// 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;
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" );
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;
}