import org.forester.sdi.SDIR;
import org.forester.sdi.TestGSDI;
import org.forester.sequence.BasicSequence;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.species.BasicSpecies;
import org.forester.species.Species;
import org.forester.surfacing.TestSurfacing;
public final class Test {
private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
- + ForesterUtil.getFileSeparator() + "resources"
- + ForesterUtil.getFileSeparator();
+ + ForesterUtil.getFileSeparator() + "resources"
+ + ForesterUtil.getFileSeparator();
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;
+ + ForesterUtil.getFileSeparator() + "test_data"
+ + ForesterUtil.getFileSeparator();
+ 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 + "/"
- + ForesterConstants.PHYLO_XML_XSD;
+ + ForesterConstants.PHYLO_XML_VERSION + "/"
+ + ForesterConstants.PHYLO_XML_XSD;
private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
- + ForesterConstants.PHYLO_XML_VERSION + "/"
- + ForesterConstants.PHYLO_XML_XSD;
+ + ForesterConstants.PHYLO_XML_VERSION + "/"
+ + ForesterConstants.PHYLO_XML_XSD;
private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
private final static double ZERO_DIFF = 1.0E-9;
public static void main( final String[] args ) {
System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
- + "]" );
+ + "]" );
Locale.setDefault( Locale.US );
System.out.println( "[Locale: " + Locale.getDefault() + "]" );
int failed = 0;
System.exit( -1 );
}
final long start_time = new Date().getTime();
- System.out.print( "MSA entropy: " );
- if ( Test.testMsaEntropy() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
System.out.print( "Basic node methods: " );
if ( Test.testBasicNodeMethods() ) {
System.out.println( "OK." );
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." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "MSA entropy: " );
+ if ( Test.testMsaEntropy() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
if ( PERFORM_DB_TESTS ) {
System.out.print( "Uniprot Entry Retrieval: " );
if ( Test.testUniprotEntryRetrieval() ) {
}
catch ( final Exception e ) {
e.printStackTrace();
+ return false;
}
return true;
}
System.out.println( phys[ 1 ].toNewHampshire() );
return false;
}
- final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
+ final URL u2 = new URL( s );
+ final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() );
if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
return false;
}
}
final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
final NHXParser p = new NHXParser();
- final URL u2 = new URL( s );
- p.setSource( u2 );
+ final URL u3 = new URL( s );
+ p.setSource( u3 );
if ( !p.hasNext() ) {
return false;
}
}
}
catch ( final Exception e ) {
+ System.out.println( e.toString() );
e.printStackTrace();
+ return false;
}
return true;
}
private static boolean testAminoAcidSequence() {
try {
- final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
+ final MolecularSequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
if ( aa1.getLength() != 13 ) {
return false;
}
if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
return false;
}
- final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
- if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
+ final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
+ if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) {
return false;
}
- final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
+ final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
return false;
}
- final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
+ final MolecularSequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
return false;
}
if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
return false;
}
+ if ( !t3.getNode( "root node" ).isDuplication() ) {
+ return false;
+ }
+ if ( !t3.getNode( "node a" ).isDuplication() ) {
+ return false;
+ }
+ if ( t3.getNode( "node a" ).isSpeciation() ) {
+ return false;
+ }
+ if ( t3.getNode( "node bc" ).isDuplication() ) {
+ return false;
+ }
+ if ( !t3.getNode( "node bc" ).isSpeciation() ) {
+ return false;
+ }
if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
return false;
}
return false;
}
if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
- .getConfidence() != 2144 ) {
+ .getConfidence() != 0 ) {
return false;
}
if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
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;
System.out.println( entry.getAnnotations().first().getRefSource() );
return false;
}
- if ( entry.getCrossReferences().size() != 5 ) {
+ if ( entry.getCrossReferences().size() < 1 ) {
return false;
}
- //
final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
return false;
System.out.println( entry1.getGeneName() );
return false;
}
- if ( entry1.getCrossReferences().size() != 6 ) {
+ if ( entry1.getCrossReferences().size() < 1 ) {
return false;
}
- //
final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
if ( !entry2.getAccession().equals( "NM_184234" ) ) {
return false;
System.out.println( entry2.getGeneName() );
return false;
}
- if ( entry2.getCrossReferences().size() != 3 ) {
+ if ( entry2.getCrossReferences().size() < 1 ) {
+ return false;
+ }
+ if ( !entry2.getChromosome().equals( "20" ) ) {
+ return false;
+ }
+ if ( !entry2.getMap().equals( "20q11.22" ) ) {
return false;
}
- //
final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
if ( !entry3.getAccession().equals( "HM043801" ) ) {
return false;
if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
return false;
}
- if ( entry3.getCrossReferences().size() != 8 ) {
+ if ( entry3.getCrossReferences().size() < 1 ) {
return false;
}
- //
- //
final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
if ( !entry4.getAccession().equals( "AAA36557" ) ) {
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;
- // }
- //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;
System.out.println( entry5.getTaxonomyIdentifier() );
return false;
}
+ final SequenceDatabaseEntry entry6 = SequenceDbWsTools.obtainEntry( "M30539" );
+ if ( !entry6.getAccession().equals( "M30539" ) ) {
+ return false;
+ }
+ if ( !entry6.getGeneName().equals( "ras" ) ) {
+ return false;
+ }
+ if ( !entry6.getSequenceName().equals( "Human SK2 c-Ha-ras-1 oncogene-encoded protein gene, exon 1" ) ) {
+ return false;
+ }
+ if ( !entry6.getTaxonomyIdentifier().equals( "9606" ) ) {
+ return false;
+ }
+ if ( !entry6.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
+ return false;
+ }
+ if ( entry6.getCrossReferences().size() < 1 ) {
+ return false;
+ }
}
catch ( final IOException e ) {
