+
+ private static boolean testPhyloXMLparsingValidating() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ PhyloXmlParser xml_parser = null;
+ try {
+ xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+ }
+ catch ( final Exception e ) {
+ // Do nothing -- means were not running from jar.
+ }
+ if ( xml_parser == null ) {
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
+ if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
+ xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
+ }
+ else {
+ xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
+ }
+ }
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_1.xml" ),
+ xml_parser );
+ if ( xml_parser.getErrorCount() > 0 ) {
+ System.out.println( xml_parser.getErrorMessages().toString() );
+ return false;
+ }
+ if ( phylogenies_0.length != 3 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testBasicProtein() {
+ try {
+ final BasicProtein p0 = new BasicProtein( "p0", "owl", 0 );
+ final Domain a = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain b = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain c = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain d = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain x = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
+ p0.addProteinDomain( y );
+ p0.addProteinDomain( e );
+ p0.addProteinDomain( b );
+ p0.addProteinDomain( c );
+ p0.addProteinDomain( d );
+ p0.addProteinDomain( a );
+ p0.addProteinDomain( x );
+ if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
+ return false;
+ }
+ if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
+ return false;
+ }
+ //
+ final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
+ final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
+ aa0.addProteinDomain( a1 );
+ if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
+ return false;
+ }
+ if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
+ return false;
+ }
+ //
+ final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
+ final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
+ aa1.addProteinDomain( a11 );
+ aa1.addProteinDomain( a12 );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
+ return false;
+ }
+ aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
+ return false;
+ }
+ aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
+ return false;
+ }
+ aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
+ return false;
+ }
+ aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
+ return false;
+ }
+ if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
+ return false;
+ }
+ //
+ final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
+ final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
+ p00.addProteinDomain( y0 );
+ p00.addProteinDomain( e0 );
+ p00.addProteinDomain( b0 );
+ p00.addProteinDomain( c0 );
+ p00.addProteinDomain( d0 );
+ p00.addProteinDomain( a0 );
+ p00.addProteinDomain( x0 );
+ p00.addProteinDomain( y1 );
+ p00.addProteinDomain( y2 );
+ p00.addProteinDomain( y3 );
+ p00.addProteinDomain( e1 );
+ p00.addProteinDomain( e2 );
+ p00.addProteinDomain( e3 );
+ p00.addProteinDomain( e4 );
+ p00.addProteinDomain( e5 );
+ p00.addProteinDomain( z0 );
+ p00.addProteinDomain( z1 );
+ p00.addProteinDomain( z2 );
+ p00.addProteinDomain( zz0 );
+ p00.addProteinDomain( zz1 );
+ if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 7, "" ).equals( "a~b~c~d~e~e~e~e~e~e~x~y~y~y~y~z~z~z~Z~Z" ) ) {
+ return false;
+ }
+ // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
+ final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final BasicProtein p = new BasicProtein( "p", "owl", 0 );
+ p.addProteinDomain( B15 );
+ p.addProteinDomain( C50 );
+ p.addProteinDomain( A60 );
+ p.addProteinDomain( A30 );
+ p.addProteinDomain( C70 );
+ p.addProteinDomain( B35 );
+ p.addProteinDomain( B40 );
+ p.addProteinDomain( A0 );
+ p.addProteinDomain( A10 );
+ p.addProteinDomain( A20 );
+ p.addProteinDomain( B25 );
+ p.addProteinDomain( D80 );
+ List<String> domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "C" );
+ if ( !p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( !p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ domains_ids.add( "X" );
+ if ( p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "C" );
+ domains_ids.add( "D" );
+ if ( !p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( !p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "D" );
+ domains_ids.add( "C" );
+ if ( !p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ if ( !p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( !p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "B" );
