// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.test;
import java.util.Set;
import org.forester.application.support_transfer;
+import org.forester.archaeopteryx.AptxUtil;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.io.parsers.nexus.NexusCharactersParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
+import org.forester.io.writers.SequenceWriter;
import org.forester.msa.BasicMsa;
import org.forester.msa.Mafft;
import org.forester.msa.Msa;
import org.forester.phylogeny.PhylogenyBranch;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.data.BranchWidth;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.protein.Protein;
+import org.forester.rio.TestRIO;
import org.forester.sdi.SDI;
import org.forester.sdi.SDIR;
-import org.forester.sdi.SDIse;
-import org.forester.sdi.TaxonomyAssigner;
import org.forester.sdi.TestGSDI;
import org.forester.sequence.BasicSequence;
import org.forester.sequence.Sequence;
import org.forester.util.ForesterUtil;
import org.forester.util.GeneralTable;
import org.forester.util.SequenceIdParser;
-import org.forester.ws.uniprot.DatabaseTools;
-import org.forester.ws.uniprot.SequenceDatabaseEntry;
-import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.seqdb.SequenceDatabaseEntry;
+import org.forester.ws.seqdb.SequenceDbWsTools;
+import org.forester.ws.seqdb.UniProtTaxonomy;
import org.forester.ws.wabi.TxSearch;
import org.forester.ws.wabi.TxSearch.RANKS;
import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
}
private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
- final PhylogenyMethods pm = PhylogenyMethods.getInstance();
- return pm.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
+ return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
}
public static boolean isEqual( final double a, final double b ) {
System.exit( -1 );
}
final long start_time = new Date().getTime();
-
-
-
+ System.out.print( "Sequence writer: " );
+ if ( testSequenceWriter() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Sequence id parsing: " );
- if ( testSequenceIdParsing() ) {
+ if ( testSequenceIdParsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
- System.exit( -1 ); //TODO FIXME remove me!! ~
failed++;
}
System.out.print( "Hmmscan output parser: " );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Taxonomy code extraction: " );
+ if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "SN extraction: " );
+ if ( Test.testExtractSNFromNodeName() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Taxonomy extraction (general): " );
+ if ( Test.testTaxonomyExtraction() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "UniProtKB id extraction: " );
+ if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Uri for Aptx web sequence accession: " );
+ if ( Test.testCreateUriForSeqWeb() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Basic node construction and parsing of NHX (node level): " );
if ( Test.testNHXNodeParsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "NHX parsing iterating: " );
+ if ( Test.testNHParsingIter() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "NH parsing: " );
if ( Test.testNHParsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Nexus tree parsing iterating: " );
+ if ( Test.testNexusTreeParsingIterating() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Nexus tree parsing: " );
if ( Test.testNexusTreeParsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Tree methods: " );
+ if ( Test.testTreeMethods() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Postorder Iterator: " );
if ( Test.testPostOrderIterator() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Node removal: " );
+ if ( Test.testNodeRemoval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Support count: " );
if ( Test.testSupportCount() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Finding of LCA 2: " );
+ if ( Test.testGetLCA2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Calculation of distance between nodes: " );
if ( Test.testGetDistance() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- System.out.print( "SDIse: " );
- if ( Test.testSDIse() ) {
+ System.out.print( "Descriptive statistics: " );
+ if ( Test.testDescriptiveStatistics() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "Taxonomy assigner: " );
- if ( Test.testTaxonomyAssigner() ) {
+ System.out.print( "Data objects and methods: " );
+ if ( Test.testDataObjects() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "SDIunrooted: " );
- if ( Test.testSDIunrooted() ) {
+ System.out.print( "Properties map: " );
+ if ( Test.testPropertiesMap() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "GSDI: " );
- if ( TestGSDI.test() ) {
+ System.out.print( "SDIse: " );
+ if ( Test.testSDIse() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "Descriptive statistics: " );
- if ( Test.testDescriptiveStatistics() ) {
+ System.out.print( "SDIunrooted: " );
+ if ( Test.testSDIunrooted() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "Data objects and methods: " );
- if ( Test.testDataObjects() ) {
+ System.out.print( "GSDI: " );
+ if ( TestGSDI.test() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "Properties map: " );
- if ( Test.testPropertiesMap() ) {
+ System.out.print( "RIO: " );
+ if ( TestRIO.test() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- if ( Mafft.isInstalled() ) {
+ //----
+ String path = "";
+ final String os = ForesterUtil.OS_NAME.toLowerCase();
+ if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
+ path = "/usr/local/bin/mafft";
+ }
+ else if ( os.indexOf( "win" ) >= 0 ) {
+ path = "C:\\Program Files\\mafft-win\\mafft.bat";
+ }
+ else {
+ path = "/home/czmasek/bin/mafft";
+ }
+ if ( !MsaInferrer.isInstalled( path ) ) {
+ path = "mafft";
+ }
+ if ( !MsaInferrer.isInstalled( path ) ) {
+ path = "/usr/local/bin/mafft";
+ }
+ if ( MsaInferrer.isInstalled( path ) ) {
System.out.print( "MAFFT (external program): " );
- if ( Test.testMafft() ) {
+ if ( Test.testMafft( path ) ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed [will not count towards failed tests]" );
}
}
+ //----
System.out.print( "Next nodes with collapsed: " );
if ( Test.testNextNodeWithCollapsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- // System.out.print( "WABI TxSearch: " );
- // if ( Test.testWabiTxSearch() ) {
- // System.out.println( "OK." );
- // succeeded++;
- // }
- // else {
- // System.out
- // .println( "failed [will not count towards failed tests since it might be due to absence internet connection]" );
- // }
System.out.println();
final Runtime rt = java.lang.Runtime.getRuntime();
final long free_memory = rt.freeMemory() / 1000000;
else {
System.out.println( "Not OK." );
}
- // System.out.println();
- // Development.setTime( true );
- //try {
- // final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- // final String clc = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
- // + "examples" + ForesterUtil.getFileSeparator() + "CLC.nhx";
- // final String multi = Test.PATH_TO_EXAMPLE_FILES +
- // "multifurcations_ex_1.nhx";
- // final String domains = Test.PATH_TO_EXAMPLE_FILES + "domains1.nhx";
- // final Phylogeny t1 = factory.create( new File( domains ), new
- // NHXParser() )[ 0 ];
- // final Phylogeny t2 = factory.create( new File( clc ), new NHXParser() )[ 0 ];
- // }
- // catch ( final Exception e ) {
- // e.printStackTrace();
- // }
- // t1.getRoot().preorderPrint();
- // final PhylogenyFactory factory = ParserBasedPhylogenyFactory
- // .getInstance();
- // try {
- //
- // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
- // + "\\AtNBSpos.nhx" ) );
- // factory.create(
- // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
- // new NHXParser() );
- // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
- // + "\\AtNBSpos.nhx" ) );
- // factory.create(
- // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
- // new NHXParser() );
- //
- //
- // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
- // + "\\big_tree.nhx" ) );
- // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
- // + "\\big_tree.nhx" ) );
- // factory.create(
- // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
- // new NHXParser() );
- // factory.create(
- // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
- // new NHXParser() );
- //
- // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
- // + "\\big_tree.nhx" ) );
- // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
- // + "\\big_tree.nhx" ) );
- //
- // factory.create(
- // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
- // new NHXParser() );
- // factory.create(
- // new File( PATH_TO_EXAMPLE_FILES + "\\big_tree.nhx" ),
- // new NHXParser() );
- //
- // Helper.readNHtree( new File( PATH_TO_EXAMPLE_FILES
- // + "\\AtNBSpos.nhx" ) );
- // factory.create(
- // new File( PATH_TO_EXAMPLE_FILES + "\\AtNBSpos.nhx" ),
- // new NHXParser() );
- //
- // }
- // catch ( IOException e ) {
- // // TODO Auto-generated catch block
- // e.printStackTrace();
- // }
}
- private static boolean testBasicNodeMethods() {
+ private static boolean testExtractUniProtKbProteinSeqIdentifier() {
try {
- if ( PhylogenyNode.getNodeCount() != 0 ) {
+ PhylogenyNode n = new PhylogenyNode();
+ n.setName( "tr|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
return false;
}
- final PhylogenyNode n1 = new PhylogenyNode();
- final PhylogenyNode n2 = PhylogenyNode
- .createInstanceFromNhxString( "", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- final PhylogenyNode n3 = PhylogenyNode
- .createInstanceFromNhxString( "n3", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- final PhylogenyNode n4 = PhylogenyNode
- .createInstanceFromNhxString( "n4:0.01", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( n1.isHasAssignedEvent() ) {
+ n.setName( "tr.B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
return false;
}
- if ( PhylogenyNode.getNodeCount() != 4 ) {
+ n.setName( "tr=B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
return false;
}
- if ( n3.getIndicator() != 0 ) {
+ n.setName( "tr-B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
return false;
}
- if ( n3.getNumberOfExternalNodes() != 1 ) {
+ n.setName( "tr/B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
return false;
}
- if ( !n3.isExternal() ) {
+ n.setName( "tr\\B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
return false;
}
- if ( !n3.isRoot() ) {
+ n.setName( "tr_B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
return false;
}
- if ( !n4.getName().equals( "n4" ) ) {
+ n.setName( " tr|B3RJ64 " );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "-tr|B3RJ64-" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "-tr=B3RJ64-" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "_tr=B3RJ64_" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( " tr_tr|B3RJ64_sp|123 " );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "ssp|B3RJ64" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ64C" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp B3RJ64" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ6X" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ6" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "K1PYK7_CRAGI" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ n.setName( "K1PYK7_PEA" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PEA" ) ) {
+ return false;
+ }
+ n.setName( "K1PYK7_RAT" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_RAT" ) ) {
+ return false;
+ }
+ n.setName( "K1PYK7_PIG" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ return false;
+ }
+ n.setName( "~K1PYK7_PIG~" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ return false;
+ }
+ n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ n.setName( "K1PYKX_CRAGI" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "XXXXX_CRAGI" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "XXXXX_CRAGI" ) ) {
+ return false;
+ }
+ n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "H3IB65" ) ) {
+ return false;
+ }
+ n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "Q86U06" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
+ seq.setSymbol( "K1PYK7_CRAGI" );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ seq.setSymbol( "tr|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ seq = new org.forester.phylogeny.data.Sequence();
+ seq.setName( "K1PYK7_CRAGI" );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ seq.setName( "tr|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ seq = new org.forester.phylogeny.data.Sequence();
+ seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK8_CRAGI" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ seq = new org.forester.phylogeny.data.Sequence();
+ seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ //
+ n = new PhylogenyNode();
+ n.setName( "ACP19736" );
+ if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ n.setName( "_ACP19736_" );
+ if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
return false;
}
}
return true;
}
- private static boolean testBasicPhyloXMLparsing() {
+ private static boolean testCreateUriForSeqWeb() {
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhyloXmlParser xml_parser = new PhyloXmlParser();
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
- xml_parser );
- if ( xml_parser.getErrorCount() > 0 ) {
- System.out.println( xml_parser.getErrorMessages().toString() );
+ final PhylogenyNode n = new PhylogenyNode();
+ n.setName( "tr|B3RJ64" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
return false;
}
- if ( phylogenies_0.length != 4 ) {
+ n.setName( "B0LM41_HUMAN" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
return false;
}
- final Phylogeny t1 = phylogenies_0[ 0 ];
- final Phylogeny t2 = phylogenies_0[ 1 ];
- final Phylogeny t3 = phylogenies_0[ 2 ];
- final Phylogeny t4 = phylogenies_0[ 3 ];
- if ( t1.getNumberOfExternalNodes() != 1 ) {
+ n.setName( "NP_001025424" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
return false;
}
- if ( !t1.isRooted() ) {
+ n.setName( "_NM_001030253-" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
return false;
}
- if ( t1.isRerootable() ) {
+ n.setName( "XM_002122186" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
return false;
}
- if ( !t1.getType().equals( "gene_tree" ) ) {
+ n.setName( "dgh_AAA34956_gdg" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
return false;
}
- if ( t2.getNumberOfExternalNodes() != 2 ) {
+ n.setName( "j40f4_Q06891.1_fndn2 fnr3" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891.1" ) ) {
return false;
}
- if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
+ n.setName( "GI:394892" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
- if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
+ n.setName( "gi_394892" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
- if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
+ n.setName( "gi6335_gi_394892_56635_Gi_43" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
- if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testExtractSNFromNodeName() {
+ try {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
return false;
}
- if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" )
+ .equals( "Mus musculus musculus" ) ) {
return false;
}
- if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" )
+ .equals( "Mus musculus musculus" ) ) {
return false;
}
- if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
- .startsWith( "actgtgggggt" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) {
return false;
}
- if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
- .startsWith( "ctgtgatgcat" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" )
+ .equals( "Mus musculus" ) ) {
return false;
}
- if ( t3.getNumberOfExternalNodes() != 4 ) {
+ }
+ 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 ) {
return false;
}
- if ( !t1.getName().equals( "t1" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !t2.getName().equals( "t2" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "ARATH" ) ) {
return false;
}
- if ( !t3.getName().equals( "t3" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "ARATH" ) ) {
return false;
}
- if ( !t4.getName().equals( "t4" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
return false;
}
- if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
return false;
}
- if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
- .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
- .equals( "apoptosis" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
- .equals( "GO:0006915" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
- .equals( "UniProtKB" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
- .equals( "experimental" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
- .equals( "function" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
- .getValue() != 1 ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
- .getType().equals( "ml" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "9YX45" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
- .equals( "apoptosis" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "MOUSE" ) ) {
return false;
}
- if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
- .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "MOUSE" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
- .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "MOUSE" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
- .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
- .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
- .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
- .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
- .equals( "GO:0005829" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
- .equals( "intracellular organelle" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
- .equals( "UniProt link" ) ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "RAT" ) ) {
return false;
}
- if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
+ .equals( "PIG" ) ) {
+ return false;
+ }
+ if ( !ParserUtils
+ .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "MOUSE" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
+ .equals( "MOUSE" ) ) {
+ return false;
+ }
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- //if ( !( t3.getNode( "root node" ).getNodeData().getDistribution().getDesc().equals( "irgendwo" ) ) ) {
- // return false;
- //}
- // if ( !( t3.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1074/jbc.M005889200" ) ) ) {
- // return false;
- // }
- // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getType().equals( "host" ) ) {
- // return false;
- // }
- // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
- // return false;
- // }
- // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
- // return false;
- // }
- // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
- // return false;
- // }
- // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
- // return false;
- // }
- // if ( !t3.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getType().equals( "ncbi" ) ) {
- // return false;
- // }
- // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
- // return false;
- // }
- // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getName()
- // .equals( "B" ) ) {
- // return false;
- // }
- // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getFrom() != 21 ) {
- // return false;
- // }
- // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
- // return false;
- // }
- // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getLength() != 24 ) {
- // return false;
- // }
- // if ( t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
- // .getConfidence() != 2144 ) {
- // return false;
- // }
- // if ( !t3.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
- // .equals( "pfam" ) ) {
- // return false;
- // }
- // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
- // return false;
- // }
- // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
- // return false;
- // }
- // if ( t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
- // return false;
- // }
- // if ( !t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
- // return false;
- // }
- // if ( ( ( BinaryCharacters ) t3.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
- // .getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
- // ;
- // return false;
- // }
- // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
- // return false;
- // }
- // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
- // return false;
- // }
- // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
- // return false;
- // }
- // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
- // return false;
- // }
- // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
- // return false;
- // }
- // if ( t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
- // return false;
- // }
- // if ( !t3.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
- // return false;
- // }
- // final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
- // xml_parser );
- // if ( xml_parser.getErrorCount() > 0 ) {
- // System.out.println( xml_parser.getErrorMessages().toString() );
- // return false;
- // }
- // if ( phylogenies_1.length != 2 ) {
- // return false;
- // }
- // final Phylogeny a = phylogenies_1[ 0 ];
- // if ( !a.getName().equals( "tree 4" ) ) {
- // return false;
- // }
- // if ( a.getNumberOfExternalNodes() != 3 ) {
- // return false;
- // }
- // if ( !a.getNode( "node b1" ).getNodeData().getSequence().getName().equals( "b1 gene" ) ) {
- // return false;
- // }
- // if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
- // return false;
- // }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return true;
}
- private static boolean testBasicPhyloXMLparsingRoundtrip() {
+ private static boolean testBasicNodeMethods() {
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhyloXmlParser xml_parser = new PhyloXmlParser();
- if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
- xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
+ if ( PhylogenyNode.getNodeCount() != 0 ) {
+ return false;
}
- else {
- xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
+ final PhylogenyNode n1 = new PhylogenyNode();
+ final PhylogenyNode n2 = PhylogenyNode
+ .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ final PhylogenyNode n3 = PhylogenyNode
+ .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ final PhylogenyNode n4 = PhylogenyNode
+ .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( n1.isHasAssignedEvent() ) {
+ return false;
+ }
+ if ( PhylogenyNode.getNodeCount() != 4 ) {
+ return false;
+ }
+ if ( n3.getIndicator() != 0 ) {
+ return false;
+ }
+ if ( n3.getNumberOfExternalNodes() != 1 ) {
+ return false;
+ }
+ if ( !n3.isExternal() ) {
+ return false;
+ }
+ if ( !n3.isRoot() ) {
+ return false;
}
+ if ( !n4.getName().equals( "n4" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testBasicPhyloXMLparsing() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhyloXmlParser xml_parser = new PhyloXmlParser();
final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
if ( phylogenies_0.length != 4 ) {
return false;
}
- final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
- final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
- if ( phylogenies_t1.length != 1 ) {
+ final Phylogeny t1 = phylogenies_0[ 0 ];
+ final Phylogeny t2 = phylogenies_0[ 1 ];
+ final Phylogeny t3 = phylogenies_0[ 2 ];
+ final Phylogeny t4 = phylogenies_0[ 3 ];
+ if ( t1.getNumberOfExternalNodes() != 1 ) {
return false;
}
- final Phylogeny t1_rt = phylogenies_t1[ 0 ];
- if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
+ if ( !t1.isRooted() ) {
return false;
}
- if ( !t1_rt.isRooted() ) {
+ if ( t1.isRerootable() ) {
return false;
}
- if ( t1_rt.isRerootable() ) {
+ if ( !t1.getType().equals( "gene_tree" ) ) {
return false;
}
- if ( !t1_rt.getType().equals( "gene_tree" ) ) {
+ if ( t2.getNumberOfExternalNodes() != 2 ) {
return false;
}
- final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
- final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
- final Phylogeny t2_rt = phylogenies_t2[ 0 ];
- if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
+ if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
return false;
}
- if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
+ if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
return false;
}
- if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
+ if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
return false;
}
- if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
+ if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
return false;
}
- if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
+ if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
+ return false;
+ }
+ if ( t2.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
+ return false;
+ }
+ if ( !t2.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
.startsWith( "actgtgggggt" ) ) {
return false;
}
- if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
+ if ( !t2.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
.startsWith( "ctgtgatgcat" ) ) {
return false;
}
- final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
- final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
- final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
- final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
- if ( phylogenies_1.length != 1 ) {
+ if ( t3.getNumberOfExternalNodes() != 4 ) {
return false;
}
- final Phylogeny t3_rt = phylogenies_1[ 0 ];
- if ( !t3_rt.getName().equals( "t3" ) ) {
+ if ( !t1.getName().equals( "t1" ) ) {
return false;
}
- if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
+ if ( !t2.getName().equals( "t2" ) ) {
return false;
}
- if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
+ if ( !t3.getName().equals( "t3" ) ) {
return false;
}
- if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
+ if ( !t4.getName().equals( "t4" ) ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
+ if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
+ if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
+ return false;
+ }
+ if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
+ return false;
+ }
+ if ( !t3.getNode( "root node" ).getNodeData().getSequence().getName()
.equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
+ if ( !t3.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
+ if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
- .equals( "UniProtKB" ) ) {
+ if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
.equals( "apoptosis" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
.equals( "GO:0006915" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
.equals( "UniProtKB" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
.equals( "experimental" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
.equals( "function" ) ) {
return false;
}
- if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
+ if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
.getValue() != 1 ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
.getType().equals( "ml" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
.equals( "apoptosis" ) ) {
return false;
}
- if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
+ if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
.getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
.getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
.getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
.getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
.getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
.getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
.equals( "GO:0005829" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
.equals( "intracellular organelle" ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
.equals( "UniProt link" ) ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
+ if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
return false;
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
- return false;
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testBasicPhyloXMLparsingRoundtrip() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhyloXmlParser xml_parser = new PhyloXmlParser();
+ if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
+ xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
}
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
- .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
+ else {
+ xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
+ }
+ final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+ xml_parser );
+ if ( xml_parser.getErrorCount() > 0 ) {
+ System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
+ if ( phylogenies_0.length != 4 ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
+ final StringBuffer t1_sb = new StringBuffer( phylogenies_0[ 0 ].toPhyloXML( 0 ) );
+ final Phylogeny[] phylogenies_t1 = factory.create( t1_sb, xml_parser );
+ if ( phylogenies_t1.length != 1 ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
+ final Phylogeny t1_rt = phylogenies_t1[ 0 ];
+ if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
+ if ( !t1_rt.isRooted() ) {
return false;
}
- if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
- .equals( "ncbi" ) ) {
+ if ( t1_rt.isRerootable() ) {
return false;
}
- if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
+ if ( !t1_rt.getType().equals( "gene_tree" ) ) {
return false;
}
- if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
- .getName().equals( "B" ) ) {
+ final StringBuffer t2_sb = new StringBuffer( phylogenies_0[ 1 ].toPhyloXML( 0 ) );
+ final Phylogeny[] phylogenies_t2 = factory.create( t2_sb, xml_parser );
+ final Phylogeny t2_rt = phylogenies_t2[ 0 ];
+ if ( t2_rt.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
return false;
}
- if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
- .getFrom() != 21 ) {
+ if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
return false;
}
- if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
+ if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
return false;
}
- if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
- .getLength() != 24 ) {
+ if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
return false;
}
- if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
+ if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 0 ).getMolecularSequence()
+ .startsWith( "actgtgggggt" ) ) {
+ return false;
+ }
+ if ( !t2_rt.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
+ .startsWith( "ctgtgatgcat" ) ) {
+ return false;
+ }
+ final StringBuffer t3_sb_0 = new StringBuffer( phylogenies_0[ 2 ].toPhyloXML( 0 ) );
+ final Phylogeny[] phylogenies_1_0 = factory.create( t3_sb_0, xml_parser );
+ final StringBuffer t3_sb = new StringBuffer( phylogenies_1_0[ 0 ].toPhyloXML( 0 ) );
+ final Phylogeny[] phylogenies_1 = factory.create( t3_sb, xml_parser );
+ if ( phylogenies_1.length != 1 ) {
+ return false;
+ }
+ final Phylogeny t3_rt = phylogenies_1[ 0 ];
+ if ( !t3_rt.getName().equals( "t3" ) ) {
+ return false;
+ }
+ if ( t3_rt.getNumberOfExternalNodes() != 4 ) {
+ return false;
+ }
+ if ( !t3_rt.getIdentifier().getValue().equals( "1-1" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getIdentifier().getProvider().equals( "treebank" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getName()
+ .equals( "Apoptosis facilitator Bcl-2-like 14 protein" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource()
+ .equals( "UniProtKB" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
+ .equals( "apoptosis" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getRef()
+ .equals( "GO:0006915" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getSource()
+ .equals( "UniProtKB" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getEvidence()
+ .equals( "experimental" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getType()
+ .equals( "function" ) ) {
+ return false;
+ }
+ if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
+ .getValue() != 1 ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getConfidence()
+ .getType().equals( "ml" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
+ .equals( "apoptosis" ) ) {
+ return false;
+ }
+ if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
+ .getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
+ .getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
+ .getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
+ .getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
+ .getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getProperties()
+ .getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
+ .equals( "GO:0005829" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getDesc()
+ .equals( "intracellular organelle" ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
+ .equals( "UniProt link" ) ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDoi().equals( "10.1038/387489a0" ) ) ) {
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
+ .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getScientificName().equals( "ecdysozoa" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getCommonName().equals( "molting animals" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getIdentifier().getProvider()
+ .equals( "ncbi" ) ) {
+ return false;
+ }
+ if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getTotalLength() != 124 ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
+ .getName().equals( "B" ) ) {
+ return false;
+ }
+ if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
+ .getFrom() != 21 ) {
+ return false;
+ }
+ if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getTo() != 44 ) {
+ return false;
+ }
+ if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
+ .getLength() != 24 ) {
+ return false;
+ }
+ if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
.getConfidence() != 2144 ) {
return false;
}
source.append( "40 41 42 43" + l );
source.append( " # 1 1 1 1 1 " + l );
source.append( "50 51 52 53 54" + l );
- final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
+ final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
if ( t1.getNumberOfColumns() != 5 ) {
return false;
}
source1.append( "40;41;42;43" + l );
source1.append( " # 1 1 1 1 1 " + l );
source1.append( ";;;50 ; ;52; 53;;54 " + l );
- final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
+ final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
if ( t2.getNumberOfColumns() != 5 ) {
return false;
}
source2.append( " comment: 1 1 1 1 1 " + l );
source2.append( ";;;50 ; 52; 53;;54 " + l );
final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
- ";",
+ ';',
+ false,
false,
"comment:",
false );
return false;
}
final PhylogenyNode n = t3.getNode( "ABC" );
- PhylogenyNodeIterator it;
- for( it = n.iterateChildNodesForward(); it.hasNext(); ) {
- it.next();
- }
- for( it.reset(); it.hasNext(); ) {
- it.next();
- }
- final PhylogenyNodeIterator it2 = n.iterateChildNodesForward();
- if ( !it2.next().getName().equals( "A" ) ) {
- return false;
- }
- if ( !it2.next().getName().equals( "B" ) ) {
- return false;
- }
- if ( !it2.next().getName().equals( "C" ) ) {
- return false;
- }
- if ( it2.hasNext() ) {
- return false;
- }
final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ];
if ( t4.getNumberOfExternalNodes() != 9 ) {
return false;
if ( t8.getHeight() != 15 ) {
return false;
}
- final char[] a9 = new char[] {};
+ final char[] a9 = new char[] { 'a' };
final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
if ( t9.getHeight() != 0 ) {
return false;
return true;
}
+ private static boolean testTreeMethods() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
+ if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
+ System.out.println( t0.toNewHampshireX() );
+ return false;
+ }
+ final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
+ if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testConfidenceAssessor() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
.create( "((A,C),X);((A,X),C);(A,C);((((A,B),C),D),E);((A,B),((E,D),C));(((A,B),C),(E,D));(A,(((E,D),C),B));(B,(A,((E,D),C)));(C,((E,D),(A,B)));(D,(E,((A,B),C)));((((A,C)ac,D)acd,E)acde,B)abcd",
new NHXParser() );
ConfidenceAssessor.evaluate( "bootstrap", ev_b, t_b, false, 1 );
- // Archaeopteryx.createApplication( t_b ); //TODO use me again me working here...
if ( !isEqual( t_b.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 4 ) ) {
return false;
}
return false;
}
t2.setIdentifier( new Identifier( "ecoli" ) );
- t2.setTaxonomyCode( "other" );
+ t2.setTaxonomyCode( "OTHER" );
t2.setScientificName( "what" );
t2.setCommonName( "something" );
if ( !t1.isEqual( t2 ) ) {
for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
}
+ final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
+ final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
+ if ( !iter.next().getName().equals( "A" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "B" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "C" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "D" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "E" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "F" ) ) {
+ return false;
+ }
+ if ( iter.hasNext() ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p1 = factory.create( "(((A:1,B:2,X:100)ab:3,C:4)abc:5,(D:7,(E:9,F:10)ef:8)def:6)r",
new NHXParser() )[ 0 ];
- final PhylogenyMethods pm = PhylogenyMethods.getInstance();
- if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "C" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
return false;
}
- if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
+ if ( PhylogenyMethods.calculateDistance( p1.getNode( "def" ), p1.getNode( "abc" ) ) != 11 ) {
return false;
}
final Phylogeny p2 = factory.create( "((A:4,B:5,C:6)abc:1,(D:7,E:8,F:9)def:2,(G:10,H:11,I:12)ghi:3)r",
new NHXParser() )[ 0 ];
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "B" ) ) != 9 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
return false;
}
- if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
+ if ( PhylogenyMethods.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
return false;
}
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
new NHXParser() )[ 0 ];
- final PhylogenyMethods pm = PhylogenyMethods.getInstance();
- final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
+ final PhylogenyNode A = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "A" ) );
if ( !A.getName().equals( "A" ) ) {
return false;
}
- final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
+ final PhylogenyNode gh = PhylogenyMethods.calculateLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
if ( !gh.getName().equals( "gh" ) ) {
return false;
}
- final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
+ final PhylogenyNode ab = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
if ( !ab.getName().equals( "ab" ) ) {
return false;
}
- final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
+ final PhylogenyNode ab2 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
if ( !ab2.getName().equals( "ab" ) ) {
return false;
}
- final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
+ final PhylogenyNode gh2 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
if ( !gh2.getName().equals( "gh" ) ) {
return false;
}
- final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
+ final PhylogenyNode gh3 = PhylogenyMethods.calculateLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
if ( !gh3.getName().equals( "gh" ) ) {
return false;
}
- final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
+ final PhylogenyNode abc = PhylogenyMethods.calculateLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
if ( !abc.getName().equals( "abc" ) ) {
return false;
}
- final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
+ final PhylogenyNode abc2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
if ( !abc2.getName().equals( "abc" ) ) {
return false;
}
- final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
+ final PhylogenyNode abcd = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
if ( !abcd.getName().equals( "abcd" ) ) {
return false;
}
- final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
+ final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
if ( !abcd2.getName().equals( "abcd" ) ) {
return false;
}
- final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
+ final PhylogenyNode abcdef = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
if ( !abcdef.getName().equals( "abcdef" ) ) {
return false;
}
- final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
+ final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
if ( !abcdef2.getName().equals( "abcdef" ) ) {
return false;
}
- final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
+ final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
if ( !abcdef3.getName().equals( "abcdef" ) ) {
return false;
}
- final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
+ final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
if ( !abcdef4.getName().equals( "abcdef" ) ) {
return false;
}
- final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
+ final PhylogenyNode abcde = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
if ( !abcde.getName().equals( "abcde" ) ) {
return false;
}
- final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
+ final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
if ( !abcde2.getName().equals( "abcde" ) ) {
return false;
}
- final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
+ final PhylogenyNode r = PhylogenyMethods.calculateLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
if ( !r.getName().equals( "abcdefgh" ) ) {
return false;
}
- final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
+ final PhylogenyNode r2 = PhylogenyMethods.calculateLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
if ( !r2.getName().equals( "abcdefgh" ) ) {
return false;
}
- final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
+ final PhylogenyNode r3 = PhylogenyMethods.calculateLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
if ( !r3.getName().equals( "abcdefgh" ) ) {
return false;
}
- final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
+ final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
if ( !abcde3.getName().equals( "abcde" ) ) {
return false;
}
- final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
+ final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
if ( !abcde4.getName().equals( "abcde" ) ) {
return false;
}
- final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
+ final PhylogenyNode ab3 = PhylogenyMethods.calculateLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
if ( !ab3.getName().equals( "ab" ) ) {
return false;
}
- final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
+ final PhylogenyNode ab4 = PhylogenyMethods.calculateLCA( p1.getNode( "B" ), p1.getNode( "ab" ) );
if ( !ab4.getName().equals( "ab" ) ) {
return false;
}
final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
- final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
+ final PhylogenyNode cd = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "d" ) );
if ( !cd.getName().equals( "cd" ) ) {
return false;
}
- final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
+ final PhylogenyNode cd2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
if ( !cd2.getName().equals( "cd" ) ) {
return false;
}
- final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
+ final PhylogenyNode cde = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
if ( !cde.getName().equals( "cde" ) ) {
return false;
}
- final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
+ final PhylogenyNode cde2 = PhylogenyMethods.calculateLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
if ( !cde2.getName().equals( "cde" ) ) {
return false;
}
- final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
+ final PhylogenyNode cdef = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
if ( !cdef.getName().equals( "cdef" ) ) {
return false;
}
- final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
+ final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
if ( !cdef2.getName().equals( "cdef" ) ) {
return false;
}
- final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
+ final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
if ( !cdef3.getName().equals( "cdef" ) ) {
return false;
}
- final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
+ final PhylogenyNode rt = PhylogenyMethods.calculateLCA( p2.getNode( "c" ), p2.getNode( "a" ) );
if ( !rt.getName().equals( "r" ) ) {
return false;
}
final Phylogeny p3 = factory
.create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
new NHXParser() )[ 0 ];
- final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
+ final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCA( p3.getNode( "b" ), p3.getNode( "c" ) );
if ( !bc_3.getName().equals( "bc" ) ) {
return false;
}
- final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
+ final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "c" ) );
if ( !ac_3.getName().equals( "abc" ) ) {
return false;
}
- final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
+ final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "d" ) );
if ( !ad_3.getName().equals( "abcde" ) ) {
return false;
}
- final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
+ final PhylogenyNode af_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "f" ) );
if ( !af_3.getName().equals( "abcdef" ) ) {
return false;
}
- final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
+ final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "g" ) );
if ( !ag_3.getName().equals( "" ) ) {
return false;
}
if ( !ag_3.isRoot() ) {
return false;
}
- final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
+ final PhylogenyNode al_3 = PhylogenyMethods.calculateLCA( p3.getNode( "a" ), p3.getNode( "l" ) );
if ( !al_3.getName().equals( "" ) ) {
return false;
}
if ( !al_3.isRoot() ) {
return false;
}
- final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
+ final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "k" ), p3.getNode( "l" ) );
if ( !kl_3.getName().equals( "" ) ) {
return false;
}
if ( !kl_3.isRoot() ) {
return false;
}
- final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
+ final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCA( p3.getNode( "f" ), p3.getNode( "l" ) );
if ( !fl_3.getName().equals( "" ) ) {
return false;
}
if ( !fl_3.isRoot() ) {
return false;
}
- final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
+ final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCA( p3.getNode( "g" ), p3.getNode( "k" ) );
if ( !gk_3.getName().equals( "ghijk" ) ) {
return false;
}
final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
- final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
+ final PhylogenyNode r_4 = PhylogenyMethods.calculateLCA( p4.getNode( "b" ), p4.getNode( "c" ) );
if ( !r_4.getName().equals( "r" ) ) {
return false;
}
final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
- final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
+ final PhylogenyNode r_5 = PhylogenyMethods.calculateLCA( p5.getNode( "a" ), p5.getNode( "c" ) );
if ( !r_5.getName().equals( "root" ) ) {
return false;
}
final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
- final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
+ final PhylogenyNode r_6 = PhylogenyMethods.calculateLCA( p6.getNode( "c" ), p6.getNode( "a" ) );
if ( !r_6.getName().equals( "rot" ) ) {
return false;
}
final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
- final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
+ final PhylogenyNode r_7 = PhylogenyMethods.calculateLCA( p7.getNode( "a" ), p7.getNode( "e" ) );
if ( !r_7.getName().equals( "rott" ) ) {
return false;
}
return true;
}
- private static boolean testHmmscanOutputParser() {
- final String test_dir = Test.PATH_TO_TEST_DATA;
+ private static boolean testGetLCA2() {
try {
- final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
- + 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 );
- final List<Protein> proteins = parser2.parse();
- if ( parser2.getProteinsEncountered() != 4 ) {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p_a );
+ final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
+ p_a.getNode( "a" ) );
+ if ( !p_a_1.getName().equals( "a" ) ) {
return false;
}
- if ( proteins.size() != 4 ) {
+ final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p_b );
+ final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
+ p_b.getNode( "a" ) );
+ if ( !p_b_1.getName().equals( "b" ) ) {
return false;
}
- if ( parser2.getDomainsEncountered() != 69 ) {
+ final PhylogenyNode p_b_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "a" ),
+ p_b.getNode( "b" ) );
+ if ( !p_b_2.getName().equals( "b" ) ) {
return false;
}
- if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
+ final Phylogeny p_c = factory.create( "(((a)b)c)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p_c );
+ final PhylogenyNode p_c_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "b" ),
+ p_c.getNode( "a" ) );
+ if ( !p_c_1.getName().equals( "b" ) ) {
return false;
}
- if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
+ final PhylogenyNode p_c_2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
+ p_c.getNode( "c" ) );
+ if ( !p_c_2.getName().equals( "c" ) ) {
+ System.out.println( p_c_2.getName() );
+ System.exit( -1 );
return false;
}
- final Protein p1 = proteins.get( 0 );
- if ( p1.getNumberOfProteinDomains() != 15 ) {
+ final PhylogenyNode p_c_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "a" ),
+ p_c.getNode( "b" ) );
+ if ( !p_c_3.getName().equals( "b" ) ) {
return false;
}
- if ( p1.getLength() != 850 ) {
+ final PhylogenyNode p_c_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_c.getNode( "c" ),
+ p_c.getNode( "a" ) );
+ if ( !p_c_4.getName().equals( "c" ) ) {
return false;
}
- final Protein p2 = proteins.get( 1 );
- if ( p2.getNumberOfProteinDomains() != 51 ) {
+ final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh",
+ new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p1 );
+ final PhylogenyNode A = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
+ p1.getNode( "A" ) );
+ if ( !A.getName().equals( "A" ) ) {
return false;
}
- if ( p2.getLength() != 1291 ) {
+ final PhylogenyNode gh = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "gh" ),
+ p1.getNode( "gh" ) );
+ if ( !gh.getName().equals( "gh" ) ) {
return false;
}
- final Protein p3 = proteins.get( 2 );
- if ( p3.getNumberOfProteinDomains() != 2 ) {
+ final PhylogenyNode ab = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
+ p1.getNode( "B" ) );
+ if ( !ab.getName().equals( "ab" ) ) {
return false;
}
- final Protein p4 = proteins.get( 3 );
- if ( p4.getNumberOfProteinDomains() != 1 ) {
+ final PhylogenyNode ab2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
+ p1.getNode( "A" ) );
+ if ( !ab2.getName().equals( "ab" ) ) {
return false;
}
- if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
+ final PhylogenyNode gh2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
+ p1.getNode( "G" ) );
+ if ( !gh2.getName().equals( "gh" ) ) {
return false;
}
- if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
+ final PhylogenyNode gh3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "G" ),
+ p1.getNode( "H" ) );
+ if ( !gh3.getName().equals( "gh" ) ) {
return false;
}
- if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
+ final PhylogenyNode abc = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "C" ),
+ p1.getNode( "A" ) );
+ if ( !abc.getName().equals( "abc" ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
+ final PhylogenyNode abc2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
+ p1.getNode( "C" ) );
+ if ( !abc2.getName().equals( "abc" ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
+ final PhylogenyNode abcd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
+ p1.getNode( "D" ) );
+ if ( !abcd.getName().equals( "abcd" ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
+ final PhylogenyNode abcd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "D" ),
+ p1.getNode( "A" ) );
+ if ( !abcd2.getName().equals( "abcd" ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
+ final PhylogenyNode abcdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
+ p1.getNode( "F" ) );
+ if ( !abcdef.getName().equals( "abcdef" ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
+ final PhylogenyNode abcdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
+ p1.getNode( "A" ) );
+ if ( !abcdef2.getName().equals( "abcdef" ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
+ final PhylogenyNode abcdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
+ p1.getNode( "F" ) );
+ if ( !abcdef3.getName().equals( "abcdef" ) ) {
return false;
}
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
- private static boolean testLastExternalNodeMethods() {
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
- final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
- final PhylogenyNode n1 = t0.getNode( "A" );
- if ( n1.isLastExternalNode() ) {
+ final PhylogenyNode abcdef4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "F" ),
+ p1.getNode( "ab" ) );
+ if ( !abcdef4.getName().equals( "abcdef" ) ) {
+ return false;
+ }
+ final PhylogenyNode abcde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
+ p1.getNode( "E" ) );
+ if ( !abcde.getName().equals( "abcde" ) ) {
+ return false;
+ }
+ final PhylogenyNode abcde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
+ p1.getNode( "A" ) );
+ if ( !abcde2.getName().equals( "abcde" ) ) {
+ return false;
+ }
+ final PhylogenyNode r = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcdefgh" ),
+ p1.getNode( "abcdefgh" ) );
+ if ( !r.getName().equals( "abcdefgh" ) ) {
+ return false;
+ }
+ final PhylogenyNode r2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "A" ),
+ p1.getNode( "H" ) );
+ if ( !r2.getName().equals( "abcdefgh" ) ) {
+ return false;
+ }
+ final PhylogenyNode r3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "H" ),
+ p1.getNode( "A" ) );
+ if ( !r3.getName().equals( "abcdefgh" ) ) {
+ return false;
+ }
+ final PhylogenyNode abcde3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "E" ),
+ p1.getNode( "abcde" ) );
+ if ( !abcde3.getName().equals( "abcde" ) ) {
+ return false;
+ }
+ final PhylogenyNode abcde4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "abcde" ),
+ p1.getNode( "E" ) );
+ if ( !abcde4.getName().equals( "abcde" ) ) {
+ return false;
+ }
+ final PhylogenyNode ab3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "ab" ),
+ p1.getNode( "B" ) );
+ if ( !ab3.getName().equals( "ab" ) ) {
+ return false;
+ }
+ final PhylogenyNode ab4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p1.getNode( "B" ),
+ p1.getNode( "ab" ) );
+ if ( !ab4.getName().equals( "ab" ) ) {
+ return false;
+ }
+ final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p2 );
+ final PhylogenyNode cd = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
+ p2.getNode( "d" ) );
+ if ( !cd.getName().equals( "cd" ) ) {
+ return false;
+ }
+ final PhylogenyNode cd2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
+ p2.getNode( "c" ) );
+ if ( !cd2.getName().equals( "cd" ) ) {
+ return false;
+ }
+ final PhylogenyNode cde = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
+ p2.getNode( "e" ) );
+ if ( !cde.getName().equals( "cde" ) ) {
+ return false;
+ }
+ final PhylogenyNode cde2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "e" ),
+ p2.getNode( "c" ) );
+ if ( !cde2.getName().equals( "cde" ) ) {
+ return false;
+ }
+ final PhylogenyNode cdef = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
+ p2.getNode( "f" ) );
+ if ( !cdef.getName().equals( "cdef" ) ) {
+ return false;
+ }
+ final PhylogenyNode cdef2 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "d" ),
+ p2.getNode( "f" ) );
+ if ( !cdef2.getName().equals( "cdef" ) ) {
+ return false;
+ }
+ final PhylogenyNode cdef3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "f" ),
+ p2.getNode( "d" ) );
+ if ( !cdef3.getName().equals( "cdef" ) ) {
+ return false;
+ }
+ final PhylogenyNode rt = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p2.getNode( "c" ),
+ p2.getNode( "a" ) );
+ if ( !rt.getName().equals( "r" ) ) {
+ return false;
+ }
+ final Phylogeny p3 = factory
+ .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)",
+ new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p3 );
+ final PhylogenyNode bc_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "b" ),
+ p3.getNode( "c" ) );
+ if ( !bc_3.getName().equals( "bc" ) ) {
+ return false;
+ }
+ final PhylogenyNode ac_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
+ p3.getNode( "c" ) );
+ if ( !ac_3.getName().equals( "abc" ) ) {
+ return false;
+ }
+ final PhylogenyNode ad_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
+ p3.getNode( "d" ) );
+ if ( !ad_3.getName().equals( "abcde" ) ) {
+ return false;
+ }
+ final PhylogenyNode af_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
+ p3.getNode( "f" ) );
+ if ( !af_3.getName().equals( "abcdef" ) ) {
+ return false;
+ }
+ final PhylogenyNode ag_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
+ p3.getNode( "g" ) );
+ if ( !ag_3.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !ag_3.isRoot() ) {
+ return false;
+ }
+ final PhylogenyNode al_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "a" ),
+ p3.getNode( "l" ) );
+ if ( !al_3.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !al_3.isRoot() ) {
+ return false;
+ }
+ final PhylogenyNode kl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "k" ),
+ p3.getNode( "l" ) );
+ if ( !kl_3.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !kl_3.isRoot() ) {
+ return false;
+ }
+ final PhylogenyNode fl_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "f" ),
+ p3.getNode( "l" ) );
+ if ( !fl_3.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !fl_3.isRoot() ) {
+ return false;
+ }
+ final PhylogenyNode gk_3 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p3.getNode( "g" ),
+ p3.getNode( "k" ) );
+ if ( !gk_3.getName().equals( "ghijk" ) ) {
+ return false;
+ }
+ final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p4 );
+ final PhylogenyNode r_4 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p4.getNode( "b" ),
+ p4.getNode( "c" ) );
+ if ( !r_4.getName().equals( "r" ) ) {
+ return false;
+ }
+ final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p5 );
+ final PhylogenyNode r_5 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p5.getNode( "a" ),
+ p5.getNode( "c" ) );
+ if ( !r_5.getName().equals( "root" ) ) {
+ return false;
+ }
+ final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p6 );
+ final PhylogenyNode r_6 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p6.getNode( "c" ),
+ p6.getNode( "a" ) );
+ if ( !r_6.getName().equals( "rot" ) ) {
+ return false;
+ }
+ final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ];
+ PhylogenyMethods.preOrderReId( p7 );
+ final PhylogenyNode r_7 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "a" ),
+ p7.getNode( "e" ) );
+ if ( !r_7.getName().equals( "rott" ) ) {
+ return false;
+ }
+ final PhylogenyNode r_71 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
+ p7.getNode( "a" ) );
+ if ( !r_71.getName().equals( "rott" ) ) {
+ return false;
+ }
+ final PhylogenyNode r_72 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
+ p7.getNode( "rott" ) );
+ if ( !r_72.getName().equals( "rott" ) ) {
+ return false;
+ }
+ final PhylogenyNode r_73 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
+ p7.getNode( "a" ) );
+ if ( !r_73.getName().equals( "rott" ) ) {
+ return false;
+ }
+ final PhylogenyNode r_74 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "rott" ),
+ p7.getNode( "rott" ) );
+ if ( !r_74.getName().equals( "rott" ) ) {
+ return false;
+ }
+ final PhylogenyNode r_75 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p7.getNode( "e" ),
+ p7.getNode( "e" ) );
+ if ( !r_75.getName().equals( "e" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testHmmscanOutputParser() {
+ 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 );
+ parser1.parse();
+ final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
+ + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
+ final List<Protein> proteins = parser2.parse();
+ if ( parser2.getProteinsEncountered() != 4 ) {
+ return false;
+ }
+ if ( proteins.size() != 4 ) {
+ return false;
+ }
+ if ( parser2.getDomainsEncountered() != 69 ) {
+ return false;
+ }
+ if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
+ return false;
+ }
+ if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
+ return false;
+ }
+ final Protein p1 = proteins.get( 0 );
+ if ( p1.getNumberOfProteinDomains() != 15 ) {
+ return false;
+ }
+ if ( p1.getLength() != 850 ) {
+ return false;
+ }
+ final Protein p2 = proteins.get( 1 );
+ if ( p2.getNumberOfProteinDomains() != 51 ) {
+ return false;
+ }
+ if ( p2.getLength() != 1291 ) {
+ return false;
+ }
+ final Protein p3 = proteins.get( 2 );
+ if ( p3.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ final Protein p4 = proteins.get( 3 );
+ if ( p4.getNumberOfProteinDomains() != 1 ) {
+ return false;
+ }
+ if ( !p4.getProteinDomain( 0 ).getDomainId().toString().equals( "DNA_pol_B_new" ) ) {
+ return false;
+ }
+ if ( p4.getProteinDomain( 0 ).getFrom() != 51 ) {
+ return false;
+ }
+ if ( p4.getProteinDomain( 0 ).getTo() != 395 ) {
+ return false;
+ }
+ if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainEvalue(), 1.2e-39 ) ) {
+ return false;
+ }
+ 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;
+ }
+ if ( !Test.isEqual( p4.getProteinDomain( 0 ).getTotalCount(), 1 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testLastExternalNodeMethods() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final char[] a0 = { '(', '(', 'A', ',', 'B', ')', ',', '(', 'C', ',', 'D', ')', ')', };
+ final Phylogeny t0 = factory.create( a0, new NHXParser() )[ 0 ];
+ final PhylogenyNode n1 = t0.getNode( "A" );
+ if ( n1.isLastExternalNode() ) {
return false;
}
final PhylogenyNode n2 = t0.getNode( "B" );
return true;
}
+ private static boolean testNodeRemoval() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((a)b)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.removeNode( t0.getNode( "b" ), t0 );
+ if ( !t0.toNewHampshire().equals( "(a);" ) ) {
+ return false;
+ }
+ final Phylogeny t1 = factory.create( "((a:2)b:4)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.removeNode( t1.getNode( "b" ), t1 );
+ if ( !t1.toNewHampshire().equals( "(a:6.0);" ) ) {
+ return false;
+ }
+ final Phylogeny t2 = factory.create( "((a,b),c)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.removeNode( t2.getNode( "b" ), t2 );
+ if ( !t2.toNewHampshire().equals( "((a),c);" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testMidpointrooting() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "(A:1,B:4,C:2,D:2,E:6,F:1,G:1,H:1)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.midpointRoot( t0 );
+ if ( !isEqual( t0.getNode( "E" ).getDistanceToParent(), 5 ) ) {
+ return false;
+ }
+ if ( !isEqual( t0.getNode( "B" ).getDistanceToParent(), 4 ) ) {
+ return false;
+ }
+ if ( !isEqual( PhylogenyMethods.calculateLCA( t0.getNode( "F" ), t0.getNode( "G" ) ).getDistanceToParent(),
+ 1 ) ) {
+ return false;
+ }
final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:4)CD:3[&&NHX:B=10])ABCD:0.5",
new NHXParser() )[ 0 ];
if ( !t1.isRooted() ) {
return false;
}
if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
+ System.exit( -1 );
return false;
}
if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
return false;
}
- if ( !phylogenies[ 9 ].isRooted() ) {
+ if ( !phylogenies[ 9 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 10 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 11 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 12 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 13 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 14 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 15 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 16 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 17 ].isRooted() ) {
+ return false;
+ }
+ if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNexusTreeParsingIterating() {
+ try {
+ final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 25 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 25 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "name" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "name" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
+ // if ( phylogenies.length != 18 ) {
+ // return false;
+ // }
+ //0
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 0" ) ) {
+ return false;
+ }
+ //1
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 1" ) ) {
+ return false;
+ }
+ //2
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //3
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 4 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //4
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 5 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //5
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //6
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 2 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //7
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //8
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 8" ) ) {
+ return false;
+ }
+ //9
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 9" ) ) {
+ return false;
+ }
+ //10
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 10" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //11
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 11" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //12
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 12" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //13
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 13" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //14
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 14" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //15
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 15" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //16
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 16" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //17
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 17" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ p.reset();
+ //0
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 0" ) ) {
+ return false;
+ }
+ //1
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 1" ) ) {
+ return false;
+ }
+ //2
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //3
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 4 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //4
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 5 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //5
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNexusTreeParsingTranslating() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
+ Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
+ if ( phylogenies.length != 1 ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ phylogenies = null;
+ phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
+ if ( phylogenies.length != 3 ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ phylogenies = null;
+ phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
+ if ( phylogenies.length != 3 ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHParsing() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
+ if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
+ return false;
+ }
+ final NHXParser nhxp = new NHXParser();
+ nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
+ nhxp.setReplaceUnderscores( true );
+ final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
+ if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
+ return false;
+ }
+ if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
+ return false;
+ }
+ final Phylogeny p1b = factory
+ .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ",
+ new NHXParser() )[ 0 ];
+ if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
+ return false;
+ }
+ if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
+ return false;
+ }
+ final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
+ final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
+ final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
+ final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
+ final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
+ final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
+ final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
+ 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() );
+ if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
+ return false;
+ }
+ if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
+ return false;
+ }
+ if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
+ return false;
+ }
+ if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
+ return false;
+ }
+ final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
+ final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
+ final String p16_S = "((A,B),C)";
+ final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
+ if ( p16.length != 1 ) {
+ return false;
+ }
+ if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
+ return false;
+ }
+ final String p17_S = "(C,(A,B))";
+ final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
+ if ( p17.length != 1 ) {
+ return false;
+ }
+ if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
+ return false;
+ }
+ final String p18_S = "((A,B),(C,D))";
+ final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
+ if ( p18.length != 1 ) {
+ return false;
+ }
+ if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
+ return false;
+ }
+ final String p19_S = "(((A,B),C),D)";
+ final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
+ if ( p19.length != 1 ) {
+ return false;
+ }
+ if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
+ return false;
+ }
+ final String p20_S = "(A,(B,(C,D)))";
+ final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
+ if ( p20.length != 1 ) {
+ return false;
+ }
+ if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
+ return false;
+ }
+ final String p21_S = "(A,(B,(C,(D,E))))";
+ final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
+ if ( p21.length != 1 ) {
+ return false;
+ }
+ if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
+ return false;
+ }
+ final String p22_S = "((((A,B),C),D),E)";
+ final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
+ if ( p22.length != 1 ) {
+ return false;
+ }
+ if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
+ return false;
+ }
+ final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
+ if ( p23.length != 1 ) {
+ System.out.println( "xl=" + p23.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
+ return false;
+ }
+ final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
+ if ( p24.length != 1 ) {
+ return false;
+ }
+ if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
+ return false;
+ }
+ final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
+ if ( p241.length != 2 ) {
+ return false;
+ }
+ if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
+ return false;
+ }
+ if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
+ return false;
+ }
+ final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
+ + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
+ + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
+ + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
+ + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
+ + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
+ + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
+ + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
+ final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
+ if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
+ return false;
+ }
+ final String p26_S = "(A,B)ab";
+ final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
+ if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
+ return false;
+ }
+ final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
+ if ( p27s.length != 1 ) {
+ System.out.println( "xxl=" + p27s.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ System.out.println( p27s[ 0 ].toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
+ new NHXParser() );
+ if ( p27.length != 1 ) {
+ System.out.println( "yl=" + p27.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ System.out.println( p27[ 0 ].toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ final String p28_S3 = "(A,B)ab";
+ final String p28_S4 = "((((A,B),C),D),;E;)";
+ final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
+ new NHXParser() );
+ if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
+ return false;
+ }
+ if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
+ return false;
+ }
+ if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
+ return false;
+ }
+ if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
+ return false;
+ }
+ if ( p28.length != 4 ) {
+ return false;
+ }
+ final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345";
+ final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
+ if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
+ return false;
+ }
+ final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72";
+ final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
+ if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
+ return false;
+ }
+ final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
+ final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
+ if ( ( p32.length != 0 ) ) {
+ return false;
+ }
+ final String p33_S = "A";
+ final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
+ if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
return false;
}
- if ( phylogenies[ 9 ].getNumberOfExternalNodes() != 3 ) {
+ final String p34_S = "B;";
+ final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
+ if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
return false;
}
- if ( !phylogenies[ 10 ].getName().equals( "tree 10" ) ) {
+ final String p35_S = "B:0.2";
+ final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
+ if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
return false;
}
- if ( !phylogenies[ 10 ].isRooted() ) {
+ final String p36_S = "(A)";
+ final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
+ if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
return false;
}
- if ( phylogenies[ 10 ].getNumberOfExternalNodes() != 3 ) {
+ final String p37_S = "((A))";
+ final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
+ if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
return false;
}
- if ( !phylogenies[ 11 ].getName().equals( "tree 11" ) ) {
+ final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
+ final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
+ if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
return false;
}
- if ( phylogenies[ 11 ].isRooted() ) {
+ final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
+ final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
+ if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
return false;
}
- if ( phylogenies[ 11 ].getNumberOfExternalNodes() != 3 ) {
+ final String p40_S = "(A,B,C)";
+ final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
+ if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
return false;
}
- if ( !phylogenies[ 12 ].getName().equals( "tree 12" ) ) {
+ final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
+ final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
+ if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
return false;
}
- if ( !phylogenies[ 12 ].isRooted() ) {
+ final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
+ final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
+ if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
return false;
}
- if ( phylogenies[ 12 ].getNumberOfExternalNodes() != 3 ) {
+ final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
+ final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
+ if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
return false;
}
- if ( !phylogenies[ 13 ].getName().equals( "tree 13" ) ) {
+ final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
+ final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
+ if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
return false;
}
- if ( !phylogenies[ 13 ].isRooted() ) {
+ final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
+ final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
+ if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
return false;
}
- if ( phylogenies[ 13 ].getNumberOfExternalNodes() != 3 ) {
+ final String p46_S = "";
+ final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
+ if ( p46.length != 0 ) {
return false;
}
- if ( !phylogenies[ 14 ].getName().equals( "tree 14" ) ) {
+ final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
+ if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- if ( !phylogenies[ 14 ].isRooted() ) {
+ final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- if ( phylogenies[ 14 ].getNumberOfExternalNodes() != 10 ) {
+ final Phylogeny p49 = factory
+ .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
+ new NHXParser() )[ 0 ];
+ if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- if ( !phylogenies[ 15 ].getName().equals( "tree 15" ) ) {
+ final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p50.getNode( "A" ) == null ) {
return false;
}
- if ( phylogenies[ 15 ].isRooted() ) {
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ .equals( "((A,B)ab:2.0[88],C);" ) ) {
return false;
}
- if ( phylogenies[ 15 ].getNumberOfExternalNodes() != 10 ) {
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
return false;
}
- if ( !phylogenies[ 16 ].getName().equals( "tree 16" ) ) {
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
+ .equals( "((A,B)88:2.0,C);" ) ) {
return false;
}
- if ( !phylogenies[ 16 ].isRooted() ) {
+ final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p51.getNode( "A(A" ) == null ) {
return false;
}
- if ( phylogenies[ 16 ].getNumberOfExternalNodes() != 10 ) {
+ final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p52.getNode( "A(A" ) == null ) {
return false;
}
- if ( !phylogenies[ 17 ].getName().equals( "tree 17" ) ) {
+ final Phylogeny p53 = factory
+ .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
+ new NHXParser() )[ 0 ];
+ if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
return false;
}
- if ( phylogenies[ 17 ].isRooted() ) {
+ //
+ final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p54.getNode( "A" ) == null ) {
return false;
}
- if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
+ if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ .equals( "((A,B)[88],C);" ) ) {
return false;
}
}
return true;
}
- private static boolean testNexusTreeParsingTranslating() {
+ private static boolean testNHParsingIter() {
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
- Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
- if ( phylogenies.length != 1 ) {
- return false;
- }
- if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
- return false;
- }
- if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
- return false;
- }
- if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
- return false;
- }
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
- return false;
- }
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
- return false;
- }
- phylogenies = null;
- phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
- if ( phylogenies.length != 3 ) {
- return false;
- }
- if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
- return false;
- }
- if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ final String p0_str = "(A,B);";
+ final NHXParser p = new NHXParser();
+ p.setSource( p0_str );
+ if ( !p.hasNext() ) {
return false;
}
- if ( phylogenies[ 0 ].isRooted() ) {
+ final Phylogeny p0 = p.next();
+ if ( !p0.toNewHampshire().equals( p0_str ) ) {
+ System.out.println( p0.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ //
+ final String p00_str = "(A,B)root;";
+ p.setSource( p00_str );
+ final Phylogeny p00 = p.next();
+ if ( !p00.toNewHampshire().equals( p00_str ) ) {
+ System.out.println( p00.toNewHampshire() );
return false;
}
- if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ //
+ final String p000_str = "A;";
+ p.setSource( p000_str );
+ final Phylogeny p000 = p.next();
+ if ( !p000.toNewHampshire().equals( p000_str ) ) {
+ System.out.println( p000.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ //
+ final String p0000_str = "A";
+ p.setSource( p0000_str );
+ final Phylogeny p0000 = p.next();
+ if ( !p0000.toNewHampshire().equals( "A;" ) ) {
+ System.out.println( p0000.toNewHampshire() );
return false;
}
- if ( phylogenies[ 1 ].isRooted() ) {
+ //
+ p.setSource( "(A)" );
+ final Phylogeny p00000 = p.next();
+ if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
+ System.out.println( p00000.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ //
+ final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
+ p.setSource( p1_str );
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ final Phylogeny p1_0 = p.next();
+ if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
+ System.out.println( p1_0.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ final Phylogeny p1_1 = p.next();
+ if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].isRooted() ) {
+ final Phylogeny p1_2 = p.next();
+ if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
+ System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ final Phylogeny p1_3 = p.next();
+ if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- phylogenies = null;
- phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
- if ( phylogenies.length != 3 ) {
+ if ( p.next() != null ) {
return false;
}
- if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ //
+ final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
+ p.setSource( p2_str );
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ Phylogeny p2_0 = p.next();
+ if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
+ System.out.println( p2_0.toNewHampshire() );
return false;
}
- if ( phylogenies[ 0 ].isRooted() ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ Phylogeny p2_1 = p.next();
+ if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ Phylogeny p2_2 = p.next();
+ if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
+ System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
return false;
}
- if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ Phylogeny p2_3 = p.next();
+ if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
return false;
}
- if ( phylogenies[ 1 ].isRooted() ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ Phylogeny p2_4 = p.next();
+ if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
+ System.out.println( "(X) != " + p2_4.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ ////
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ p2_0 = p.next();
+ if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
+ System.out.println( p2_0.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 2 ].isRooted() ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ p2_1 = p.next();
+ if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ p2_2 = p.next();
+ if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
+ System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
return false;
}
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
- private static boolean testNHParsing() {
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
- if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final NHXParser nhxp = new NHXParser();
- nhxp.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
- nhxp.setReplaceUnderscores( true );
- final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
- if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
+ p2_3 = p.next();
+ if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
return false;
}
- if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p1b = factory
- .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ",
- new NHXParser() )[ 0 ];
- if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
+ p2_4 = p.next();
+ if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
+ System.out.println( "(X) != " + p2_4.toNewHampshire() );
return false;
}
- if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
- final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
- final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
- final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
- final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
- final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
- final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
- final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
- 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() );
- if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
+ //
+ final String p3_str = "((A,B),C)abc";
+ p.setSource( p3_str );
+ if ( !p.hasNext() ) {
return false;
}
- if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
+ final Phylogeny p3_0 = p.next();
+ if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
return false;
}
- if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
- final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
- final String p16_S = "((A,B),C)";
- final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
- if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p17_S = "(C,(A,B))";
- final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
- if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
+ //
+ final String p4_str = "((A,B)ab,C)abc";
+ p.setSource( p4_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p18_S = "((A,B),(C,D))";
- final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
- if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
+ final Phylogeny p4_0 = p.next();
+ if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
return false;
}
- final String p19_S = "(((A,B),C),D)";
- final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
- if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p20_S = "(A,(B,(C,D)))";
- final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
- if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p21_S = "(A,(B,(C,(D,E))))";
- final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
- if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
+ //
+ final String p5_str = "(((A,B)ab,C)abc,D)abcd";
+ p.setSource( p5_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p22_S = "((((A,B),C),D),E)";
- final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
- if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
+ final Phylogeny p5_0 = p.next();
+ if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
return false;
}
- final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
- final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
- if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
- if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
- final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
- if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
+ //
+ final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ p.setSource( p6_str );
+ if ( !p.hasNext() ) {
return false;
}
- if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
+ Phylogeny p6_0 = p.next();
+ if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
return false;
}
- final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
- + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
- + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
- + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
- + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
- + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
- + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
- + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
- final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
- if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p26_S = "(A,B)ab";
- final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
- if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
- new NHXParser() );
- if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
- final String p28_S3 = "(A,B)ab";
- final String p28_S4 = "((((A,B),C),D),;E;)";
- final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
- new NHXParser() );
- if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
+ p6_0 = p.next();
+ if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
return false;
}
- if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
+ //
+ final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ p.setSource( p7_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345";
- final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
- if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
+ Phylogeny p7_0 = p.next();
+ if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72";
- final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
- if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
- final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
- if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
+ if ( p.next() != null ) {
return false;
}
- final String p33_S = "A";
- final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
- if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- final String p34_S = "B;";
- final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
- if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
+ p7_0 = p.next();
+ if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- final String p35_S = "B:0.2";
- final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
- if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p36_S = "(A)";
- final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
- if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p37_S = "((A))";
- final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
- if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
+ //
+ final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
+ p.setSource( p8_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
- final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
- if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
+ Phylogeny p8_0 = p.next();
+ if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
- final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
- if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final String p40_S = "(A,B,C)";
- final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
- if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
- final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
- if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
+ Phylogeny p8_1 = p.next();
+ if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
return false;
}
- final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
- final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
- if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
- final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
- if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
- final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
- if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
- final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
- if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
+ p8_0 = p.next();
+ if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- final String p46_S = "";
- final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
- if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
- if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ p8_1 = p.next();
+ if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
return false;
}
- final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final Phylogeny p49 = factory
- .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
- new NHXParser() )[ 0 ];
- if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ if ( p.next() != null ) {
return false;
}
- final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( p50.getNode( "A" ) == null ) {
+ p.reset();
+ //
+ p.setSource( "" );
+ if ( p.hasNext() ) {
return false;
}
- if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
- .equals( "((A,B)ab:2.0[88],C);" ) ) {
+ //
+ p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
+ if ( !p.hasNext() ) {
return false;
}
- if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
+ Phylogeny p_27 = p.next();
+ if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
+ System.out.println( p_27.toNewHampshireX() );
+ System.exit( -1 );
return false;
}
- if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
- .equals( "((A,B)88:2.0,C);" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( p51.getNode( "A(A" ) == null ) {
+ if ( p.next() != null ) {
return false;
}
- final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( p52.getNode( "A(A" ) == null ) {
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p53 = factory
- .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
- new NHXParser() )[ 0 ];
- if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
+ p_27 = p.next();
+ if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
+ System.out.println( p_27.toNewHampshireX() );
+ System.exit( -1 );
return false;
}
- //
- final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
- if ( p54.getNode( "A" ) == null ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
- .equals( "((A,B)[88],C);" ) ) {
+ if ( p.next() != null ) {
return false;
}
}
final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
final PhylogenyNode n5 = PhylogenyNode
- .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
+ .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
final PhylogenyNode n6 = PhylogenyNode
- .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
+ .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
if ( !n1.toNewHampshireX().equals( "" ) ) {
return false;
}
if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
return false;
}
- if ( !n5.toNewHampshireX()
- .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
+ if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
+ return false;
+ }
+ if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
+ System.out.println( n6.toNewHampshireX() );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testTaxonomyExtraction() {
+ try {
+ final PhylogenyNode n0 = PhylogenyNode
+ .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n0.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n1 = PhylogenyNode
+ .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n1.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n1.toString() );
+ return false;
+ }
+ final PhylogenyNode n2x = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n2x.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n3 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
+ System.out.println( n3.toString() );
+ return false;
+ }
+ final PhylogenyNode n4 = PhylogenyNode
+ .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n4.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n4.toString() );
+ return false;
+ }
+ final PhylogenyNode n5 = PhylogenyNode
+ .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n5.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n5.toString() );
+ return false;
+ }
+ final PhylogenyNode n6 = PhylogenyNode
+ .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n6.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n6.toString() );
+ return false;
+ }
+ final PhylogenyNode n7 = PhylogenyNode
+ .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n7.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n7.toString() );
+ return false;
+ }
+ final PhylogenyNode n8 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
+ System.out.println( n8.toString() );
+ return false;
+ }
+ final PhylogenyNode n9 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
+ System.out.println( n9.toString() );
+ return false;
+ }
+ final PhylogenyNode n10x = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n10x.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n10x.toString() );
+ return false;
+ }
+ final PhylogenyNode n10xx = PhylogenyNode
+ .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n10xx.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n10xx.toString() );
+ return false;
+ }
+ final PhylogenyNode n10 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
+ System.out.println( n10.toString() );
+ return false;
+ }
+ final PhylogenyNode n11 = PhylogenyNode
+ .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n11.toString() );
return false;
}
- if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
+ final PhylogenyNode n12 = PhylogenyNode
+ .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n12.toString() );
+ return false;
+ }
+ final PhylogenyNode n13 = PhylogenyNode
+ .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( n13.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n13.toString() );
return false;
}
}
if ( !n5.isHasAssignedEvent() ) {
return false;
}
- if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
- return false;
- }
- if ( n5.getNodeData().getProperties().getPropertyRefs().length != 2 ) {
- return false;
- }
final PhylogenyNode n8 = PhylogenyNode
- .createInstanceFromNhxString( "n8_ECOLI/12:0.01",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
return false;
}
final PhylogenyNode n9 = PhylogenyNode
- .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
return false;
}
final PhylogenyNode n10 = PhylogenyNode
- .createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n10.getName().equals( "n10.ECOLI" ) ) {
return false;
}
final PhylogenyNode n20 = PhylogenyNode
- .createInstanceFromNhxString( "n20_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
return false;
}
final PhylogenyNode n20x = PhylogenyNode
- .createInstanceFromNhxString( "n20_ECOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
- if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
+ .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
return false;
}
final PhylogenyNode n20xx = PhylogenyNode
- .createInstanceFromNhxString( "n20_eCOL1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
+ .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
return false;
}
final PhylogenyNode n20xxx = PhylogenyNode
- .createInstanceFromNhxString( "n20_ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
return false;
}
return false;
}
final PhylogenyNode n20xxxx = PhylogenyNode
- .createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
return false;
}
return false;
}
final PhylogenyNode n21 = PhylogenyNode
- .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
- if ( !n21.getName().equals( "n21_PIG" ) ) {
+ .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n21.getName().equals( "N21_PIG" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
return false;
}
final PhylogenyNode n21x = PhylogenyNode
- .createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n21x.getName().equals( "n21_PIG" ) ) {
return false;
}
return false;
}
final PhylogenyNode n22 = PhylogenyNode
- .createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n22.getName().equals( "n22/PIG" ) ) {
return false;
}
return false;
}
final PhylogenyNode n23 = PhylogenyNode
- .createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n23.getName().equals( "n23/PIG_1" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
return false;
}
- if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) {
- final PhylogenyNode a = PhylogenyNode
- .createInstanceFromNhxString( "n10_ECOLI/1-2",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
- return false;
- }
- if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
- return false;
- }
- final PhylogenyNode b = PhylogenyNode
- .createInstanceFromNhxString( "n10_ECOLI1/1-2",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
- return false;
- }
- if ( !PhylogenyMethods.getSpecies( b ).equals( "" ) ) {
- return false;
- }
- final PhylogenyNode c = PhylogenyNode
- .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
- return false;
- }
- if ( !PhylogenyMethods.getSpecies( c ).equals( "" ) ) {
- return false;
- }
- final PhylogenyNode c1 = PhylogenyNode
- .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
- return false;
- }
- if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
- return false;
- }
- final PhylogenyNode c2 = PhylogenyNode
- .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
- return false;
- }
- if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
- return false;
- }
- final PhylogenyNode d = PhylogenyNode
- .createInstanceFromNhxString( "n10_RAT1/1-2",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
- return false;
- }
- if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
- return false;
- }
- final PhylogenyNode e = PhylogenyNode
- .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !e.getName().equals( "n10_RAT1" ) ) {
- return false;
- }
- if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
- return false;
- }
+ final PhylogenyNode a = PhylogenyNode
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
+ return false;
}
- final PhylogenyNode n11 = PhylogenyNode
- .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
+ if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
return false;
}
- if ( n11.getDistanceToParent() != 0.4 ) {
+ final PhylogenyNode c1 = PhylogenyNode
+ .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
return false;
}
- if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
+ if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
return false;
}
- final PhylogenyNode n12 = PhylogenyNode
- .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
+ final PhylogenyNode c2 = PhylogenyNode
+ .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
return false;
}
- if ( n12.getDistanceToParent() != 0.4 ) {
+ if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
return false;
}
- if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
+ final PhylogenyNode e3 = PhylogenyNode
+ .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !e3.getName().equals( "n10_RAT~" ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
return false;
}
- final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
- final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
- if ( !tvu1.getRef().equals( "tag1" ) ) {
+ final PhylogenyNode n11 = PhylogenyNode
+ .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
return false;
}
- if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
+ if ( n11.getDistanceToParent() != 0.4 ) {
return false;
}
- if ( !tvu1.getUnit().equals( "unit1" ) ) {
+ if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
return false;
}
- if ( !tvu1.getValue().equals( "value1" ) ) {
+ final PhylogenyNode n12 = PhylogenyNode
+ .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
return false;
}
- if ( !tvu3.getRef().equals( "tag3" ) ) {
+ if ( n12.getDistanceToParent() != 0.4 ) {
return false;
}
- if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
+ if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
return false;
}
- if ( !tvu3.getUnit().equals( "unit3" ) ) {
+ final PhylogenyNode o = PhylogenyNode
+ .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
return false;
}
- if ( !tvu3.getValue().equals( "value3" ) ) {
+ if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
return false;
}
if ( n1.getName().compareTo( "" ) != 0 ) {
return false;
}
final PhylogenyNode n00 = PhylogenyNode
- .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
- if ( !n00.getNodeData().getNodeIdentifier().getValue().equals( "node_identifier" ) ) {
- return false;
- }
+ .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
return false;
}
if ( !n00.getNodeData().getSequence().getAccession().getValue().equals( "accession123" ) ) {
return false;
}
- if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getRef().equals( "url_tag" ) ) {
- return false;
- }
- if ( n00.getNodeData().getProperties().getProperty( "url_tag" ).getAppliesTo() != Property.AppliesTo.NODE ) {
- return false;
- }
- if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getDataType().equals( "xsd:anyURI" ) ) {
- return false;
- }
- if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getValue().equals( "www.yahoo.com" ) ) {
- return false;
- }
- if ( !n00.getNodeData().getProperties().getProperty( "url_tag" ).getUnit().equals( "" ) ) {
- return false;
- }
final PhylogenyNode nx = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:GN=gene_1]" );
if ( !nx.getNodeData().getSequence().getName().equals( "gene_1" ) ) {
return false;
}
- final PhylogenyNode nx2 = PhylogenyNode.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:G=gene_2]" );
- if ( !nx2.getNodeData().getSequence().getName().equals( "gene_2" ) ) {
- return false;
- }
final PhylogenyNode n13 = PhylogenyNode
- .createInstanceFromNhxString( "blah_12345/1-2",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
return false;
}
- if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) {
+ if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
+ return false;
+ }
+ if ( !n13.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
+ return false;
+ }
+ if ( !n13.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
return false;
}
final PhylogenyNode n14 = PhylogenyNode
- .createInstanceFromNhxString( "blah_12X45/1-2",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
+ .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
return false;
}
- if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
+ if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
return false;
}
final PhylogenyNode n15 = PhylogenyNode
.createInstanceFromNhxString( "something_wicked[123]",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n15.getName().equals( "something_wicked" ) ) {
return false;
}
}
final PhylogenyNode n16 = PhylogenyNode
.createInstanceFromNhxString( "something_wicked2[9]",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n16.getName().equals( "something_wicked2" ) ) {
return false;
}
- if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
+ if ( n16.getBranchData().getNumberOfConfidences() != 1 ) {
+ return false;
+ }
+ if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
+ return false;
+ }
+ final PhylogenyNode n17 = PhylogenyNode
+ .createInstanceFromNhxString( "something_wicked3[a]",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n17.getName().equals( "something_wicked3" ) ) {
+ return false;
+ }
+ if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
+ return false;
+ }
+ final PhylogenyNode n18 = PhylogenyNode
+ .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
+ return false;
+ }
+ if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
+ return false;
+ }
+ if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
+ return false;
+ }
+ final PhylogenyNode n19 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
+ return false;
+ }
+ if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
+ return false;
+ }
+ final PhylogenyNode n30 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_1234567-roejojoej",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
+ return false;
+ }
+ if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
+ return false;
+ }
+ final PhylogenyNode n31 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_12345678-roejojoej",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n31.getNodeData().isHasTaxonomy() ) {
return false;
}
- if ( !isEqual( n16.getBranchData().getConfidence( 0 ).getValue(), 9 ) ) {
+ final PhylogenyNode n32 = PhylogenyNode
+ .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n32.getNodeData().isHasTaxonomy() ) {
return false;
}
- final PhylogenyNode n17 = PhylogenyNode
- .createInstanceFromNhxString( "something_wicked3[a]",
- PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n17.getName().equals( "something_wicked3" ) ) {
+ final PhylogenyNode n40 = PhylogenyNode
+ .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
return false;
}
- if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
+ final PhylogenyNode n41 = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n41.getNodeData().isHasTaxonomy() ) {
return false;
}
- final PhylogenyNode n18 = PhylogenyNode
- .createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
+ final PhylogenyNode n42 = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( n42.getNodeData().isHasTaxonomy() ) {
return false;
}
- if ( n18.getBranchData().getNumberOfConfidences() != 1 ) {
+ final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
+ NHXParser.TAXONOMY_EXTRACTION.NO );
+ if ( n43.getNodeData().isHasTaxonomy() ) {
return false;
}
- if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
+ final PhylogenyNode n44 = PhylogenyNode
+ .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n44.getNodeData().isHasTaxonomy() ) {
return false;
}
}
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
- final int count = PhylogenyNode.getNodeCount();
+ final long count = PhylogenyNode.getNodeCount();
p.levelOrderReID();
if ( p.getNode( "r" ).getId() != count ) {
return false;
}
- if ( p.getNode( "A" ).getId() != count + 1 ) {
+ if ( p.getNode( "A" ).getId() != ( count + 1 ) ) {
return false;
}
- if ( p.getNode( "B" ).getId() != count + 1 ) {
+ if ( p.getNode( "B" ).getId() != ( count + 1 ) ) {
return false;
}
- if ( p.getNode( "C" ).getId() != count + 1 ) {
+ if ( p.getNode( "C" ).getId() != ( count + 1 ) ) {
return false;
}
- if ( p.getNode( "1" ).getId() != count + 2 ) {
+ if ( p.getNode( "1" ).getId() != ( count + 2 ) ) {
return false;
}
- if ( p.getNode( "2" ).getId() != count + 2 ) {
+ if ( p.getNode( "2" ).getId() != ( count + 2 ) ) {
return false;
}
- if ( p.getNode( "3" ).getId() != count + 2 ) {
+ if ( p.getNode( "3" ).getId() != ( count + 2 ) ) {
return false;
}
- if ( p.getNode( "4" ).getId() != count + 2 ) {
+ if ( p.getNode( "4" ).getId() != ( count + 2 ) ) {
return false;
}
- if ( p.getNode( "5" ).getId() != count + 2 ) {
+ if ( p.getNode( "5" ).getId() != ( count + 2 ) ) {
return false;
}
- if ( p.getNode( "6" ).getId() != count + 2 ) {
+ if ( p.getNode( "6" ).getId() != ( count + 2 ) ) {
return false;
}
- if ( p.getNode( "a" ).getId() != count + 3 ) {
+ if ( p.getNode( "a" ).getId() != ( count + 3 ) ) {
return false;
}
- if ( p.getNode( "b" ).getId() != count + 3 ) {
+ if ( p.getNode( "b" ).getId() != ( count + 3 ) ) {
return false;
}
- if ( p.getNode( "X" ).getId() != count + 4 ) {
+ if ( p.getNode( "X" ).getId() != ( count + 4 ) ) {
return false;
}
- if ( p.getNode( "Y" ).getId() != count + 4 ) {
+ if ( p.getNode( "Y" ).getId() != ( count + 4 ) ) {
return false;
}
- if ( p.getNode( "Z" ).getId() != count + 4 ) {
+ if ( p.getNode( "Z" ).getId() != ( count + 4 ) ) {
return false;
}
}
final Phylogeny gene1 = factory.create( "(A1[&&NHX:S=yeast],A2[&&NHX:S=yeast])", new NHXParser() )[ 0 ];
gene1.setRooted( true );
species1.setRooted( true );
- final SDI sdi = new SDIse( gene1, species1 );
+ final SDI sdi = new SDI( gene1, species1 );
if ( !gene1.getRoot().isDuplication() ) {
return false;
}
new NHXParser() )[ 0 ];
species2.setRooted( true );
gene2.setRooted( true );
- final SDI sdi2 = new SDIse( gene2, species2 );
+ final SDI sdi2 = new SDI( gene2, species2 );
if ( sdi2.getDuplicationsSum() != 0 ) {
return false;
}
new NHXParser() )[ 0 ];
species3.setRooted( true );
gene3.setRooted( true );
- final SDI sdi3 = new SDIse( gene3, species3 );
+ final SDI sdi3 = new SDI( gene3, species3 );
if ( sdi3.getDuplicationsSum() != 1 ) {
return false;
}
new NHXParser() )[ 0 ];
species4.setRooted( true );
gene4.setRooted( true );
- final SDI sdi4 = new SDIse( gene4, species4 );
+ final SDI sdi4 = new SDI( gene4, species4 );
if ( sdi4.getDuplicationsSum() != 1 ) {
return false;
}
new NHXParser() )[ 0 ];
species5.setRooted( true );
gene5.setRooted( true );
- final SDI sdi5 = new SDIse( gene5, species5 );
+ final SDI sdi5 = new SDI( gene5, species5 );
if ( sdi5.getDuplicationsSum() != 2 ) {
return false;
}
new NHXParser() )[ 0 ];
species6.setRooted( true );
gene6.setRooted( true );
- final SDI sdi6 = new SDIse( gene6, species6 );
+ final SDI sdi6 = new SDI( gene6, species6 );
if ( sdi6.getDuplicationsSum() != 3 ) {
return false;
}
final Phylogeny gene7_1 = Test
.createPhylogeny( "((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
gene7_1.setRooted( true );
- final SDI sdi7 = new SDIse( gene7_1, species7 );
+ final SDI sdi7 = new SDI( gene7_1, species7 );
if ( sdi7.getDuplicationsSum() != 0 ) {
return false;
}
final Phylogeny gene7_2 = Test
.createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
gene7_2.setRooted( true );
- final SDI sdi7_2 = new SDIse( gene7_2, species7 );
+ final SDI sdi7_2 = new SDI( gene7_2, species7 );
if ( sdi7_2.getDuplicationsSum() != 1 ) {
return false;
}
return true;
}
- private static boolean testTaxonomyAssigner() {
- try {
- String s0_str = "(((([&&NHX:S=A],[&&NHX:S=B])[&&NHX:S=AB],[&&NHX:S=C])[&&NHX:S=ABC],[&&NHX:S=D])[&&NHX:S=ABCD],[&&NHX:S=E])[&&NHX:S=ABCDE]";
- String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c";
- Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
- Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- s0.setRooted( true );
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) {
- return false;
- }
- s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD],"
- + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH],"
- + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], "
- + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]";
- s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
- s0.setRooted( true );
- g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
- + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b,"
- + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, "
- + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
- + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, "
- + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a,"
- + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b,"
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
- + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a,"
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b,"
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, "
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a,"
- + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
- + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
- + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, "
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) {
- return false;
- }
- if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
- + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
- + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) {
- return false;
- }
- if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) {
- return false;
- }
- s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D]),"
- + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H]),"
- + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), "
- + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))";
- s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ];
- s0.setRooted( true );
- g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a,"
- + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab,"
- + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, "
- + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r";
- g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ];
- g0.setRooted( true );
- TaxonomyAssigner.execute( g0, s0 );
- if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) {
- return false;
- }
- if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
private static boolean testUniprotTaxonomySearch() {
try {
- List<UniProtTaxonomy> results = UniProtWsTools
- .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
+ List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
+ 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
if ( results.size() != 1 ) {
return false;
}
if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861.2" ).equals( "AY423861.2" ) ) {
+ return false;
+ }
+ if ( !SequenceIdParser.parseGenbankAccessor( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
}
private static boolean testUniprotEntryRetrieval() {
- if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
- return false;
- }
- if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
- return false;
- }
- if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
- return false;
- }
- if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
- return false;
- }
- if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
- return false;
- }
- if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
- return false;
- }
- if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
- return false;
- }
- if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
- return false;
- }
- if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
- return false;
- }
- if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
- return false;
- }
- if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
- return false;
- }
- if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
- return false;
- }
- if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
- return false;
- }
try {
- final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
+ final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
if ( !entry.getAccession().equals( "P12345" ) ) {
return false;
}
if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
return false;
}
- if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
- return false;
- }
if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
return false;
}
return true;
}
+ private static boolean testSequenceWriter() {
+ try {
+ final String n = ForesterUtil.LINE_SEPARATOR;
+ if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
+ .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
+ .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
private static boolean testCreateBalancedPhylogeny() {
try {
final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
return true;
}
- private static boolean testMafft() {
+ private static boolean testMafft( final String path ) {
try {
final List<String> opts = new ArrayList<String>();
opts.add( "--maxiterate" );
opts.add( "--localpair" );
opts.add( "--quiet" );
Msa msa = null;
- final MsaInferrer mafft = Mafft.createInstance();
+ final MsaInferrer mafft = Mafft.createInstance( path );
msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
return false;
private static boolean testMsaQualityMethod() {
try {
final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
- final Sequence s1 = BasicSequence.createAaSequence( "a", "ABBXEFGHIJ" );
- final Sequence s2 = BasicSequence.createAaSequence( "a", "AXCXEFGHIJ" );
- final Sequence s3 = BasicSequence.createAaSequence( "a", "AXDDEFGHIJ" );
+ final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
+ final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
+ final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
final List<Sequence> l = new ArrayList<Sequence>();
l.add( s0 );
l.add( s1 );
}
return true;
}
-
+
private static boolean testSequenceIdParsing() {
try {
Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" );
- if ( id == null
- || ForesterUtil.isEmpty( id.getValue() )
- || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "ADF31344" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
//
id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" );
- if ( id == null
- || ForesterUtil.isEmpty( id.getValue() )
- || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "ADF31344" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
//
id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" );
- if ( id == null
- || ForesterUtil.isEmpty( id.getValue() )
- || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "ADF31344" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
return false;
}
-
//
id = SequenceIdParser.parse( "gb_AAA96518_1" );
- if ( id == null
- || ForesterUtil.isEmpty( id.getValue() )
- || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "AAA96518" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
//
id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" );
- if ( id == null
- || ForesterUtil.isEmpty( id.getValue() )
- || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "EHB07727" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
//
id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" );
- if ( id == null
- || ForesterUtil.isEmpty( id.getValue() )
- || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "BAF37827" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
//
id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" );
- if ( id == null
- || ForesterUtil.isEmpty( id.getValue() )
- || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "CAA73223" )
- || !id.getProvider().equals( "ncbi" ) ) {
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
return false;
}
//
-// id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
-// if ( id == null
-// || ForesterUtil.isEmpty( id.getValue() )
-// || ForesterUtil.isEmpty( id.getProvider() )
-// || !id.getValue().equals( "002434188" )
-// || !id.getProvider().equals( "genbank" ) ) {
-// if ( id != null ) {
-// System.out.println( "value =" + id.getValue() );
-// System.out.println( "provider=" + id.getProvider() );
-// }
-// return false;
-// }
-
+ id = SequenceIdParser.parse( "P4A123" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
+ || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ }
+ return false;
+ }
+ //
+ id = SequenceIdParser.parse( "XP_12345" );
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getProvider() );
+ return false;
+ }
// lcl_91970_unknown_
}
catch ( final Exception e ) {
git://source.jalview.org / jalview.git / blobdiff