System.out.println();
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 ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
+ .equals( "MOUSE" ) ) {
return false;
}
if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
+ .equals( "MOUSE" ) ) {
return false;
}
if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
+ .equals( "MOUSE" ) ) {
return false;
}
if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
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" ) ) {
final String test_dir = Test.PATH_TO_TEST_DATA;
try {
final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
- + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
+ + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
parser1.parse();
final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
- + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
+ + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
final List<Protein> proteins = parser2.parse();
if ( parser2.getProteinsEncountered() != 4 ) {
return false;
private static boolean testMsaQualityMethod() {
try {
- final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
- final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
- final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
- final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
- final List<Sequence> l = new ArrayList<Sequence>();
+ final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
+ final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
+ final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
+ final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
+ final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
l.add( s0 );
l.add( s1 );
l.add( s2 );
private static boolean testMsaEntropy() {
try {
- final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
- final Sequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
- final Sequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
- final Sequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
- final List<Sequence> l = new ArrayList<Sequence>();
+ final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
+ final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
+ final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
+ final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
+ final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
l.add( s0 );
l.add( s1 );
l.add( s2 );
l.add( s3 );
final Msa msa = BasicMsa.createInstance( l );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
- System.out.println();
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
- final List<Sequence> l2 = new ArrayList<Sequence>();
+ //TODO need to DO the tests!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ //FIXME
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
+ // System.out.println();
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
+ final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
final Msa msa2 = BasicMsa.createInstance( l2 );
- System.out.println();
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
+ // System.out.println();
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
private static boolean testDeleteableMsa() {
try {
- final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
- final Sequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
- final Sequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
- final Sequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
- final Sequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
- final Sequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
- final List<Sequence> l0 = new ArrayList<Sequence>();
+ final MolecularSequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
+ final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
+ final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
+ final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
+ final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
+ final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
+ final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
l0.add( s0 );
l0.add( s1 );
l0.add( s2 );
return false;
}
//
- final Sequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
- final Sequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
- final Sequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
- final Sequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
- final Sequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
- final Sequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
- final List<Sequence> l1 = new ArrayList<Sequence>();
+ final MolecularSequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
+ final MolecularSequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
+ final MolecularSequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
+ final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
+ final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
+ final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
+ final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
l1.add( s_0 );
l1.add( s_1 );
l1.add( s_2 );
if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
return false;
}
- //
- final Sequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
- final Sequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
- final Sequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
- final Sequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
- final Sequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
- final Sequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
- final List<Sequence> l2 = new ArrayList<Sequence>();
+ final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
+ final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
+ final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
+ final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
+ final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
+ final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
+ final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
l2.add( s__0 );
l2.add( s__1 );
l2.add( s__2 );
dmsa2.setIdentifier( 0, "new_c" );
dmsa2.setIdentifier( 1, "new_d" );
dmsa2.setResidueAt( 0, 0, 'x' );
- final Sequence s = dmsa2.deleteRow( "new_d", true );
+ final MolecularSequence s = dmsa2.deleteRow( "new_d", true );
if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
return false;
}
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();
return false;
}
if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
- .getDistanceToParent() ) ) {
