package org.forester.clade_analysis;
import java.io.File;
-import java.util.List;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
System.out.println( "Clade analysis 3 failed" );
failed = true;
}
+ if ( !testCladeAnalysis4() ) {
+ System.out.println( "Clade analysis 4 failed" );
+ failed = true;
+ }
+ if ( !testCladeAnalysis5() ) {
+ System.out.println( "Clade analysis 5 failed" );
+ failed = true;
+ }
+ if ( !testCladeAnalysis6() ) {
+ System.out.println( "Clade analysis 6 failed" );
+ failed = true;
+ }
if ( !failed ) {
System.out.println( "OK" );
}
+ else {
+ System.out.println( "NOT OK" );
+ }
}
public static boolean test() {
if ( !testCladeAnalysis3() ) {
return false;
}
+ if ( !testCladeAnalysis4() ) {
+ return false;
+ }
+ if ( !testCladeAnalysis5() ) {
+ return false;
+ }
+ if ( !testCladeAnalysis6() ) {
+ return false;
+ }
return true;
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
- Result res = Analysis.execute( p1, "A.1.1.1", "." );
+ ResultSingle res = AnalysisSingle.execute( p1, "A.1.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.1.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.1.3", "." );
+ res = AnalysisSingle.execute( p1, "A.1.1.3", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.1.4", "." );
+ res = AnalysisSingle.execute( p1, "A.1.1.4", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.2.1", "." );
+ res = AnalysisSingle.execute( p1, "A.1.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.2.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.2.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.2.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.2.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.3.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.3.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.2.1", "." );
+ res = AnalysisSingle.execute( p1, "A.3.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.3.1", "." );
+ res = AnalysisSingle.execute( p1, "A.3.3.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.4.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.4.1.1.a", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.1.a", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.4.1.2", "." );
- res = Analysis.execute( p1, "A.4.1.2.a", "." );
- res = Analysis.execute( p1, "A.5.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.2.a", "." );
+ res = AnalysisSingle.execute( p1, "A.5.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.5.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.5.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.6.3.12", "." );
+ res = AnalysisSingle.execute( p1, "A.6.3.12", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "B.1.1.1", "." );
+ res = AnalysisSingle.execute( p1, "B.1.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
if ( res.getWarnings().size() != 2 ) {
return false;
}
- res = Analysis.execute( p1, "B.1.234.3", "." );
+ res = AnalysisSingle.execute( p1, "B.1.234.3", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
if ( res.getWarnings().size() != 2 ) {
return false;
}
- res = Analysis.execute( p1, "C.1.1.1", "." );
+ res = AnalysisSingle.execute( p1, "C.1.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.1.1.2", "." );
+ res = AnalysisSingle.execute( p1, "C.1.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.1.2.1", "." );
+ res = AnalysisSingle.execute( p1, "C.1.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.2.1", "." );
+ res = AnalysisSingle.execute( p1, "C.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.3", "." );
+ res = AnalysisSingle.execute( p1, "C.3", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
if ( res.getWarnings().size() != 1 ) {
return false;
}
- res = Analysis.execute( p1, "QE.1.1.1.2.1", "." );
+ res = AnalysisSingle.execute( p1, "QE.1.1.1.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
- Result res = Analysis.execute( p1, "6_DQ278891", null );
+ ResultSingle res = AnalysisSingle.execute( p1, "6_DQ278891", null );
if ( !res.getGreatestCommonPrefix().equals( "6_" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "6xa_EU408330", null );
+ res = AnalysisSingle.execute( p1, "6xa_EU408330", null );
if ( !res.getGreatestCommonPrefix().equals( "6xa_EU40833" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "7a_EF108306", null );
+ res = AnalysisSingle.execute( p1, "7a_EF108306", null );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
}
return true;
}
-
+
private static boolean testCladeAnalysis3() {
try {
- final Result2 res1 = new Result2();
- res1.addGreatestCommonPrefix( "A.1.1", 0.3 );
- res1.addGreatestCommonPrefix( "A.1.2", 0.3 );
- res1.addGreatestCommonPrefix( "A.1.3", 0.3 );
- res1.addGreatestCommonPrefix( "B.1", 0.1 );
-
- List<String> x = ForesterUtil.spliIntoPrefixes( "A.1.2.3.4", "." );
- // System.out.println( x );
- x =ForesterUtil.spliIntoPrefixes( "A", "." );
- // System.out.println( x );
-
-
- res1.analyzeGreatestCommonPrefixes( "." );
-
- final Result2 res2 = new Result2();
- res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
- res2.addGreatestCommonPrefix( "A.1", 0.7 );
- res2.addGreatestCommonPrefix( "A.1.2", 0.1 );
- res2.addGreatestCommonPrefix( "B.1", 0.1 );
- res2.analyzeGreatestCommonPrefixes( "." );
-
- final Result2 res3 = new Result2();
- res3.addGreatestCommonPrefix( "A.1.1.1", 0.7 );
- res3.addGreatestCommonPrefix( "A.1", 0.1 );
- res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
- res3.addGreatestCommonPrefix( "B.1", 0.1 );
- res3.analyzeGreatestCommonPrefixes( "." );
-
-
- final Result2 res4 = new Result2();
- res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35);
- res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 );
- res4.addGreatestCommonPrefix( "A.1", 0.1 );
- res4.addGreatestCommonPrefix( "A.1.2", 0.1 );
- res4.addGreatestCommonPrefix( "B.1", 0.1 );
- res4.analyzeGreatestCommonPrefixes( "." );
-
