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 );
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 );
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." );
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." );
System.exit( -1 );
}
}
+ // System.exit( 0 );
System.out.print( "Hmmscan output parser: " );
if ( testHmmscanOutputParser() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
-
-
-
System.out.print( "Tree copy: " );
if ( Test.testTreeCopy() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
-
-
-
-
-
-
System.out.print( "Basic tree methods: " );
if ( Test.testBasicTreeMethods() ) {
System.out.println( "OK." );
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 ) {
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 );
}
// 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 );
}
}
return true;
}
-
-
+
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() ) ) {
+ if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
return false;
}
- if ( !t1.toNewHampshireX().equals( str_0 )) {
+ if ( !t1.toNewHampshireX().equals( str_0 ) ) {
return false;
}
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 )) {
+ 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 )) {
+ if ( !t1.toNewHampshireX().equals( str_0 ) ) {
return false;
}
-
}
catch ( final Exception e ) {
e.printStackTrace();
}
return true;
}
-
private static boolean testCreateBalancedPhylogeny() {
try {
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 );
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;
}
// 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 );
}
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;
}
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;
}
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;
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();