package org.forester.clade_analysis;
import java.io.File;
-import java.util.List;
-import java.util.regex.Pattern;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
if ( !failed ) {
System.out.println( "OK" );
}
+ else {
+ System.out.println( "NOT OK" );
+ }
}
public static boolean test() {
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;
}
private static boolean testCladeAnalysis3() {
try {
- final Result2 res1 = new Result2();
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res1.toString());
- System.out.println( "------------------------- ");
+ res1.analyze( 0.5 );
+ System.out.print( res1.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res2 = new Result2( "." );
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res2.toString());
- System.out.println( "------------------------- ");
+ res2.analyze( 0.3 );
+ System.out.print( res2.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res3 = new Result2( "." );
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res3.toString());
- System.out.println( "------------------------- ");
+ res3.analyze( 0.3 );
+ System.out.print( res3.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res33 = new Result2( "." );
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res33.toString());
- System.out.println( "------------------------- ");
+ res33.analyze( 0.3 );
+ System.out.print( res33.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res4 = new Result2();
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res4.toString());
- System.out.println( "------------------------- ");
+ res4.analyze( 0.3 );
+ System.out.print( res4.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res5 = new Result2();
+ 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( "B.1.1", 0.2 );
res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
- res5.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res5.toString());
- System.out.println( "------------------------- ");
+ res5.analyze( 0.3 );
+ System.out.print( res5.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res6 = new Result2();
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res6.toString());
- System.out.println( "------------------------- ");
+ res6.analyze( 0.3 );
+ System.out.print( res6.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res7 = new Result2();
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res7.toString());
- System.out.println( "------------------------- ");
+ res7.analyze( 0.3 );
+ System.out.print( res7.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res8 = new Result2( "_/_" );
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res8.toString());
- System.out.println( "------------------------- ");
+ res8.analyze( 0.3 );
+ System.out.print( res8.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res9 = new Result2( "_/_" );
+ 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.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res9.toString());
- System.out.println( "------------------------- ");
+ res9.analyze( 0.3 );
+ System.out.print( res9.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
}
catch ( final Exception e ) {
}
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 ];
- Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
- Result2 res = Analysis2.execute( p1, query, "." );
-
- res.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res.toString());
- System.out.println( "------------------------- ");
+ final ResultMulti res2 = AnalysisMulti.execute( p1 );
+ res2.analyze( 0.3 );
+ System.out.print( res2.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- // Result res = Analysis.execute( p1, "A.1.1.1", "." );
- /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
- return false;
- }
- if ( res.getLeastEncompassingCladeSize() != 4 ) {
- return false;
- }
- if ( res.getTreeSize() != 25 ) {
- return false;
- }
- if ( res.getWarnings().size() != 0 ) {
- return false;
- }*/
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
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 ];
- Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
- Result2 res = Analysis2.execute( p1, query, "." );
-
- res.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res.toString());
- System.out.println( "------------------------- ");
+ final ResultMulti res = AnalysisMulti.execute( p1 );
+ res.analyze( 0.3 );
+ System.out.print( res.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- // Result res = Analysis.execute( p1, "A.1.1.1", "." );
- /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
- return false;
- }
- if ( res.getLeastEncompassingCladeSize() != 4 ) {
- return false;
- }
- if ( res.getTreeSize() != 25 ) {
- return false;
- }
- if ( res.getWarnings().size() != 0 ) {
- return false;
- }*/
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
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 ];
- Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
- Result2 res = Analysis2.execute( p1, query, "." );
-
- res.analyzeGreatestCommonPrefixes( 0.45 );
- System.out.print( res.toString());
- System.out.println( "------------------------- ");
+ final ResultMulti res = AnalysisMulti.execute( p1, 0.45 );
+ System.out.print( res.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- // Result res = Analysis.execute( p1, "A.1.1.1", "." );
- /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
- return false;
- }
- if ( res.getLeastEncompassingCladeSize() != 4 ) {
- return false;
- }
- if ( res.getTreeSize() != 25 ) {
- return false;
- }
- if ( res.getWarnings().size() != 0 ) {
- return false;
- }*/
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
git://source.jalview.org / jalview.git / blobdiff