- final Result2 res5 = new Result2();
- res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2);
- res5.addGreatestCommonPrefix( "C.2.3", 0.2 );
- res5.addGreatestCommonPrefix( "A.1.5", 0.1 );
- res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 );
- res5.addGreatestCommonPrefix( "B.1.1", 0.2 );
- res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
- res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
- res5.analyzeGreatestCommonPrefixes( "." );
+ final ResultMulti res1 = new ResultMulti();
+ res1.addGreatestCommonPrefix( "A.1.1", 0.3 );
+ res1.addGreatestCommonPrefix( "A.1.2", 0.3 );
+ res1.addGreatestCommonPrefix( "A.1.3", 0.3 );
+ res1.addGreatestCommonPrefix( "B.1", 0.1 );
+ res1.analyze( 0.5 );
+ System.out.print( res1.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res2 = new ResultMulti( "." );
+ res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
+ res2.addGreatestCommonPrefix( "A.1", 0.7 );
+ res2.addGreatestCommonPrefix( "A.1.2", 0.1 );
+ res2.addGreatestCommonPrefix( "B.1", 0.1 );
+ res2.analyze( 0.3 );
+ System.out.print( res2.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res3 = new ResultMulti( "." );
+ res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
+ res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 );
+ res3.addGreatestCommonPrefix( "A.1", 0.1 );
+ res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
+ res3.addGreatestCommonPrefix( "B.1", 0.1 );
+ res3.analyze( 0.3 );
+ System.out.print( res3.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res33 = new ResultMulti( "." );
+ res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
+ res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 );
+ res33.addGreatestCommonPrefix( "A.1", 0.1 );
+ res33.addGreatestCommonPrefix( "A.1.2", 0.1 );
+ res33.addGreatestCommonPrefix( "B.1", 0.1 );
+ res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 );
+ res33.analyze( 0.3 );
+ System.out.print( res33.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res4 = new ResultMulti();
+ res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35 );
+ res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 );
+ res4.addGreatestCommonPrefix( "A.1", 0.1 );
+ res4.addGreatestCommonPrefix( "A.1.2", 0.1 );
+ res4.addGreatestCommonPrefix( "B.1", 0.1 );
+ res4.analyze( 0.3 );
+ System.out.print( res4.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res5 = new ResultMulti();
+ res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2 );
+ res5.addGreatestCommonPrefix( "C.2.3", 0.2 );
+ res5.addGreatestCommonPrefix( "A.1.5", 0.1 );
+ res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 );
+ res5.addGreatestCommonPrefix( "B.1.1", 0.2 );
+ res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
+ res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
+ res5.analyze( 0.3 );
+ System.out.print( res5.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res6 = new ResultMulti();
+ res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 );
+ res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 );
+ res6.addGreatestCommonPrefix( "A.1", 0.1 );
+ res6.addGreatestCommonPrefix( "A.1.2", 0.1 );
+ res6.addGreatestCommonPrefix( "B.1", 0.1 );
+ res6.analyze( 0.3 );
+ System.out.print( res6.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res7 = new ResultMulti();
+ res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 );
+ res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 );
+ res7.addGreatestCommonPrefix( "A.1", 0.01 );
+ res7.addGreatestCommonPrefix( "A.1.2", 0.01 );
+ res7.addGreatestCommonPrefix( "B.1", 0.01 );
+ res7.analyze( 0.3 );
+ System.out.print( res7.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res8 = new ResultMulti( "_/_" );
+ res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
+ res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 );
+ res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
+ res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
+ res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
+ res8.analyze( 0.3 );
+ System.out.print( res8.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ final ResultMulti res9 = new ResultMulti( "_/_" );
+ res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
+ res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 );
+ res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
+ res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
+ res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
+ res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 );
+ res9.analyze( 0.3 );
+ System.out.print( res9.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testCladeAnalysis4() {
+ try {
+ final File intreefile1 = new File( PATH_TO_TEST_DATA + "pplacer_2.tre" );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
+ final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
+ ResultMulti res2 = AnalysisMulti.execute( p1 );
+ res2.analyze( 0.3 );
+ System.out.print( res2.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testCladeAnalysis5() {
+ try {
+ final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_3.xml" );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
+ final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
+ ResultMulti res = AnalysisMulti.execute( p1 );
+ res.analyze( 0.3 );
+ System.out.print( res.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testCladeAnalysis6() {
+ try {
+ final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_4.xml" );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
+ final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
+ ResultMulti res = AnalysisMulti.execute( p1, 0.45 );
+ System.out.print( res.toString() );
+ System.out.println( "------------------------- " );
+ System.out.println();
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
git://source.jalview.org / jalview.git / blobdiff