+ .getDistanceToParent() ) ) {
return false;
}
if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
- .getDistanceToParent() ) ) {
+ .getDistanceToParent() ) ) {
return false;
}
if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
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 Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
- + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
- + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
- new NHXParser() );
+ + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
+ + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
+ new NHXParser() );
if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
return false;
}
if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
.equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
System.out.println( n7
- .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
+ .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
return false;
}
}
if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
return false;
}
+ final Phylogeny p12 = factory.create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
+ new NHXParser() )[ 0 ];
+ if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
final Phylogeny p2 = factory
.create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
- + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
- + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
- + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
- + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
- + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
- + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
- + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
- + "7.369400000000000e-02}])",
- new NHXParser() )[ 0 ];
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
+ + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
+ + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
+ + "7.369400000000000e-02}])",
+ new NHXParser() )[ 0 ];
if ( p2.getNode( "1" ) == null ) {
return false;
}
// J. of Comput Bio. Vol. 4, No 2, pp.177-187
final Phylogeny species6 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene6 = factory
.create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1,"
- + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
- new NHXParser() )[ 0 ];
+ + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
+ new NHXParser() )[ 0 ];
species6.setRooted( true );
gene6.setRooted( true );
final SDI sdi6 = new SDI( gene6, species6 );
}
final Phylogeny species6 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene6 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
- + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
- + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
- + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
- new NHXParser() )[ 0 ];
+ + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
+ new NHXParser() )[ 0 ];
species6.setRooted( true );
gene6.setRooted( true );
Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
p6 = null;
final Phylogeny species7 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene7 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
- + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
- + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
- + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
- new NHXParser() )[ 0 ];
+ + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
+ new NHXParser() )[ 0 ];
species7.setRooted( true );
gene7.setRooted( true );
Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
p7 = null;
final Phylogeny species8 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene8 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
- + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
- + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
- + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
- new NHXParser() )[ 0 ];
+ + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
+ new NHXParser() )[ 0 ];
species8.setRooted( true );
gene8.setRooted( true );
Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
}
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" ) );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
- + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
- + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
- + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
- + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
- new NHXParser() );
+ + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
+ + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
+ + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
+ + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
+ new NHXParser() );
SupportCount.count( t0_1, phylogenies_1, true, false );
final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),((F,G),X))"
- + "(((((A,Y),B),C),D),((F,G),E))"
- + "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),(F,G),Z)"
- + "(((((A,B),C),D),E),(F,G))"
- + "((((((A,B),C),D),E),F),G)"
- + "(((((X,Y),F,G),E),((A,B),C)),D)",
- new NHXParser() );
+ + "(((((A,B),C),D),E),((F,G),X))"
+ + "(((((A,Y),B),C),D),((F,G),E))"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "(((((A,B),C),D),E),(F,G),Z)"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "((((((A,B),C),D),E),F),G)"
+ + "(((((X,Y),F,G),E),((A,B),C)),D)",
+ new NHXParser() );
SupportCount.count( t0_2, phylogenies_2, true, false );
final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
while ( it.hasNext() ) {
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 );
private static boolean testUniprotEntryRetrieval() {
try {
- final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
+ final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 );
if ( !entry.getAccession().equals( "P12345" ) ) {
return false;
}
if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
return false;
}
+ if ( entry.getMolecularSequence() == null ) {
+ return false;
+ }
+ if ( !entry
+ .getMolecularSequence()
+ .getMolecularSequenceAsString()
+ .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
+ || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
+ System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() );
+ System.out.println( "expected something else." );
+ return false;
+ }
}
catch ( final IOException e ) {
System.out.println();
e.printStackTrace( System.out );
return true;
}
+ catch ( final NullPointerException f ) {
+ f.printStackTrace( System.out );
+ return false;
+ }
catch ( final Exception e ) {
return false;
}
git://source.jalview.org / jalview.git / blobdiff