ( 1.0 / 7 ) + ( 1.0 / 7 ) + ( 1.0 / 5 ) ) / 9 ) ) { return false; } names.add( "G" ); cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx - .isEqual( cov.getScore(), - ( 1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 / 4 + 1.0 / 4 + 1.0 + 1.0 / 2 + 1.0 / 4 ) / 9 ) ) { + if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 + ( 1.0 / 3 ) + ( 1.0 / 4 ) + ( 1.0 / 4 ) + ( 1.0 / 4 ) + + 1.0 + ( 1.0 / 2 ) + ( 1.0 / 4 ) ) / 9 ) ) { return false; } names.add( "E" ); cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx.isEqual( cov.getScore(), - ( 1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0 / 4 ) / 9 ) ) { + if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 + ( 1.0 / 3 ) + ( 1.0 / 4 ) + 1.0 + ( 1.0 / 2 ) + 1.0 + + ( 1.0 / 2 ) + ( 1.0 / 4 ) ) / 9 ) ) { return false; } names.add( "X" ); cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx.isEqual( cov.getScore(), - ( 1.0 + 1.0 + 1.0 / 3 + 1.0 / 3 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0 ) / 9 ) ) { + if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 + ( 1.0 / 3 ) + ( 1.0 / 3 ) + 1.0 + ( 1.0 / 2 ) + 1.0 + + ( 1.0 / 2 ) + 1.0 ) / 9 ) ) { return false; } names.add( "C" ); names.add( "C" ); names.add( "C" ); cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx.isEqual( cov.getScore(), - ( 1.0 + 1.0 + 1.0 + 1.0 / 3 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0 ) / 9 ) ) { + if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 + 1.0 + ( 1.0 / 3 ) + 1.0 + ( 1.0 / 2 ) + 1.0 + + ( 1.0 / 2 ) + 1.0 ) / 9 ) ) { return false; } names.add( "D" ); cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx - .isEqual( cov.getScore(), ( 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0 ) / 9 ) ) { + if ( !TestPccx.isEqual( cov.getScore(), + ( 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + ( 1.0 / 2 ) + 1.0 + ( 1.0 / 2 ) + 1.0 ) / 9 ) ) { return false; } names.add( "F" ); cov = cc.calculateCoverage( phylogenies, names, false ); - if ( !TestPccx.isEqual( cov.getScore(), ( 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 / 2 + 1.0 ) / 9 ) ) { + if ( !TestPccx + .isEqual( cov.getScore(), ( 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + ( 1.0 / 2 ) + 1.0 ) / 9 ) ) { return false; } names.add( "H" ); @@ -195,23 +195,27 @@ public class TestPccx { final CoverageCalculator cc2 = CoverageCalculator.getInstance( new ExternalNodeBasedCoverageMethod(), options2 ); Coverage cov2 = cc2.calculateCoverage( phylogenies2, names2, false ); - final double nf = 1 / ( 1 / 0.1 + 1 / 0.7 + 1 / 1.0 + 1 / 1.7 + 1 / 0.3 + 1 / 0.4 + 1 / 0.5 + 1 / 0.6 + 1 / 2.0 ); - if ( !TestPccx.isEqual( cov2.getScore(), ( 1 / 0.1 + ( 1 / 0.8 + 1 / 0.2 + 1 / 0.15 ) / 3 + 1 / 1.3 + 1 - / 4.0 + 1 / 6.4 + 1 / 6.5 + 1 / 6.7 + 1 / 6.8 + 1 / 5.6 ) + final double nf = 1 / ( ( 1 / 0.1 ) + ( 1 / 0.7 ) + ( 1 / 1.0 ) + ( 1 / 1.7 ) + ( 1 / 0.3 ) + ( 1 / 0.4 ) + + ( 1 / 0.5 ) + ( 1 / 0.6 ) + ( 1 / 2.0 ) ); + if ( !TestPccx.isEqual( cov2.getScore(), ( ( 1 / 0.1 ) + + ( ( ( 1 / 0.8 ) + ( 1 / 0.2 ) + ( 1 / 0.15 ) ) / 3 ) + ( 1 / 1.3 ) + ( 1 / 4.0 ) + ( 1 / 6.4 ) + + ( 1 / 6.5 ) + ( 1 / 6.7 ) + ( 1 / 6.8 ) + ( 1 / 5.6 ) ) * nf ) ) { return false; } names2.add( "C" ); cov2 = cc2.calculateCoverage( phylogenies2, names2, false ); - if ( !TestPccx.isEqual( cov2.getScore(), ( 1 / 0.1 + ( 1 / 0.8 + 1 / 0.2 + 1 / 0.15 ) / 3 + 1 / 1.0 + 1 - / 4.0 + 1 / 6.4 + 1 / 6.5 + 1 / 6.7 + 1 / 6.8 + 1 / 5.6 ) + if ( !TestPccx.isEqual( cov2.getScore(), ( ( 1 / 0.1 ) + + ( ( ( 1 / 0.8 ) + ( 1 / 0.2 ) + ( 1 / 0.15 ) ) / 3 ) + ( 1 / 1.0 ) + ( 1 / 4.0 ) + ( 1 / 6.4 ) + + ( 1 / 6.5 ) + ( 1 / 6.7 ) + ( 1 / 6.8 ) + ( 1 / 5.6 ) ) * nf ) ) { return false; } names2.add( "E" ); cov2 = cc2.calculateCoverage( phylogenies2, names2, false ); - if ( !TestPccx.isEqual( cov2.getScore(), ( 1 / 0.1 + ( 1 / 0.8 + 1 / 0.2 + 1 / 0.15 ) / 3 + 1 / 1.0 + +1 - / 4.0 + 1 / 0.3 + 1 / 0.7 + 1 / 3.1 + 1 / 3.2 + 1 / 4.8 ) + if ( !TestPccx.isEqual( cov2.getScore(), ( ( 1 / 0.1 ) + + ( ( ( 1 / 0.8 ) + ( 1 / 0.2 ) + ( 1 / 0.15 ) ) / 3 ) + ( 1 / 1.0 ) + ( +1 / 4.0 ) + ( 1 / 0.3 ) + + ( 1 / 0.7 ) + ( 1 / 3.1 ) + ( 1 / 3.2 ) + ( 1 / 4.8 ) ) * nf ) ) { return false; }