in progress

[jalview.git] / forester / java / src / org / forester / pccx / TestPccx.java

diff --git a/forester/java/src/org/forester/pccx/TestPccx.java b/forester/java/src/org/forester/pccx/TestPccx.java
index d5bdbdc..2e36f25 100644 (file)
--- a/forester/java/src/org/forester/pccx/TestPccx.java
+++ b/forester/java/src/org/forester/pccx/TestPccx.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,13 +15,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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" );
@@ -158,12 +158,11 @@ public class TestPccx {
             already_covered.add( "X" );
             already_covered.add( "H" );
             already_covered.add( "C" );
-            l = ce
-                    .find( phylogenies,
-                           already_covered,
-                           0,
-                           new ExternalNodeBasedCoverageMethodOptions( "org.forester.pccx.BranchCountingBasedScoringMethod" ),
-                           null );
+            l = ce.find( phylogenies,
+                         already_covered,
+                         0,
+                         new ExternalNodeBasedCoverageMethodOptions( "org.forester.pccx.BranchCountingBasedScoringMethod" ),
+                         null );
             if ( !l.get( 0 ).equals( "E" ) ) {
                 return false;
             }
@@ -196,23 +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;
             }