private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
+ ForesterUtil.getFileSeparator() + "test_data"
+ ForesterUtil.getFileSeparator();
- private final static boolean PERFORM_DB_TESTS = false;
+ private final static boolean PERFORM_DB_TESTS = true;
private static final boolean PERFORM_WEB_TREE_ACCESS = true;
private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
+ ForesterConstants.PHYLO_XML_VERSION + "/"
succeeded++;
}
System.out.println( "OK." );
+ System.out.print( "Taxonomy data extraction: " );
+ if ( Test.testExtractTaxonomyDataFromNodeName() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Taxonomy code extraction: " );
if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
System.out.println( "OK." );
return false;
}
final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
- if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
+ if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) {
return false;
}
final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
return false;
}
- //
if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
return false;
}
if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
return false;
}
- //
final Phylogeny[] t2 = factory
.create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);",
new NHXParser() );
for( final Phylogeny target : t2 ) {
ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
}
- //
final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
new NHXParser() )[ 0 ];
final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
System.out.println( entry.getSequenceName() );
return false;
}
- // if ( !entry.getSequenceSymbol().equals( "" ) ) {
- // System.out.println( entry.getSequenceSymbol() );
- // return false;
- // }
if ( !entry.getGeneName().equals( "treX-like" ) ) {
System.out.println( entry.getGeneName() );
return false;
if ( entry.getCrossReferences().size() != 5 ) {
return false;
}
- //
final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
return false;
if ( entry1.getCrossReferences().size() != 6 ) {
return false;
}
- //
final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
if ( !entry2.getAccession().equals( "NM_184234" ) ) {
return false;
if ( entry3.getCrossReferences().size() != 8 ) {
return false;
}
- //
- //
final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
if ( !entry4.getAccession().equals( "AAA36557" ) ) {
return false;
return true;
}
+ private static boolean testExtractTaxonomyDataFromNodeName() {
+ try {
+ PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" );
+ if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" );
+ if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" );
+ if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" );
+ if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" );
+ if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode( "HNRPR_HUMAN" );
+ if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode( "HNRPR_HUMAN_X" );
+ if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testExtractTaxonomyCodeFromNodeName() {
try {
if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
return false;
}
- if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
+ if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) {
return false;
}
if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
return false;
}
- //
final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
if ( !ext.get( 4 ).getName().equals( "h" ) ) {
return false;
}
- //
- //
ext.clear();
final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
return false;
}
- //
- //
ext.clear();
final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
return false;
}
- //
- //
ext.clear();
final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
return false;
}
- //
- //
final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 7 ).getName().equals( "h" ) ) {
return false;
}
- //
- //
final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 6 ).getName().equals( "h" ) ) {
return false;
}
- //
- //
final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 6 ).getName().equals( "h" ) ) {
return false;
}
- //
- //
final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 6 ).getName().equals( "h" ) ) {
return false;
}
- //
- //
final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
return false;
}
- //
- //
final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
return false;
}
- //
- //
final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
return false;
}
- //
- //
final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
return false;
}
- //
- //
final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
return false;
}
- //
- //
final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
ext.clear();
if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
return false;
}
- //
- //
final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
ext.clear();
if ( phy != null ) {
return false;
}
- //
p.reset();
if ( !p.hasNext() ) {
return false;
if ( phy != null ) {
return false;
}
- ////
p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
if ( !p.hasNext() ) {
return false;
if ( phy != null ) {
return false;
}
- //
p.reset();
if ( !p.hasNext() ) {
return false;
if ( phy != null ) {
return false;
}
- //
p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
if ( !p.hasNext() ) {
return false;
}
final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
SequenceDbWsTools.obtainSeqInformation( n2 );
- if ( !n2.getNodeData().getSequence().getName()
- .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
+ if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) {
return false;
}
if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
System.out.println( "provider=" + id.getSource() );
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
if ( !s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
System.out.println( n17.toString() );
return false;
}
- //
final PhylogenyNode n18 = PhylogenyNode
.createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
System.out.println( n21.toString() );
return false;
}
- final PhylogenyNode n22 = PhylogenyNode
- .createInstanceFromNhxString( "NEMVE_Nematostella_vectensis",
- NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
- if ( !n22.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
- System.out.println( n22.toString() );
- return false;
- }
final PhylogenyNode n23 = PhylogenyNode
.createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
return false;
}
+ if ( !entry
+ .getMolecularSequence()
+ .getMolecularSequenceAsString()
+ .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
+ || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
+ System.out.println( entry.getMolecularSequence().getMolecularSequenceAsString() );
+ return false;
+ }
}
catch ( final IOException e ) {
System.out.println();