X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=cd648f8add22824bdc5d8ecda2a8130e485ad2ee;hb=91d1f3e69ae616d45f4f2f421cbb436aaccc7cfc;hp=66bff3d70843385d710f8107bd71ef34cd7b2b97;hpb=380f98efacccdaeff5a86ba6b9b05367df133b79;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 66bff3d..cd648f8 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -175,8 +175,8 @@ public final class Test { if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) { return false; } - final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.01, 1 ); - final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 ); + 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 ); @@ -187,7 +187,7 @@ public final class Test { if ( ab_s0.getNumberOfProteinDomains() != 1 ) { return false; } - if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) { + if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) { return false; } final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab ); @@ -490,18 +490,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - if ( PERFORM_DB_TESTS ) { - System.out.print( "Ebi Entry Retrieval: " ); - if ( Test.testEbiEntryRetrieval() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } - } - ///////////////////////////////////////// System.exit( 0 ); System.out.print( "UniProtKB id extraction: " ); if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) { System.out.println( "OK." ); @@ -521,6 +509,18 @@ public final class Test { failed++; } if ( PERFORM_DB_TESTS ) { + System.out.print( "Ebi Entry Retrieval: " ); + if ( Test.testEbiEntryRetrieval() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } + } + // System.exit( 0 ); + if ( PERFORM_DB_TESTS ) { System.out.print( "Sequence DB tools 2: " ); if ( testSequenceDbWsTools2() ) { System.out.println( "OK." ); @@ -532,6 +532,7 @@ public final class Test { System.exit( -1 ); } } + // System.exit( 0 ); System.out.print( "Hmmscan output parser: " ); if ( testHmmscanOutputParser() ) { System.out.println( "OK." ); @@ -1364,7 +1365,7 @@ public final class Test { private static boolean testBasicPhyloXMLparsing() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final PhyloXmlParser xml_parser = new PhyloXmlParser(); + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml", xml_parser ); if ( xml_parser.getErrorCount() > 0 ) { @@ -1557,7 +1558,7 @@ public final class Test { private static boolean testBasicPhyloXMLparsingRoundtrip() { try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final PhyloXmlParser xml_parser = new PhyloXmlParser(); + final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser(); if ( USE_LOCAL_PHYLOXML_SCHEMA ) { xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); } @@ -1909,7 +1910,7 @@ public final class Test { // Do nothing -- means were not running from jar. } if ( xml_parser == null ) { - xml_parser = new PhyloXmlParser(); + xml_parser = PhyloXmlParser.createPhyloXmlParser(); if ( USE_LOCAL_PHYLOXML_SCHEMA ) { xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); } @@ -2776,7 +2777,7 @@ public final class Test { private static boolean testTreeCopy() { try { - final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])"; + final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]"; final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 ); final Phylogeny t1 = t0.copy(); if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) { @@ -2787,14 +2788,16 @@ public final class Test { } t0.deleteSubtree( t0.getNode( "c" ), true ); t0.deleteSubtree( t0.getNode( "a" ), true ); - t0.deleteSubtree( t0.getNode( "e" ), true ); - if ( !t0.toNewHampshireX().equals( "(b,d)[&&NHX:S=lizards]" ) ) { + t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" ); + t0.getNode( "b" ).setName( "Bee" ); + if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) { return false; } if ( !t1.toNewHampshireX().equals( str_0 ) ) { return false; } - t0.deleteSubtree( t0.getNode( "b" ), true ); + t0.deleteSubtree( t0.getNode( "e" ), true ); + t0.deleteSubtree( t0.getNode( "Bee" ), true ); t0.deleteSubtree( t0.getNode( "d" ), true ); if ( !t1.toNewHampshireX().equals( str_0 ) ) { return false; @@ -5100,7 +5103,10 @@ public final class Test { if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) { return false; } - if ( parser2.getDomainsIgnoredDueToEval() != 0 ) { + if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) { + return false; + } + if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) { return false; } final Protein p1 = proteins.get( 0 ); @@ -5140,12 +5146,6 @@ public final class Test { if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) { return false; } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) { - return false; - } - if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) { - return false; - } if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) { return false; } @@ -8537,7 +8537,7 @@ public final class Test { // Do nothing -- means were not running from jar. } if ( xml_parser == null ) { - xml_parser = new PhyloXmlParser(); + xml_parser = PhyloXmlParser.createPhyloXmlParser(); if ( USE_LOCAL_PHYLOXML_SCHEMA ) { xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD ); } @@ -11295,6 +11295,20 @@ public final class Test { System.out.println( acc.toString() ); return false; } + n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() ) + || !acc.getValue().equals( "71845847" ) ) { + System.out.println( acc.toString() ); + return false; + } + n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" ); + acc = SequenceDbWsTools.obtainSeqAccession( n ); + if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() ) + || !acc.getValue().equals( "AAZ45343.1" ) ) { + System.out.println( acc.toString() ); + return false; + } } catch ( final Exception e ) { return false; @@ -11320,7 +11334,6 @@ public final class Test { } final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); SequenceDbWsTools.obtainSeqInformation( n2 ); - System.out.println( n2.toString() ); if ( !n2.getNodeData().getSequence().getName() .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) { return false; @@ -11336,7 +11349,6 @@ public final class Test { } final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" ); SequenceDbWsTools.obtainSeqInformation( n3 ); - System.out.println( "n=" + n3.toString() ); if ( !n3.getNodeData().getSequence().getName() .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) { return false; @@ -11501,20 +11513,37 @@ public final class Test { System.out.println( entry4.getGeneName() ); return false; } - // if ( !entry4.getChromosome().equals( "ras" ) ) { - // System.out.println( entry4.getChromosome() ); - // return false; - // } - // if ( !entry4.getMap().equals( "ras" ) ) { - // System.out.println( entry4.getMap() ); - // return false; - // } + // if ( !entry4.getChromosome().equals( "ras" ) ) { + // System.out.println( entry4.getChromosome() ); + // return false; + // } + // if ( !entry4.getMap().equals( "ras" ) ) { + // System.out.println( entry4.getMap() ); + // return false; + // } + //TODO FIXME gi... // //TODO fails: // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" ); // if ( !entry5.getAccession().equals( "HM043801" ) ) { // return false; // } + final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" ); + if ( !entry5.getAccession().equals( "AAZ45343" ) ) { + return false; + } + if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) { + System.out.println( entry5.getTaxonomyScientificName() ); + return false; + } + if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) { + System.out.println( entry5.getSequenceName() ); + return false; + } + if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) { + System.out.println( entry5.getTaxonomyIdentifier() ); + return false; + } } catch ( final IOException e ) { System.out.println();