+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Ebi Entry Retrieval: " );
+ if ( Test.testEbiEntryRetrieval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Sequence DB tools 2: " );
+ if ( testSequenceDbWsTools2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ System.exit( -1 );
+ }
+ System.out.print( "Uniprot Taxonomy Search: " );
+ if ( Test.testUniprotTaxonomySearch() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ }
+ if ( PERFORM_WEB_TREE_ACCESS ) {
+ System.out.print( "NHX parsing from URL: " );
+ if ( Test.testNHXparsingFromURL() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "NHX parsing from URL 2: " );
+ if ( Test.testNHXparsingFromURL2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "phyloXML parsing from URL: " );
+ if ( Test.testPhyloXMLparsingFromURL() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "TreeBase acccess: " );
+ if ( Test.testTreeBaseReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ System.out.print( "ToL access: " );
+ if ( Test.testToLReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ System.out.print( "TreeFam access: " );
+ if ( Test.testTreeFamReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ //
+ System.out.print( "Pfam tree access: " );
+ if ( Test.testPfamTreeReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ }
+ System.out.println();
+ final Runtime rt = java.lang.Runtime.getRuntime();
+ final long free_memory = rt.freeMemory() / 1000000;
+ final long total_memory = rt.totalMemory() / 1000000;
+ System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
+ + free_memory + "MB, total memory: " + total_memory + "MB)" );
+ System.out.println();
+ System.out.println( "Successful tests: " + succeeded );
+ System.out.println( "Failed tests: " + failed );
+ System.out.println();
+ if ( failed < 1 ) {
+ System.out.println( "OK." );
+ }
+ else {
+ System.out.println( "Not OK." );
+ }
+ }
+
+ public static boolean testEngulfingOverlapRemoval() {
+ try {
+ final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final List<Boolean> covered = new ArrayList<Boolean>();
+ covered.add( true ); // 0
+ covered.add( false ); // 1
+ covered.add( true ); // 2
+ covered.add( false ); // 3
+ covered.add( true ); // 4
+ covered.add( true ); // 5
+ covered.add( false ); // 6
+ covered.add( true ); // 7
+ covered.add( true ); // 8
+ if ( ForesterUtil.isEngulfed( d0, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d1, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d2, covered ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d4, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d5, covered ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
+ return false;
+ }
+ final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
+ final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
+ final Protein abc = new BasicProtein( "abc", "nemve", 0 );
+ abc.addProteinDomain( a );
+ abc.addProteinDomain( b );
+ abc.addProteinDomain( c );
+ final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
+ final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
+ if ( abc.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
+ return false;
+ }
+ if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
+ return false;
+ }
+ final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
+ final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
+ final Protein def = new BasicProtein( "def", "nemve", 0 );
+ def.addProteinDomain( d );
+ def.addProteinDomain( e );
+ def.addProteinDomain( f );
+ final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
+ final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
+ if ( def.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( def_r1.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( def_r2.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
+ return false;
+ }
+ if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
+ return false;
+ }
+ if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ public static final boolean testNHXparsingFromURL2() {
+ try {
+ final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
+ final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
+ false,
+ false,
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ if ( ( phys == null ) || ( phys.length != 5 ) ) {
+ return false;
+ }
+ if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ System.out.println( phys[ 0 ].toNewHampshire() );
+ return false;
+ }
+ if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ System.out.println( phys[ 1 ].toNewHampshire() );
+ return false;
+ }
+ final Phylogeny phys2[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
+ false,
+ false,
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
+ return false;
+ }
+ if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ System.out.println( phys2[ 0 ].toNewHampshire() );
+ return false;
+ }
+ if ( !phys2[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ System.out.println( phys2[ 1 ].toNewHampshire() );
+ return false;
+ }
+ final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
+ + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
+ if ( ( phys3 == null ) || ( phys3.length != 1 ) ) {
+ return false;
+ }
+ if ( !phys3[ 0 ]
+ .toNewHampshire()
+ .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
+ System.out.println( phys3[ 0 ].toNewHampshire() );
+ return false;
+ }
+ final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
+ + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
+ if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
+ return false;
+ }
+ if ( !phys4[ 0 ]
+ .toNewHampshire()
+ .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
+ System.out.println( phys4[ 0 ].toNewHampshire() );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ public static final boolean testNHXparsingFromURL() {
+ try {
+ final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
+ final URL u = new URL( s );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u, new NHXParser() );
+ if ( ( phys == null ) || ( phys.length != 5 ) ) {
+ return false;
+ }
+ if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ System.out.println( phys[ 0 ].toNewHampshire() );
+ return false;
+ }
+ if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ System.out.println( phys[ 1 ].toNewHampshire() );
+ return false;
+ }
+ final URL u2 = new URL( s );
+ final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() );
+ if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
+ return false;
+ }
+ if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ System.out.println( phys2[ 0 ].toNewHampshire() );
+ return false;
+ }
+ final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
+ final NHXParser p = new NHXParser();
+ final URL u3 = new URL( s );
+ p.setSource( u3 );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ System.out.println( e.toString() );
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ public static boolean testOverlapRemoval() {
+ try {
+ final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final List<Boolean> covered = new ArrayList<Boolean>();
+ covered.add( true ); // 0
+ covered.add( false ); // 1
+ covered.add( true ); // 2
+ covered.add( false ); // 3
+ covered.add( true ); // 4
+ covered.add( true ); // 5
+ covered.add( false ); // 6
+ covered.add( true ); // 7
+ covered.add( true ); // 8
+ if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
+ return false;
+ }
+ final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
+ final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
+ final Protein ab = new BasicProtein( "ab", "varanus", 0 );
+ ab.addProteinDomain( a );
+ ab.addProteinDomain( b );
+ final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
+ if ( ab.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
+ return false;
+ }
+ if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
+ return false;
+ }
+ final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
+ if ( ab.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
+ final Domain d = new BasicDomain( "d",
+ ( short ) 10000,
+ ( short ) 10500,
+ ( short ) 1,
+ ( short ) 1,
+ 0.0000001,
+ 1 );
+ final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
+ final Protein cde = new BasicProtein( "cde", "varanus", 0 );
+ cde.addProteinDomain( c );
+ cde.addProteinDomain( d );
+ cde.addProteinDomain( e );
+ final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
+ if ( cde.getNumberOfProteinDomains() != 3 ) {
+ return false;