+ if ( !p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( !p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "B" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "C" );
+ domains_ids.add( "A" );
+ domains_ids.add( "C" );
+ domains_ids.add( "D" );
+ if ( !p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testBasicTable() {
+ try {
+ final BasicTable<String> t0 = new BasicTable<String>();
+ if ( t0.getNumberOfColumns() != 0 ) {
+ return false;
+ }
+ if ( t0.getNumberOfRows() != 0 ) {
+ return false;
+ }
+ t0.setValue( 3, 2, "23" );
+ t0.setValue( 10, 1, "error" );
+ t0.setValue( 10, 1, "110" );
+ t0.setValue( 9, 1, "19" );
+ t0.setValue( 1, 10, "101" );
+ t0.setValue( 10, 10, "1010" );
+ t0.setValue( 100, 10, "10100" );
+ t0.setValue( 0, 0, "00" );
+ if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
+ return false;
+ }
+ if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
+ return false;
+ }
+ if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
+ return false;
+ }
+ if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
+ return false;
+ }
+ if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
+ return false;
+ }
+ if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
+ return false;
+ }
+ if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
+ return false;
+ }
+ if ( t0.getNumberOfColumns() != 101 ) {
+ return false;
+ }
+ if ( t0.getNumberOfRows() != 11 ) {
+ return false;
+ }
+ if ( t0.getValueAsString( 49, 4 ) != null ) {
+ return false;
+ }
+ final String l = ForesterUtil.getLineSeparator();
+ final StringBuffer source = new StringBuffer();
+ source.append( "" + l );
+ source.append( "# 1 1 1 1 1 1 1 1" + l );
+ source.append( " 00 01 02 03" + l );
+ source.append( " 10 11 12 13 " + l );
+ source.append( "20 21 22 23 " + l );
+ source.append( " 30 31 32 33" + l );
+ source.append( "40 41 42 43" + l );
+ source.append( " # 1 1 1 1 1 " + l );
+ source.append( "50 51 52 53 54" + l );
+ final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
+ if ( t1.getNumberOfColumns() != 5 ) {
+ return false;
+ }
+ if ( t1.getNumberOfRows() != 6 ) {
+ return false;
+ }
+ if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
+ return false;
+ }
+ if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
+ return false;
+ }
+ if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
+ return false;
+ }
+ if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
+ return false;
+ }
+ final StringBuffer source1 = new StringBuffer();
+ source1.append( "" + l );
+ source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
+ source1.append( " 00; 01 ;02;03" + l );
+ source1.append( " 10; 11; 12; 13 " + l );
+ source1.append( "20; 21; 22; 23 " + l );
+ source1.append( " 30; 31; 32; 33" + l );
+ source1.append( "40;41;42;43" + l );
+ source1.append( " # 1 1 1 1 1 " + l );
+ source1.append( ";;;50 ; ;52; 53;;54 " + l );
+ final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
+ if ( t2.getNumberOfColumns() != 5 ) {
+ return false;
+ }
+ if ( t2.getNumberOfRows() != 6 ) {
+ return false;
+ }
+ if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
+ return false;
+ }
+ if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
+ return false;
+ }
+ if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
+ return false;
+ }
+ if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
+ return false;
+ }
+ if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
+ return false;
+ }
+ if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
+ return false;
+ }
+ final StringBuffer source2 = new StringBuffer();
+ source2.append( "" + l );
+ source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
+ source2.append( " 00; 01 ;02;03" + l );
+ source2.append( " 10; 11; 12; 13 " + l );
+ source2.append( "20; 21; 22; 23 " + l );
+ source2.append( " " + l );
+ source2.append( " 30; 31; 32; 33" + l );
+ source2.append( "40;41;42;43" + l );
+ source2.append( " comment: 1 1 1 1 1 " + l );
+ source2.append( ";;;50 ; 52; 53;;54 " + l );
+ final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
+ ';',
+ false,
+ false,
+ "comment:",
+ false );
+ if ( tl.size() != 2 ) {
+ return false;
+ }
+ final BasicTable<String> t3 = tl.get( 0 );
+ final BasicTable<String> t4 = tl.get( 1 );
+ if ( t3.getNumberOfColumns() != 4 ) {
+ return false;
+ }
+ if ( t3.getNumberOfRows() != 3 ) {
+ return false;
+ }
+ if ( t4.getNumberOfColumns() != 4 ) {
+ return false;
+ }
+ if ( t4.getNumberOfRows() != 3 ) {
+ return false;
+ }
+ if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
+ return false;
+ }
+ if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }