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Applications and software libraries for evolutionary biology and comparative genomics research
// $Id:
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// WWW: www.phylosoft.org/forester
package org.forester.test;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.Set;
import org.forester.application.support_transfer;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
import org.forester.go.TestGo;
import org.forester.io.parsers.FastaParser;
import org.forester.io.parsers.GeneralMsaParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser;
import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
import org.forester.io.parsers.nexus.NexusBinaryStatesMatrixParser;
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.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.msa.BasicMsa;
import org.forester.msa.Mafft;
import org.forester.msa.Msa;
import org.forester.msa.MsaInferrer;
import org.forester.msa.MsaMethods;
import org.forester.pccx.TestPccx;
import org.forester.phylogeny.Phylogeny;
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.data.BinaryCharacters;
import org.forester.phylogeny.data.BranchWidth;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Distribution;
import org.forester.phylogeny.data.DomainArchitecture;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.PhylogenyData;
import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.Polygon;
import org.forester.phylogeny.data.PropertiesMap;
import org.forester.phylogeny.data.Property;
import org.forester.phylogeny.data.Property.AppliesTo;
import org.forester.phylogeny.data.ProteinDomain;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.protein.Protein;
import org.forester.sdi.SDI;
import org.forester.sdi.SDIR;
import org.forester.sdi.SDIse;
import org.forester.sdi.TestGSDI;
import org.forester.sequence.BasicSequence;
import org.forester.sequence.Sequence;
import org.forester.surfacing.TestSurfacing;
import org.forester.tools.ConfidenceAssessor;
import org.forester.tools.SupportCount;
import org.forester.tools.TreeSplitMatrix;
import org.forester.util.AsciiHistogram;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
import org.forester.util.GeneralTable;
import org.forester.util.SequenceIdParser;
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;
import org.forester.ws.wabi.TxSearch.TAX_RANK;
@SuppressWarnings( "unused")
public final class Test {
private final static double ZERO_DIFF = 1.0E-9;
private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
+ ForesterUtil.getFileSeparator() + "test_data"
+ ForesterUtil.getFileSeparator();
private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
+ ForesterUtil.getFileSeparator() + "resources"
+ ForesterUtil.getFileSeparator();
private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
+ ForesterConstants.PHYLO_XML_VERSION + "/"
+ ForesterConstants.PHYLO_XML_XSD;
private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
+ ForesterConstants.PHYLO_XML_VERSION + "/"
+ ForesterConstants.PHYLO_XML_XSD;
private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
return p;
}
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();
}
public static boolean isEqual( final double a, final double b ) {
return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
}
public static void main( final String[] args ) {
System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
+ "]" );
Locale.setDefault( Locale.US );
System.out.println( "[Locale: " + Locale.getDefault() + "]" );
int failed = 0;
int succeeded = 0;
System.out.print( "[Test if directory with files for testing exists/is readable: " );
if ( Test.testDir( PATH_TO_TEST_DATA ) ) {
System.out.println( "OK.]" );
}
else {
System.out.println( "could not find/read from directory \"" + PATH_TO_TEST_DATA + "\".]" );
System.out.println( "Testing aborted." );
System.exit( -1 );
}
System.out.print( "[Test if resources directory exists/is readable: " );
if ( testDir( PATH_TO_RESOURCES ) ) {
System.out.println( "OK.]" );
}
else {
System.out.println( "could not find/read from directory \"" + Test.PATH_TO_RESOURCES + "\".]" );
System.out.println( "Testing aborted." );
System.exit( -1 );
}
final long start_time = new Date().getTime();
System.out.print( "Sequence id parsing: " );
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: " );
if ( testHmmscanOutputParser() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Basic node methods: " );
if ( Test.testBasicNodeMethods() ) {
System.out.println( "OK." );
succeeded++;
}
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." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "NH parsing: " );
if ( Test.testNHParsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Conversion to NHX (node level): " );
if ( Test.testNHXconversion() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "NHX parsing: " );
if ( Test.testNHXParsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "NHX parsing with quotes: " );
if ( Test.testNHXParsingQuotes() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "NHX parsing (MrBayes): " );
if ( Test.testNHXParsingMB() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Nexus characters parsing: " );
if ( Test.testNexusCharactersParsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Nexus tree parsing: " );
if ( Test.testNexusTreeParsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Nexus tree parsing (translating): " );
if ( Test.testNexusTreeParsingTranslating() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Nexus matrix parsing: " );
if ( Test.testNexusMatrixParsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Basic phyloXML parsing: " );
if ( Test.testBasicPhyloXMLparsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Basic phyloXML parsing (validating against schema): " );
if ( testBasicPhyloXMLparsingValidating() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "phyloXML Distribution Element: " );
if ( Test.testPhyloXMLparsingOfDistributionElement() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Tol XML parsing: " );
if ( Test.testBasicTolXMLparsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Copying of node data: " );
if ( Test.testCopyOfNodeData() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Basic tree methods: " );
if ( Test.testBasicTreeMethods() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Postorder Iterator: " );
if ( Test.testPostOrderIterator() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Preorder Iterator: " );
if ( Test.testPreOrderIterator() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Levelorder Iterator: " );
if ( Test.testLevelOrderIterator() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Re-id methods: " );
if ( Test.testReIdMethods() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Methods on last external nodes: " );
if ( Test.testLastExternalNodeMethods() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Methods on external nodes: " );
if ( Test.testExternalNodeRelatedMethods() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Deletion of external nodes: " );
if ( Test.testDeletionOfExternalNodes() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Subtree deletion: " );
if ( Test.testSubtreeDeletion() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Phylogeny branch: " );
if ( Test.testPhylogenyBranch() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Rerooting: " );
if ( Test.testRerooting() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Mipoint rooting: " );
if ( Test.testMidpointrooting() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Support count: " );
if ( Test.testSupportCount() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Support transfer: " );
if ( Test.testSupportTransfer() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Finding of LCA: " );
if ( Test.testGetLCA() ) {
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." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "SDIse: " );
if ( Test.testSDIse() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "SDIunrooted: " );
if ( Test.testSDIunrooted() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "GSDI: " );
if ( TestGSDI.test() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Descriptive statistics: " );
if ( Test.testDescriptiveStatistics() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Data objects and methods: " );
if ( Test.testDataObjects() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Properties map: " );
if ( Test.testPropertiesMap() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Phylogeny reconstruction:" );
System.out.println();
if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Analysis of domain architectures: " );
System.out.println();
if ( TestSurfacing.test( new File( PATH_TO_TEST_DATA ) ) ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "GO: " );
System.out.println();
if ( TestGo.test( new File( PATH_TO_TEST_DATA ) ) ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Modeling tools: " );
if ( TestPccx.test() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Split Matrix strict: " );
if ( Test.testSplitStrict() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Split Matrix: " );
if ( Test.testSplit() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Confidence Assessor: " );
if ( Test.testConfidenceAssessor() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Basic table: " );
if ( Test.testBasicTable() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "General table: " );
if ( Test.testGeneralTable() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Amino acid sequence: " );
if ( Test.testAminoAcidSequence() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "General MSA parser: " );
if ( Test.testGeneralMsaParser() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Fasta parser for msa: " );
if ( Test.testFastaParser() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Creation of balanced phylogeny: " );
if ( Test.testCreateBalancedPhylogeny() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "EMBL Entry Retrieval: " );
if ( Test.testEmblEntryRetrieval() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Uniprot Entry Retrieval: " );
if ( Test.testUniprotEntryRetrieval() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Uniprot Taxonomy Search: " );
if ( Test.testUniprotTaxonomySearch() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
if ( Mafft.isInstalled() ) {
System.out.print( "MAFFT (external program): " );
if ( Test.testMafft() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed [will not count towards failed tests]" );
}
}
System.out.print( "Next nodes with collapsed: " );
if ( Test.testNextNodeWithCollapsing() ) {
System.out.println( "OK." );
succeeded++;
}
else {
System.out.println( "failed." );
failed++;
}
System.out.print( "Simple MSA quality: " );
if ( Test.testMsaQualityMethod() ) {
System.out.println( "OK." );
succeeded++;
}
else {
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;
final long total_memory = rt.totalMemory() / 1000000;
System.out.println( "Running time : " + ( new Date().getTime() - start_time ) + "ms " + "(free memory: "
+ free_memory + "MB, total memory: " + total_memory + "MB)" );
System.out.println();
System.out.println( "Successful tests: " + succeeded );
System.out.println( "Failed tests: " + failed );
System.out.println();
if ( failed < 1 ) {
System.out.println( "OK." );
}
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() {
try {
if ( PhylogenyNode.getNodeCount() != 0 ) {
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() ) {
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 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_0.length != 4 ) {
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 ) {
return false;
}
if ( !t1.isRooted() ) {
return false;
}
if ( t1.isRerootable() ) {
return false;
}
if ( !t1.getType().equals( "gene_tree" ) ) {
return false;
}
if ( t2.getNumberOfExternalNodes() != 2 ) {
return false;
}
if ( !isEqual( t2.getNode( "node a" ).getDistanceToParent(), 1.0 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "node b" ).getDistanceToParent(), 2.0 ) ) {
return false;
}
if ( t2.getNode( "node a" ).getNodeData().getTaxonomies().size() != 2 ) {
return false;
}
if ( !t2.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
return false;
}
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.getNode( "node a" ).getNodeData().getSequence( 1 ).getMolecularSequence()
.startsWith( "ctgtgatgcat" ) ) {
return false;
}
if ( t3.getNumberOfExternalNodes() != 4 ) {
return false;
}
if ( !t1.getName().equals( "t1" ) ) {
return false;
}
if ( !t2.getName().equals( "t2" ) ) {
return false;
}
if ( !t3.getName().equals( "t3" ) ) {
return false;
}
if ( !t4.getName().equals( "t4" ) ) {
return false;
}
if ( !t3.getIdentifier().getValue().equals( "1-1" ) ) {
return false;
}
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.getNode( "root node" ).getNodeData().getSequence().getSymbol().equals( "BCL2L14" ) ) {
return false;
}
if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getValue().equals( "Q9BZR8" ) ) {
return false;
}
if ( !t3.getNode( "root node" ).getNodeData().getSequence().getAccession().getSource().equals( "UniProtKB" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
.equals( "apoptosis" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
.equals( "GO:0006915" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
.equals( "UniProtKB" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
.equals( "experimental" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
.equals( "function" ) ) {
return false;
}
if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
.getValue() != 1 ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
.getType().equals( "ml" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
.equals( "apoptosis" ) ) {
return false;
}
if ( ( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
.equals( "GO:0005829" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).getDesc()
.equals( "intracellular organelle" ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getType().equals( "source" ) ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getUri( 0 ).getDescription()
.equals( "UniProt link" ) ) ) {
return false;
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
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 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 );
}
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 ( 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 ) {
return false;
}
final Phylogeny t1_rt = phylogenies_t1[ 0 ];
if ( !t1_rt.getDistanceUnit().equals( "cc" ) ) {
return false;
}
if ( !t1_rt.isRooted() ) {
return false;
}
if ( t1_rt.isRerootable() ) {
return false;
}
if ( !t1_rt.getType().equals( "gene_tree" ) ) {
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 ) {
return false;
}
if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 0 ).getCommonName().equals( "some parasite" ) ) {
return false;
}
if ( !t2_rt.getNode( "node a" ).getNodeData().getTaxonomy( 1 ).getCommonName().equals( "the host" ) ) {
return false;
}
if ( t2_rt.getNode( "node a" ).getNodeData().getSequences().size() != 2 ) {
return false;
}
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( 1 ) ).getDesc()
.equals( "apoptosis" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getRef()
.equals( "GO:0006915" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getSource()
.equals( "UniProtKB" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getEvidence()
.equals( "experimental" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getType()
.equals( "function" ) ) {
return false;
}
if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
.getValue() != 1 ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getConfidence()
.getType().equals( "ml" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getDesc()
.equals( "apoptosis" ) ) {
return false;
}
if ( ( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getAppliesTo() != AppliesTo.ANNOTATION ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getDataType().equals( "xsd:double" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getRef().equals( "AFFY:expression" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getUnit().equals( "AFFY:x" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "AFFY:expression" ).getValue().equals( "0.2" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 1 ) ).getProperties()
.getProperty( "MED:disease" ).getValue().equals( "lymphoma" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 0 ) ).getRef()
.equals( "GO:0005829" ) ) {
return false;
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getSequence().getAnnotation( 2 ) ).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;
}
if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
.equals( "pfam" ) ) {
return false;
}
if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 3 ) {
return false;
}
if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
return false;
}
if ( t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 1 ) {
return false;
}
if ( !t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().getType().equals( "domains" ) ) {
return false;
}
final Taxonomy taxbb = t3_rt.getNode( "node bb" ).getNodeData().getTaxonomy();
if ( !taxbb.getAuthority().equals( "Stephenson, 1935" ) ) {
return false;
}
if ( !taxbb.getCommonName().equals( "starlet sea anemone" ) ) {
return false;
}
if ( !taxbb.getIdentifier().getProvider().equals( "EOL" ) ) {
return false;
}
if ( !taxbb.getIdentifier().getValue().equals( "704294" ) ) {
return false;
}
if ( !taxbb.getTaxonomyCode().equals( "NEMVE" ) ) {
return false;
}
if ( !taxbb.getScientificName().equals( "Nematostella vectensis" ) ) {
return false;
}
if ( taxbb.getSynonyms().size() != 2 ) {
return false;
}
if ( !taxbb.getSynonyms().contains( "Nematostella vectensis Stephenson1935" ) ) {
return false;
}
if ( !taxbb.getSynonyms().contains( "See Anemone" ) ) {
return false;
}
if ( !taxbb.getUri( 0 ).getDescription().equals( "EOL" ) ) {
return false;
}
if ( !taxbb.getUri( 0 ).getType().equals( "linkout" ) ) {
return false;
}
if ( !taxbb.getUri( 0 ).getValue().toString().equals( "http://www.eol.org/pages/704294" ) ) {
return false;
}
if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
.getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
;
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCharacters().size() != 1 ) {
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCount() != 3 ) {
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getLostCharacters().size() != 3 ) {
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCount() != 2 ) {
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getPresentCharacters().size() != 2 ) {
return false;
}
if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) {
return false;
}
//
if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) {
return false;
}
if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getValue().toPlainString()
.equalsIgnoreCase( "435" ) ) {
return false;
}
if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMin().toPlainString().equalsIgnoreCase( "416" ) ) {
return false;
}
if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getMax().toPlainString()
.equalsIgnoreCase( "443.7" ) ) {
return false;
}
if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getUnit().equals( "mya" ) ) {
return false;
}
if ( !t3_rt.getNode( "node bb" ).getNodeData().getDate().getDesc().equals( "Triassic" ) ) {
return false;
}
if ( !t3_rt.getNode( "node bc" ).getNodeData().getDate().getValue().toPlainString()
.equalsIgnoreCase( "433" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testBasicPhyloXMLparsingValidating() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
PhyloXmlParser xml_parser = null;
try {
xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
}
catch ( final Exception e ) {
// Do nothing -- means were not running from jar.
}
if ( xml_parser == null ) {
xml_parser = new PhyloXmlParser();
if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
}
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 ( phylogenies_0.length != 4 ) {
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.getName().equals( "t1" ) ) {
return false;
}
if ( !t2.getName().equals( "t2" ) ) {
return false;
}
if ( !t3.getName().equals( "t3" ) ) {
return false;
}
if ( !t4.getName().equals( "t4" ) ) {
return false;
}
if ( t1.getNumberOfExternalNodes() != 1 ) {
return false;
}
if ( t2.getNumberOfExternalNodes() != 2 ) {
return false;
}
if ( t3.getNumberOfExternalNodes() != 4 ) {
return false;
}
final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( "errors:" );
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_1.length != 4 ) {
return false;
}
final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( "errors:" );
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_2.length != 1 ) {
return false;
}
if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
return false;
}
final Phylogeny[] phylogenies_3 = 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_3.length != 2 ) {
return false;
}
final Phylogeny a = phylogenies_3[ 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;
}
final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_4.length != 1 ) {
return false;
}
final Phylogeny s = phylogenies_4[ 0 ];
if ( s.getNumberOfExternalNodes() != 6 ) {
return false;
}
s.getNode( "first" );
s.getNode( "<>" );
s.getNode( "\"\"" );
s.getNode( "'''\"" );
s.getNode( "\"\"\"" );
s.getNode( "dick & doof" );
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testBasicTable() {
try {
final BasicTable t0 = new BasicTable();
if ( t0.getNumberOfColumns() != 0 ) {
return false;
}
if ( t0.getNumberOfRows() != 0 ) {
return false;
}
t0.setValue( 3, 2, "23" );
t0.setValue( 10, 1, "error" );
t0.setValue( 10, 1, "110" );
t0.setValue( 9, 1, "19" );
t0.setValue( 1, 10, "101" );
t0.setValue( 10, 10, "1010" );
t0.setValue( 100, 10, "10100" );
t0.setValue( 0, 0, "00" );
if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
return false;
}
if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
return false;
}
if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
return false;
}
if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
return false;
}
if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
return false;
}
if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
return false;
}
if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
return false;
}
if ( t0.getNumberOfColumns() != 101 ) {
return false;
}
if ( t0.getNumberOfRows() != 11 ) {
return false;
}
if ( t0.getValueAsString( 49, 4 ) != null ) {
return false;
}
final String l = ForesterUtil.getLineSeparator();
final StringBuffer source = new StringBuffer();
source.append( "" + l );
source.append( "# 1 1 1 1 1 1 1 1" + l );
source.append( " 00 01 02 03" + l );
source.append( " 10 11 12 13 " + l );
source.append( "20 21 22 23 " + l );
source.append( " 30 31 32 33" + l );
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 t1 = BasicTableParser.parse( source.toString(), " " );
if ( t1.getNumberOfColumns() != 5 ) {
return false;
}
if ( t1.getNumberOfRows() != 6 ) {
return false;
}
if ( !t1.getValueAsString( 0, 0 ).equals( "00" ) ) {
return false;
}
if ( !t1.getValueAsString( 1, 0 ).equals( "01" ) ) {
return false;
}
if ( !t1.getValueAsString( 3, 0 ).equals( "03" ) ) {
return false;
}
if ( !t1.getValueAsString( 4, 5 ).equals( "54" ) ) {
return false;
}
final StringBuffer source1 = new StringBuffer();
source1.append( "" + l );
source1.append( "# 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
source1.append( " 00; 01 ;02;03" + l );
source1.append( " 10; 11; 12; 13 " + l );
source1.append( "20; 21; 22; 23 " + l );
source1.append( " 30; 31; 32; 33" + l );
source1.append( "40;41;42;43" + l );
source1.append( " # 1 1 1 1 1 " + l );
source1.append( ";;;50 ; ;52; 53;;54 " + l );
final BasicTable t2 = BasicTableParser.parse( source1.toString(), ";" );
if ( t2.getNumberOfColumns() != 5 ) {
return false;
}
if ( t2.getNumberOfRows() != 6 ) {
return false;
}
if ( !t2.getValueAsString( 0, 0 ).equals( "00" ) ) {
return false;
}
if ( !t2.getValueAsString( 1, 0 ).equals( "01" ) ) {
return false;
}
if ( !t2.getValueAsString( 3, 0 ).equals( "03" ) ) {
return false;
}
if ( !t2.getValueAsString( 3, 3 ).equals( "33" ) ) {
return false;
}
if ( !t2.getValueAsString( 3, 5 ).equals( "53" ) ) {
return false;
}
if ( !t2.getValueAsString( 1, 5 ).equals( "" ) ) {
return false;
}
final StringBuffer source2 = new StringBuffer();
source2.append( "" + l );
source2.append( "comment: 1; 1; 1; 1 ;1 ;1; 1 ;1;" + l );
source2.append( " 00; 01 ;02;03" + l );
source2.append( " 10; 11; 12; 13 " + l );
source2.append( "20; 21; 22; 23 " + l );
source2.append( " " + l );
source2.append( " 30; 31; 32; 33" + l );
source2.append( "40;41;42;43" + l );
source2.append( " comment: 1 1 1 1 1 " + l );
source2.append( ";;;50 ; 52; 53;;54 " + l );
final List> tl = BasicTableParser.parse( source2.toString(),
";",
false,
"comment:",
false );
if ( tl.size() != 2 ) {
return false;
}
final BasicTable t3 = tl.get( 0 );
final BasicTable t4 = tl.get( 1 );
if ( t3.getNumberOfColumns() != 4 ) {
return false;
}
if ( t3.getNumberOfRows() != 3 ) {
return false;
}
if ( t4.getNumberOfColumns() != 4 ) {
return false;
}
if ( t4.getNumberOfRows() != 3 ) {
return false;
}
if ( !t3.getValueAsString( 0, 0 ).equals( "00" ) ) {
return false;
}
if ( !t4.getValueAsString( 0, 0 ).equals( "30" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testBasicTolXMLparsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final TolParser parser = new TolParser();
final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2484.tol", parser );
if ( parser.getErrorCount() > 0 ) {
System.out.println( parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_0.length != 1 ) {
return false;
}
final Phylogeny t1 = phylogenies_0[ 0 ];
if ( t1.getNumberOfExternalNodes() != 5 ) {
return false;
}
if ( !t1.isRooted() ) {
return false;
}
if ( !t1.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Mesozoa" ) ) {
return false;
}
if ( !t1.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2484" ) ) {
return false;
}
if ( !t1.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Rhombozoa" ) ) {
return false;
}
if ( t1.getRoot().getChildNode( 0 ).getNumberOfDescendants() != 3 ) {
return false;
}
final Phylogeny[] phylogenies_1 = factory.create( Test.PATH_TO_TEST_DATA + "tol_2.tol", parser );
if ( parser.getErrorCount() > 0 ) {
System.out.println( parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_1.length != 1 ) {
return false;
}
final Phylogeny t2 = phylogenies_1[ 0 ];
if ( t2.getNumberOfExternalNodes() != 664 ) {
return false;
}
if ( !t2.isRooted() ) {
return false;
}
if ( !t2.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Eubacteria" ) ) {
return false;
}
if ( !t2.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "2" ) ) {
return false;
}
if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
return false;
}
if ( t2.getRoot().getNumberOfDescendants() != 24 ) {
return false;
}
if ( !t2.getRoot().getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName().equals( "Aquificae" ) ) {
return false;
}
if ( !t2.getRoot().getChildNode( 0 ).getChildNode( 0 ).getNodeData().getTaxonomy().getScientificName()
.equals( "Aquifex" ) ) {
return false;
}
final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "tol_5.tol", parser );
if ( parser.getErrorCount() > 0 ) {
System.out.println( parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_2.length != 1 ) {
return false;
}
final Phylogeny t3 = phylogenies_2[ 0 ];
if ( t3.getNumberOfExternalNodes() != 184 ) {
return false;
}
if ( !t3.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Viruses" ) ) {
return false;
}
if ( !t3.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "5" ) ) {
return false;
}
if ( t3.getRoot().getNumberOfDescendants() != 6 ) {
return false;
}
final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "tol_4567.tol", parser );
if ( parser.getErrorCount() > 0 ) {
System.out.println( parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_3.length != 1 ) {
return false;
}
final Phylogeny t4 = phylogenies_3[ 0 ];
if ( t4.getNumberOfExternalNodes() != 1 ) {
return false;
}
if ( !t4.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Marpissa decorata" ) ) {
return false;
}
if ( !t4.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "4567" ) ) {
return false;
}
if ( t4.getRoot().getNumberOfDescendants() != 0 ) {
return false;
}
final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "tol_16299.tol", parser );
if ( parser.getErrorCount() > 0 ) {
System.out.println( parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_4.length != 1 ) {
return false;
}
final Phylogeny t5 = phylogenies_4[ 0 ];
if ( t5.getNumberOfExternalNodes() != 13 ) {
return false;
}
if ( !t5.getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Hominidae" ) ) {
return false;
}
if ( !t5.getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "16299" ) ) {
return false;
}
if ( t5.getRoot().getNumberOfDescendants() != 2 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testBasicTreeMethods() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t1 = factory.create();
if ( !t1.isEmpty() ) {
return false;
}
final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
if ( t2.getNumberOfExternalNodes() != 4 ) {
return false;
}
if ( t2.getHeight() != 8.5 ) {
return false;
}
if ( !t2.isCompletelyBinary() ) {
return false;
}
if ( t2.isEmpty() ) {
return false;
}
final Phylogeny t3 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3)", new NHXParser() )[ 0 ];
if ( t3.getNumberOfExternalNodes() != 5 ) {
return false;
}
if ( t3.getHeight() != 11 ) {
return false;
}
if ( t3.isCompletelyBinary() ) {
return false;
}
final PhylogenyNode n = t3.getNode( "ABC" );
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 ( t4.getHeight() != 11 ) {
return false;
}
if ( t4.isCompletelyBinary() ) {
return false;
}
final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
if ( t5.getNumberOfExternalNodes() != 8 ) {
return false;
}
if ( t5.getHeight() != 15 ) {
return false;
}
final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
if ( t6.getHeight() != 15 ) {
return false;
}
final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
if ( t7.getHeight() != 15 ) {
return false;
}
final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
if ( t8.getNumberOfExternalNodes() != 10 ) {
return false;
}
if ( t8.getHeight() != 15 ) {
return false;
}
final char[] a9 = new char[] {};
final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
if ( t9.getHeight() != 0 ) {
return false;
}
final char[] a10 = new char[] { 'a', ':', '6' };
final Phylogeny t10 = factory.create( a10, new NHXParser() )[ 0 ];
if ( t10.getHeight() != 6 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testConfidenceAssessor() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
final Phylogeny[] ev0 = factory
.create( "((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);((((A,B),C),D),E);",
new NHXParser() );
ConfidenceAssessor.evaluate( "bootstrap", ev0, t0, false, 1, 0, 2 );
if ( !isEqual( t0.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
return false;
}
if ( !isEqual( t0.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) {
return false;
}
final Phylogeny t1 = factory.create( "((((A,B)ab[&&NHX:B=50],C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
final Phylogeny[] ev1 = factory
.create( "((((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)));",
new NHXParser() );
ConfidenceAssessor.evaluate( "bootstrap", ev1, t1, false, 1 );
if ( !isEqual( t1.getNode( "ab" ).getBranchData().getConfidence( 1 ).getValue(), 7 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
return false;
}
final Phylogeny t_b = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
final Phylogeny[] ev_b = factory
.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;
}
if ( !isEqual( t_b.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
return false;
}
//
final Phylogeny t1x = factory.create( "((((A,B)ab,C)abc,D)abcd,E)abcde", new NHXParser() )[ 0 ];
final Phylogeny[] ev1x = factory
.create( "((((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)));",
new NHXParser() );
ConfidenceAssessor.evaluate( "bootstrap", ev1x, t1x, true, 1 );
if ( !isEqual( t1x.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
return false;
}
if ( !isEqual( t1x.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 7 ) ) {
return false;
}
final Phylogeny t_bx = factory.create( "((((A,C)ac,D)acd,E)acde,B)abcde", new NHXParser() )[ 0 ];
final Phylogeny[] ev_bx = factory
.create( "((((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_bx, t_bx, true, 1 );
if ( !isEqual( t_bx.getNode( "ac" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
return false;
}
if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
return false;
}
//
final Phylogeny[] t2 = factory
.create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);",
new NHXParser() );
final Phylogeny[] ev2 = factory
.create( "((((a,b),c),d),e);((((a,b),c),d),e);((((a,b),e),d),c);((((a,b),e),d),c);(((a,b),(c,d)),e);((a,b),x);((a,b),(x,y));(a,b);(a,e);(a,b,c);",
new NHXParser() );
for( final Phylogeny target : t2 ) {
ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 );
}
//
final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg",
new NHXParser() )[ 0 ];
final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() );
ConfidenceAssessor.evaluate( "bootstrap", ev4, t4, false, 1 );
if ( !isEqual( t4.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
return false;
}
if ( !isEqual( t4.getNode( "abc" ).getBranchData().getConfidence( 0 ).getValue(), 2 ) ) {
return false;
}
if ( !isEqual( t4.getNode( "abcde" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testCopyOfNodeData() {
try {
final PhylogenyNode n1 = PhylogenyNode
.createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:O=22:SO=33:SN=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
final PhylogenyNode n2 = n1.copyNodeData();
if ( !n1.toNewHampshireX().equals( n2.toNewHampshireX() ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testDataObjects() {
try {
final Confidence s0 = new Confidence();
final Confidence s1 = new Confidence();
if ( !s0.isEqual( s1 ) ) {
return false;
}
final Confidence s2 = new Confidence( 0.23, "bootstrap" );
final Confidence s3 = new Confidence( 0.23, "bootstrap" );
if ( s2.isEqual( s1 ) ) {
return false;
}
if ( !s2.isEqual( s3 ) ) {
return false;
}
final Confidence s4 = ( Confidence ) s3.copy();
if ( !s4.isEqual( s3 ) ) {
return false;
}
s3.asSimpleText();
s3.asText();
// Taxonomy
// ----------
final Taxonomy t1 = new Taxonomy();
final Taxonomy t2 = new Taxonomy();
final Taxonomy t3 = new Taxonomy();
final Taxonomy t4 = new Taxonomy();
final Taxonomy t5 = new Taxonomy();
t1.setIdentifier( new Identifier( "ecoli" ) );
t1.setTaxonomyCode( "ECOLI" );
t1.setScientificName( "E. coli" );
t1.setCommonName( "coli" );
final Taxonomy t0 = ( Taxonomy ) t1.copy();
if ( !t1.isEqual( t0 ) ) {
return false;
}
t2.setIdentifier( new Identifier( "ecoli" ) );
t2.setTaxonomyCode( "OTHER" );
t2.setScientificName( "what" );
t2.setCommonName( "something" );
if ( !t1.isEqual( t2 ) ) {
return false;
}
t2.setIdentifier( new Identifier( "nemve" ) );
if ( t1.isEqual( t2 ) ) {
return false;
}
t1.setIdentifier( null );
t3.setTaxonomyCode( "ECOLI" );
t3.setScientificName( "what" );
t3.setCommonName( "something" );
if ( !t1.isEqual( t3 ) ) {
return false;
}
t1.setIdentifier( null );
t1.setTaxonomyCode( "" );
t4.setScientificName( "E. ColI" );
t4.setCommonName( "something" );
if ( !t1.isEqual( t4 ) ) {
return false;
}
t4.setScientificName( "B. subtilis" );
t4.setCommonName( "something" );
if ( t1.isEqual( t4 ) ) {
return false;
}
t1.setIdentifier( null );
t1.setTaxonomyCode( "" );
t1.setScientificName( "" );
t5.setCommonName( "COLI" );
if ( !t1.isEqual( t5 ) ) {
return false;
}
t5.setCommonName( "vibrio" );
if ( t1.isEqual( t5 ) ) {
return false;
}
// Identifier
// ----------
final Identifier id0 = new Identifier( "123", "pfam" );
final Identifier id1 = ( Identifier ) id0.copy();
if ( !id1.isEqual( id1 ) ) {
return false;
}
if ( !id1.isEqual( id0 ) ) {
return false;
}
if ( !id0.isEqual( id1 ) ) {
return false;
}
id1.asSimpleText();
id1.asText();
// ProteinDomain
// ---------------
final ProteinDomain pd0 = new ProteinDomain( "abc", 100, 200 );
final ProteinDomain pd1 = ( ProteinDomain ) pd0.copy();
if ( !pd1.isEqual( pd1 ) ) {
return false;
}
if ( !pd1.isEqual( pd0 ) ) {
return false;
}
pd1.asSimpleText();
pd1.asText();
final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" );
final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy();
if ( !pd3.isEqual( pd3 ) ) {
return false;
}
if ( !pd2.isEqual( pd3 ) ) {
return false;
}
if ( !pd0.isEqual( pd3 ) ) {
return false;
}
pd3.asSimpleText();
pd3.asText();
// DomainArchitecture
// ------------------
final ProteinDomain d0 = new ProteinDomain( "domain0", 10, 20 );
final ProteinDomain d1 = new ProteinDomain( "domain1", 30, 40 );
final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
final ArrayList domains0 = new ArrayList();
domains0.add( d2 );
domains0.add( d0 );
domains0.add( d3 );
domains0.add( d1 );
final DomainArchitecture ds0 = new DomainArchitecture( domains0, 110 );
if ( ds0.getNumberOfDomains() != 4 ) {
return false;
}
final DomainArchitecture ds1 = ( DomainArchitecture ) ds0.copy();
if ( !ds0.isEqual( ds0 ) ) {
return false;
}
if ( !ds0.isEqual( ds1 ) ) {
return false;
}
if ( ds1.getNumberOfDomains() != 4 ) {
return false;
}
final ArrayList domains1 = new ArrayList();
domains1.add( d1 );
domains1.add( d2 );
domains1.add( d4 );
domains1.add( d0 );
final DomainArchitecture ds2 = new DomainArchitecture( domains1, 200 );
if ( ds0.isEqual( ds2 ) ) {
return false;
}
ds1.asSimpleText();
ds1.asText();
ds1.toNHX();
final DomainArchitecture ds3 = new DomainArchitecture( "120>30>40>0.9>b>50>60>0.4>c>10>20>0.1>a" );
if ( !ds3.toNHX().toString().equals( ":DS=120>10>20>0.1>a>30>40>0.9>b>50>60>0.4>c" ) ) {
System.out.println( ds3.toNHX() );
return false;
}
if ( ds3.getNumberOfDomains() != 3 ) {
return false;
}
// Event
// -----
final Event e1 = new Event( Event.EventType.fusion );
if ( e1.isDuplication() ) {
return false;
}
if ( !e1.isFusion() ) {
return false;
}
if ( !e1.asText().toString().equals( "fusion" ) ) {
return false;
}
if ( !e1.asSimpleText().toString().equals( "fusion" ) ) {
return false;
}
final Event e11 = new Event( Event.EventType.fusion );
if ( !e11.isEqual( e1 ) ) {
return false;
}
if ( !e11.toNHX().toString().equals( "" ) ) {
return false;
}
final Event e2 = new Event( Event.EventType.speciation_or_duplication );
if ( e2.isDuplication() ) {
return false;
}
if ( !e2.isSpeciationOrDuplication() ) {
return false;
}
if ( !e2.asText().toString().equals( "speciation_or_duplication" ) ) {
return false;
}
if ( !e2.asSimpleText().toString().equals( "?" ) ) {
return false;
}
if ( !e2.toNHX().toString().equals( ":D=?" ) ) {
return false;
}
if ( e11.isEqual( e2 ) ) {
return false;
}
final Event e2c = ( Event ) e2.copy();
if ( !e2c.isEqual( e2 ) ) {
return false;
}
Event e3 = new Event( 1, 2, 3 );
if ( e3.isDuplication() ) {
return false;
}
if ( e3.isSpeciation() ) {
return false;
}
if ( e3.isGeneLoss() ) {
return false;
}
if ( !e3.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
return false;
}
final Event e3c = ( Event ) e3.copy();
final Event e3cc = ( Event ) e3c.copy();
if ( !e3c.asSimpleText().toString().equals( "D2S3L" ) ) {
return false;
}
e3 = null;
if ( !e3c.isEqual( e3cc ) ) {
return false;
}
Event e4 = new Event( 1, 2, 3 );
if ( !e4.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
return false;
}
if ( !e4.asSimpleText().toString().equals( "D2S3L" ) ) {
return false;
}
final Event e4c = ( Event ) e4.copy();
e4 = null;
final Event e4cc = ( Event ) e4c.copy();
if ( !e4cc.asText().toString().equals( "duplications [1] speciations [2] gene-losses [3]" ) ) {
return false;
}
if ( !e4c.isEqual( e4cc ) ) {
return false;
}
final Event e5 = new Event();
if ( !e5.isUnassigned() ) {
return false;
}
if ( !e5.asText().toString().equals( "unassigned" ) ) {
return false;
}
if ( !e5.asSimpleText().toString().equals( "" ) ) {
return false;
}
final Event e6 = new Event( 1, 0, 0 );
if ( !e6.asText().toString().equals( "duplication" ) ) {
return false;
}
if ( !e6.asSimpleText().toString().equals( "D" ) ) {
return false;
}
final Event e7 = new Event( 0, 1, 0 );
if ( !e7.asText().toString().equals( "speciation" ) ) {
return false;
}
if ( !e7.asSimpleText().toString().equals( "S" ) ) {
return false;
}
final Event e8 = new Event( 0, 0, 1 );
if ( !e8.asText().toString().equals( "gene-loss" ) ) {
return false;
}
if ( !e8.asSimpleText().toString().equals( "L" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testDeletionOfExternalNodes() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0 = factory.create( "A", new NHXParser() )[ 0 ];
final PhylogenyWriter w = new PhylogenyWriter();
if ( t0.isEmpty() ) {
return false;
}
if ( t0.getNumberOfExternalNodes() != 1 ) {
return false;
}
t0.deleteSubtree( t0.getNode( "A" ), false );
if ( t0.getNumberOfExternalNodes() != 0 ) {
return false;
}
if ( !t0.isEmpty() ) {
return false;
}
final Phylogeny t1 = factory.create( "(A,B)r", new NHXParser() )[ 0 ];
if ( t1.getNumberOfExternalNodes() != 2 ) {
return false;
}
t1.deleteSubtree( t1.getNode( "A" ), false );
if ( t1.getNumberOfExternalNodes() != 1 ) {
return false;
}
if ( !t1.getNode( "B" ).getName().equals( "B" ) ) {
return false;
}
t1.deleteSubtree( t1.getNode( "B" ), false );
if ( t1.getNumberOfExternalNodes() != 1 ) {
return false;
}
t1.deleteSubtree( t1.getNode( "r" ), false );
if ( !t1.isEmpty() ) {
return false;
}
final Phylogeny t2 = factory.create( "((A,B),C)", new NHXParser() )[ 0 ];
if ( t2.getNumberOfExternalNodes() != 3 ) {
return false;
}
t2.deleteSubtree( t2.getNode( "B" ), false );
if ( t2.getNumberOfExternalNodes() != 2 ) {
return false;
}
t2.toNewHampshireX();
PhylogenyNode n = t2.getNode( "A" );
if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
return false;
}
t2.deleteSubtree( t2.getNode( "A" ), false );
if ( t2.getNumberOfExternalNodes() != 2 ) {
return false;
}
t2.deleteSubtree( t2.getNode( "C" ), true );
if ( t2.getNumberOfExternalNodes() != 1 ) {
return false;
}
final Phylogeny t3 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
if ( t3.getNumberOfExternalNodes() != 4 ) {
return false;
}
t3.deleteSubtree( t3.getNode( "B" ), true );
if ( t3.getNumberOfExternalNodes() != 3 ) {
return false;
}
n = t3.getNode( "A" );
if ( !n.getNextExternalNode().getName().equals( "C" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
return false;
}
t3.deleteSubtree( t3.getNode( "A" ), true );
if ( t3.getNumberOfExternalNodes() != 2 ) {
return false;
}
n = t3.getNode( "C" );
if ( !n.getNextExternalNode().getName().equals( "D" ) ) {
return false;
}
t3.deleteSubtree( t3.getNode( "C" ), true );
if ( t3.getNumberOfExternalNodes() != 1 ) {
return false;
}
t3.deleteSubtree( t3.getNode( "D" ), true );
if ( t3.getNumberOfExternalNodes() != 0 ) {
return false;
}
final Phylogeny t4 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
if ( t4.getNumberOfExternalNodes() != 6 ) {
return false;
}
t4.deleteSubtree( t4.getNode( "B2" ), true );
if ( t4.getNumberOfExternalNodes() != 5 ) {
return false;
}
String s = w.toNewHampshire( t4, false, true ).toString();
if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
return false;
}
t4.deleteSubtree( t4.getNode( "B11" ), true );
if ( t4.getNumberOfExternalNodes() != 4 ) {
return false;
}
t4.deleteSubtree( t4.getNode( "C" ), true );
if ( t4.getNumberOfExternalNodes() != 3 ) {
return false;
}
n = t4.getNode( "A" );
n = n.getNextExternalNode();
if ( !n.getName().equals( "B12" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "D" ) ) {
return false;
}
s = w.toNewHampshire( t4, false, true ).toString();
if ( !s.equals( "((A,B12),D);" ) ) {
return false;
}
final Phylogeny t5 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
t5.deleteSubtree( t5.getNode( "A" ), true );
if ( t5.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t5, false, true ).toString();
if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
return false;
}
final Phylogeny t6 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
t6.deleteSubtree( t6.getNode( "B11" ), true );
if ( t6.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t6, false, false ).toString();
if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
return false;
}
final Phylogeny t7 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
t7.deleteSubtree( t7.getNode( "B12" ), true );
if ( t7.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t7, false, true ).toString();
if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
return false;
}
final Phylogeny t8 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
t8.deleteSubtree( t8.getNode( "B2" ), true );
if ( t8.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t8, false, false ).toString();
if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
return false;
}
final Phylogeny t9 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
t9.deleteSubtree( t9.getNode( "C" ), true );
if ( t9.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t9, false, true ).toString();
if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
return false;
}
final Phylogeny t10 = factory.create( "((A,((B11,B12),B2)),(C,D))", new NHXParser() )[ 0 ];
t10.deleteSubtree( t10.getNode( "D" ), true );
if ( t10.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t10, false, true ).toString();
if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
return false;
}
final Phylogeny t11 = factory.create( "(A,B,C)", new NHXParser() )[ 0 ];
t11.deleteSubtree( t11.getNode( "A" ), true );
if ( t11.getNumberOfExternalNodes() != 2 ) {
return false;
}
s = w.toNewHampshire( t11, false, true ).toString();
if ( !s.equals( "(B,C);" ) ) {
return false;
}
t11.deleteSubtree( t11.getNode( "C" ), true );
if ( t11.getNumberOfExternalNodes() != 1 ) {
return false;
}
s = w.toNewHampshire( t11, false, false ).toString();
if ( !s.equals( "B;" ) ) {
return false;
}
final Phylogeny t12 = factory.create( "((A1,A2,A3),(B1,B2,B3),(C1,C2,C3))", new NHXParser() )[ 0 ];
t12.deleteSubtree( t12.getNode( "B2" ), true );
if ( t12.getNumberOfExternalNodes() != 8 ) {
return false;
}
s = w.toNewHampshire( t12, false, true ).toString();
if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
return false;
}
t12.deleteSubtree( t12.getNode( "B3" ), true );
if ( t12.getNumberOfExternalNodes() != 7 ) {
return false;
}
s = w.toNewHampshire( t12, false, true ).toString();
if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
return false;
}
t12.deleteSubtree( t12.getNode( "C3" ), true );
if ( t12.getNumberOfExternalNodes() != 6 ) {
return false;
}
s = w.toNewHampshire( t12, false, true ).toString();
if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
return false;
}
t12.deleteSubtree( t12.getNode( "A1" ), true );
if ( t12.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t12, false, true ).toString();
if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
return false;
}
t12.deleteSubtree( t12.getNode( "B1" ), true );
if ( t12.getNumberOfExternalNodes() != 4 ) {
return false;
}
s = w.toNewHampshire( t12, false, true ).toString();
if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
return false;
}
t12.deleteSubtree( t12.getNode( "A3" ), true );
if ( t12.getNumberOfExternalNodes() != 3 ) {
return false;
}
s = w.toNewHampshire( t12, false, true ).toString();
if ( !s.equals( "(A2,(C1,C2));" ) ) {
return false;
}
t12.deleteSubtree( t12.getNode( "A2" ), true );
if ( t12.getNumberOfExternalNodes() != 2 ) {
return false;
}
s = w.toNewHampshire( t12, false, true ).toString();
if ( !s.equals( "(C1,C2);" ) ) {
return false;
}
final Phylogeny t13 = factory.create( "(A,B,C,(D:1.0,E:2.0):3.0)", new NHXParser() )[ 0 ];
t13.deleteSubtree( t13.getNode( "D" ), true );
if ( t13.getNumberOfExternalNodes() != 4 ) {
return false;
}
s = w.toNewHampshire( t13, false, true ).toString();
if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
return false;
}
final Phylogeny t14 = factory.create( "((A,B,C,(D:0.1,E:0.4):1.0),F)", new NHXParser() )[ 0 ];
t14.deleteSubtree( t14.getNode( "E" ), true );
if ( t14.getNumberOfExternalNodes() != 5 ) {
return false;
}
s = w.toNewHampshire( t14, false, true ).toString();
if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
return false;
}
final Phylogeny t15 = factory.create( "((A1,A2,A3,A4),(B1,B2,B3,B4),(C1,C2,C3,C4))", new NHXParser() )[ 0 ];
t15.deleteSubtree( t15.getNode( "B2" ), true );
if ( t15.getNumberOfExternalNodes() != 11 ) {
return false;
}
t15.deleteSubtree( t15.getNode( "B1" ), true );
if ( t15.getNumberOfExternalNodes() != 10 ) {
return false;
}
t15.deleteSubtree( t15.getNode( "B3" ), true );
if ( t15.getNumberOfExternalNodes() != 9 ) {
return false;
}
t15.deleteSubtree( t15.getNode( "B4" ), true );
if ( t15.getNumberOfExternalNodes() != 8 ) {
return false;
}
t15.deleteSubtree( t15.getNode( "A1" ), true );
if ( t15.getNumberOfExternalNodes() != 7 ) {
return false;
}
t15.deleteSubtree( t15.getNode( "C4" ), true );
if ( t15.getNumberOfExternalNodes() != 6 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testDescriptiveStatistics() {
try {
final DescriptiveStatistics dss1 = new BasicDescriptiveStatistics();
dss1.addValue( 82 );
dss1.addValue( 78 );
dss1.addValue( 70 );
dss1.addValue( 58 );
dss1.addValue( 42 );
if ( dss1.getN() != 5 ) {
return false;
}
if ( !Test.isEqual( dss1.getMin(), 42 ) ) {
return false;
}
if ( !Test.isEqual( dss1.getMax(), 82 ) ) {
return false;
}
if ( !Test.isEqual( dss1.arithmeticMean(), 66 ) ) {
return false;
}
if ( !Test.isEqual( dss1.sampleStandardDeviation(), 16.24807680927192 ) ) {
return false;
}
if ( !Test.isEqual( dss1.median(), 70 ) ) {
return false;
}
if ( !Test.isEqual( dss1.midrange(), 62 ) ) {
return false;
}
if ( !Test.isEqual( dss1.sampleVariance(), 264 ) ) {
return false;
}
if ( !Test.isEqual( dss1.pearsonianSkewness(), -0.7385489458759964 ) ) {
return false;
}
if ( !Test.isEqual( dss1.coefficientOfVariation(), 0.24618298195866547 ) ) {
return false;
}
if ( !Test.isEqual( dss1.sampleStandardUnit( 66 - 16.24807680927192 ), -1.0 ) ) {
return false;
}
if ( !Test.isEqual( dss1.getValue( 1 ), 78 ) ) {
return false;
}
dss1.addValue( 123 );
if ( !Test.isEqual( dss1.arithmeticMean(), 75.5 ) ) {
return false;
}
if ( !Test.isEqual( dss1.getMax(), 123 ) ) {
return false;
}
if ( !Test.isEqual( dss1.standardErrorOfMean(), 11.200446419674531 ) ) {
return false;
}
final DescriptiveStatistics dss2 = new BasicDescriptiveStatistics();
dss2.addValue( -1.85 );
dss2.addValue( 57.5 );
dss2.addValue( 92.78 );
dss2.addValue( 57.78 );
if ( !Test.isEqual( dss2.median(), 57.64 ) ) {
return false;
}
if ( !Test.isEqual( dss2.sampleStandardDeviation(), 39.266984753946495 ) ) {
return false;
}
final double[] a = dss2.getDataAsDoubleArray();
if ( !Test.isEqual( a[ 3 ], 57.78 ) ) {
return false;
}
dss2.addValue( -100 );
if ( !Test.isEqual( dss2.sampleStandardDeviation(), 75.829111296388 ) ) {
return false;
}
if ( !Test.isEqual( dss2.sampleVariance(), 5750.05412 ) ) {
return false;
}
final double[] ds = new double[ 14 ];
ds[ 0 ] = 34;
ds[ 1 ] = 23;
ds[ 2 ] = 1;
ds[ 3 ] = 32;
ds[ 4 ] = 11;
ds[ 5 ] = 2;
ds[ 6 ] = 12;
ds[ 7 ] = 33;
ds[ 8 ] = 13;
ds[ 9 ] = 22;
ds[ 10 ] = 21;
ds[ 11 ] = 35;
ds[ 12 ] = 24;
ds[ 13 ] = 31;
final int[] bins = BasicDescriptiveStatistics.performBinning( ds, 0, 40, 4 );
if ( bins.length != 4 ) {
return false;
}
if ( bins[ 0 ] != 2 ) {
return false;
}
if ( bins[ 1 ] != 3 ) {
return false;
}
if ( bins[ 2 ] != 4 ) {
return false;
}
if ( bins[ 3 ] != 5 ) {
return false;
}
final double[] ds1 = new double[ 9 ];
ds1[ 0 ] = 10.0;
ds1[ 1 ] = 19.0;
ds1[ 2 ] = 9.999;
ds1[ 3 ] = 0.0;
ds1[ 4 ] = 39.9;
ds1[ 5 ] = 39.999;
ds1[ 6 ] = 30.0;
ds1[ 7 ] = 19.999;
ds1[ 8 ] = 30.1;
final int[] bins1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 4 );
if ( bins1.length != 4 ) {
return false;
}
if ( bins1[ 0 ] != 2 ) {
return false;
}
if ( bins1[ 1 ] != 3 ) {
return false;
}
if ( bins1[ 2 ] != 0 ) {
return false;
}
if ( bins1[ 3 ] != 4 ) {
return false;
}
final int[] bins1_1 = BasicDescriptiveStatistics.performBinning( ds1, 0, 40, 3 );
if ( bins1_1.length != 3 ) {
return false;
}
if ( bins1_1[ 0 ] != 3 ) {
return false;
}
if ( bins1_1[ 1 ] != 2 ) {
return false;
}
if ( bins1_1[ 2 ] != 4 ) {
return false;
}
final int[] bins1_2 = BasicDescriptiveStatistics.performBinning( ds1, 1, 39, 3 );
if ( bins1_2.length != 3 ) {
return false;
}
if ( bins1_2[ 0 ] != 2 ) {
return false;
}
if ( bins1_2[ 1 ] != 2 ) {
return false;
}
if ( bins1_2[ 2 ] != 2 ) {
return false;
}
final DescriptiveStatistics dss3 = new BasicDescriptiveStatistics();
dss3.addValue( 1 );
dss3.addValue( 1 );
dss3.addValue( 1 );
dss3.addValue( 2 );
dss3.addValue( 3 );
dss3.addValue( 4 );
dss3.addValue( 5 );
dss3.addValue( 5 );
dss3.addValue( 5 );
dss3.addValue( 6 );
dss3.addValue( 7 );
dss3.addValue( 8 );
dss3.addValue( 9 );
dss3.addValue( 10 );
dss3.addValue( 10 );
dss3.addValue( 10 );
final AsciiHistogram histo = new AsciiHistogram( dss3 );
histo.toStringBuffer( 10, '=', 40, 5 );
histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null );
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testDir( final String file ) {
try {
final File f = new File( file );
if ( !f.exists() ) {
return false;
}
if ( !f.isDirectory() ) {
return false;
}
if ( !f.canRead() ) {
return false;
}
}
catch ( final Exception e ) {
return false;
}
return true;
}
private static boolean testExternalNodeRelatedMethods() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t1 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
PhylogenyNode n = t1.getNode( "A" );
n = n.getNextExternalNode();
if ( !n.getName().equals( "B" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "C" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "D" ) ) {
return false;
}
n = t1.getNode( "B" );
while ( !n.isLastExternalNode() ) {
n = n.getNextExternalNode();
}
final Phylogeny t2 = factory.create( "(((A,B),C),D)", new NHXParser() )[ 0 ];
n = t2.getNode( "A" );
n = n.getNextExternalNode();
if ( !n.getName().equals( "B" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "C" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "D" ) ) {
return false;
}
n = t2.getNode( "B" );
while ( !n.isLastExternalNode() ) {
n = n.getNextExternalNode();
}
final Phylogeny t3 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
n = t3.getNode( "A" );
n = n.getNextExternalNode();
if ( !n.getName().equals( "B" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "C" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "D" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "E" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "F" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "G" ) ) {
return false;
}
n = n.getNextExternalNode();
if ( !n.getName().equals( "H" ) ) {
return false;
}
n = t3.getNode( "B" );
while ( !n.isLastExternalNode() ) {
n = n.getNextExternalNode();
}
final Phylogeny t4 = factory.create( "((A,B),(C,D))", new NHXParser() )[ 0 ];
for( final PhylogenyNodeIterator iter = t4.iteratorExternalForward(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
}
final Phylogeny t5 = factory.create( "(((A,B),(C,D)),((E,F),(G,H)))", new NHXParser() )[ 0 ];
for( final PhylogenyNodeIterator iter = t5.iteratorExternalForward(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testGeneralTable() {
try {
final GeneralTable t0 = new GeneralTable();
t0.setValue( 3, 2, "23" );
t0.setValue( 10, 1, "error" );
t0.setValue( 10, 1, "110" );
t0.setValue( 9, 1, "19" );
t0.setValue( 1, 10, "101" );
t0.setValue( 10, 10, "1010" );
t0.setValue( 100, 10, "10100" );
t0.setValue( 0, 0, "00" );
if ( !t0.getValue( 3, 2 ).equals( "23" ) ) {
return false;
}
if ( !t0.getValue( 10, 1 ).equals( "110" ) ) {
return false;
}
if ( !t0.getValueAsString( 1, 10 ).equals( "101" ) ) {
return false;
}
if ( !t0.getValueAsString( 10, 10 ).equals( "1010" ) ) {
return false;
}
if ( !t0.getValueAsString( 100, 10 ).equals( "10100" ) ) {
return false;
}
if ( !t0.getValueAsString( 9, 1 ).equals( "19" ) ) {
return false;
}
if ( !t0.getValueAsString( 0, 0 ).equals( "00" ) ) {
return false;
}
if ( !t0.getValueAsString( 49, 4 ).equals( "" ) ) {
return false;
}
if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
return false;
}
final GeneralTable t1 = new GeneralTable();
t1.setValue( "3", "2", "23" );
t1.setValue( "10", "1", "error" );
t1.setValue( "10", "1", "110" );
t1.setValue( "9", "1", "19" );
t1.setValue( "1", "10", "101" );
t1.setValue( "10", "10", "1010" );
t1.setValue( "100", "10", "10100" );
t1.setValue( "0", "0", "00" );
t1.setValue( "qwerty", "zxcvbnm", "asdef" );
if ( !t1.getValue( "3", "2" ).equals( "23" ) ) {
return false;
}
if ( !t1.getValue( "10", "1" ).equals( "110" ) ) {
return false;
}
if ( !t1.getValueAsString( "1", "10" ).equals( "101" ) ) {
return false;
}
if ( !t1.getValueAsString( "10", "10" ).equals( "1010" ) ) {
return false;
}
if ( !t1.getValueAsString( "100", "10" ).equals( "10100" ) ) {
return false;
}
if ( !t1.getValueAsString( "9", "1" ).equals( "19" ) ) {
return false;
}
if ( !t1.getValueAsString( "0", "0" ).equals( "00" ) ) {
return false;
}
if ( !t1.getValueAsString( "qwerty", "zxcvbnm" ).equals( "asdef" ) ) {
return false;
}
if ( !t1.getValueAsString( "49", "4" ).equals( "" ) ) {
return false;
}
if ( !t1.getValueAsString( "22349", "3434344" ).equals( "" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testGetDistance() {
try {
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 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "def" ) ) != 0 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ef" ) ) != 0 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "r" ) ) != 0 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "A" ) ) != 0 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "B" ) ) != 3 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "B" ), p1.getNode( "A" ) ) != 3 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "C" ) ) != 8 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "C" ), p1.getNode( "A" ) ) != 8 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "D" ) ) != 22 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "E" ) ) != 32 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "E" ), p1.getNode( "A" ) ) != 32 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "F" ) ) != 33 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "F" ), p1.getNode( "A" ) ) != 33 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ab" ) ) != 1 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "A" ) ) != 1 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "abc" ) ) != 4 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "abc" ), p1.getNode( "A" ) ) != 4 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "r" ) ) != 9 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "r" ), p1.getNode( "A" ) ) != 9 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "def" ) ) != 15 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "A" ) ) != 15 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "A" ), p1.getNode( "ef" ) ) != 23 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "A" ) ) != 23 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "def" ) ) != 8 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "def" ), p1.getNode( "ef" ) ) != 8 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "r" ) ) != 14 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "abc" ) ) != 19 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ef" ), p1.getNode( "ab" ) ) != 22 ) {
return false;
}
if ( pm.calculateDistance( p1.getNode( "ab" ), p1.getNode( "ef" ) ) != 22 ) {
return false;
}
if ( pm.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 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "C" ) ) != 10 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "D" ) ) != 14 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "ghi" ) ) != 8 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "A" ), p2.getNode( "I" ) ) != 20 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "ghi" ) ) != 10 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "r" ) ) != 0 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "r" ), p2.getNode( "G" ) ) != 13 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "r" ) ) != 13 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "H" ) ) != 21 ) {
return false;
}
if ( pm.calculateDistance( p2.getNode( "G" ), p2.getNode( "I" ) ) != 22 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testGetLCA() {
try {
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" ) );
if ( !A.getName().equals( "A" ) ) {
return false;
}
final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) );
if ( !gh.getName().equals( "gh" ) ) {
return false;
}
final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) );
if ( !ab.getName().equals( "ab" ) ) {
return false;
}
final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) );
if ( !ab2.getName().equals( "ab" ) ) {
return false;
}
final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) );
if ( !gh2.getName().equals( "gh" ) ) {
return false;
}
final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) );
if ( !gh3.getName().equals( "gh" ) ) {
return false;
}
final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) );
if ( !abc.getName().equals( "abc" ) ) {
return false;
}
final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) );
if ( !abc2.getName().equals( "abc" ) ) {
return false;
}
final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) );
if ( !abcd.getName().equals( "abcd" ) ) {
return false;
}
final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) );
if ( !abcd2.getName().equals( "abcd" ) ) {
return false;
}
final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) );
if ( !abcdef.getName().equals( "abcdef" ) ) {
return false;
}
final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) );
if ( !abcdef2.getName().equals( "abcdef" ) ) {
return false;
}
final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) );
if ( !abcdef3.getName().equals( "abcdef" ) ) {
return false;
}
final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) );
if ( !abcdef4.getName().equals( "abcdef" ) ) {
return false;
}
final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) );
if ( !abcde.getName().equals( "abcde" ) ) {
return false;
}
final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) );
if ( !abcde2.getName().equals( "abcde" ) ) {
return false;
}
final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) );
if ( !r.getName().equals( "abcdefgh" ) ) {
return false;
}
final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) );
if ( !r2.getName().equals( "abcdefgh" ) ) {
return false;
}
final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) );
if ( !r3.getName().equals( "abcdefgh" ) ) {
return false;
}
final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) );
if ( !abcde3.getName().equals( "abcde" ) ) {
return false;
}
final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) );
if ( !abcde4.getName().equals( "abcde" ) ) {
return false;
}
final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) );
if ( !ab3.getName().equals( "ab" ) ) {
return false;
}
final PhylogenyNode ab4 = pm.obtainLCA( 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" ) );
if ( !cd.getName().equals( "cd" ) ) {
return false;
}
final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) );
if ( !cd2.getName().equals( "cd" ) ) {
return false;
}
final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) );
if ( !cde.getName().equals( "cde" ) ) {
return false;
}
final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) );
if ( !cde2.getName().equals( "cde" ) ) {
return false;
}
final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) );
if ( !cdef.getName().equals( "cdef" ) ) {
return false;
}
final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) );
if ( !cdef2.getName().equals( "cdef" ) ) {
return false;
}
final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) );
if ( !cdef3.getName().equals( "cdef" ) ) {
return false;
}
final PhylogenyNode rt = pm.obtainLCA( 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" ) );
if ( !bc_3.getName().equals( "bc" ) ) {
return false;
}
final PhylogenyNode ac_3 = pm.obtainLCA( 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" ) );
if ( !ad_3.getName().equals( "abcde" ) ) {
return false;
}
final PhylogenyNode af_3 = pm.obtainLCA( 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" ) );
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" ) );
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" ) );
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" ) );
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" ) );
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" ) );
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" ) );
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" ) );
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" ) );
if ( !r_7.getName().equals( "rott" ) ) {
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 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" );
if ( n2.isLastExternalNode() ) {
return false;
}
final PhylogenyNode n3 = t0.getNode( "C" );
if ( n3.isLastExternalNode() ) {
return false;
}
final PhylogenyNode n4 = t0.getNode( "D" );
if ( !n4.isLastExternalNode() ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testLevelOrderIterator() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
PhylogenyNodeIterator it0;
for( it0 = t0.iteratorLevelOrder(); it0.hasNext(); ) {
it0.next();
}
for( it0.reset(); it0.hasNext(); ) {
it0.next();
}
final PhylogenyNodeIterator it = t0.iteratorLevelOrder();
if ( !it.next().getName().equals( "r" ) ) {
return false;
}
if ( !it.next().getName().equals( "ab" ) ) {
return false;
}
if ( !it.next().getName().equals( "cd" ) ) {
return false;
}
if ( !it.next().getName().equals( "A" ) ) {
return false;
}
if ( !it.next().getName().equals( "B" ) ) {
return false;
}
if ( !it.next().getName().equals( "C" ) ) {
return false;
}
if ( !it.next().getName().equals( "D" ) ) {
return false;
}
if ( it.hasNext() ) {
return false;
}
final Phylogeny t2 = factory.create( "(((1,2,(a,(X,Y,Z)b)3,4,5,6)A,B,C)abc,(D,E,(f1,(f21)f2,f3)F,G)defg)r",
new NHXParser() )[ 0 ];
PhylogenyNodeIterator it2;
for( it2 = t2.iteratorLevelOrder(); it2.hasNext(); ) {
it2.next();
}
for( it2.reset(); it2.hasNext(); ) {
it2.next();
}
final PhylogenyNodeIterator it3 = t2.iteratorLevelOrder();
if ( !it3.next().getName().equals( "r" ) ) {
return false;
}
if ( !it3.next().getName().equals( "abc" ) ) {
return false;
}
if ( !it3.next().getName().equals( "defg" ) ) {
return false;
}
if ( !it3.next().getName().equals( "A" ) ) {
return false;
}
if ( !it3.next().getName().equals( "B" ) ) {
return false;
}
if ( !it3.next().getName().equals( "C" ) ) {
return false;
}
if ( !it3.next().getName().equals( "D" ) ) {
return false;
}
if ( !it3.next().getName().equals( "E" ) ) {
return false;
}
if ( !it3.next().getName().equals( "F" ) ) {
return false;
}
if ( !it3.next().getName().equals( "G" ) ) {
return false;
}
if ( !it3.next().getName().equals( "1" ) ) {
return false;
}
if ( !it3.next().getName().equals( "2" ) ) {
return false;
}
if ( !it3.next().getName().equals( "3" ) ) {
return false;
}
if ( !it3.next().getName().equals( "4" ) ) {
return false;
}
if ( !it3.next().getName().equals( "5" ) ) {
return false;
}
if ( !it3.next().getName().equals( "6" ) ) {
return false;
}
if ( !it3.next().getName().equals( "f1" ) ) {
return false;
}
if ( !it3.next().getName().equals( "f2" ) ) {
return false;
}
if ( !it3.next().getName().equals( "f3" ) ) {
return false;
}
if ( !it3.next().getName().equals( "a" ) ) {
return false;
}
if ( !it3.next().getName().equals( "b" ) ) {
return false;
}
if ( !it3.next().getName().equals( "f21" ) ) {
return false;
}
if ( !it3.next().getName().equals( "X" ) ) {
return false;
}
if ( !it3.next().getName().equals( "Y" ) ) {
return false;
}
if ( !it3.next().getName().equals( "Z" ) ) {
return false;
}
if ( it3.hasNext() ) {
return false;
}
final Phylogeny t4 = factory.create( "((((D)C)B)A)r", new NHXParser() )[ 0 ];
PhylogenyNodeIterator it4;
for( it4 = t4.iteratorLevelOrder(); it4.hasNext(); ) {
it4.next();
}
for( it4.reset(); it4.hasNext(); ) {
it4.next();
}
final PhylogenyNodeIterator it5 = t4.iteratorLevelOrder();
if ( !it5.next().getName().equals( "r" ) ) {
return false;
}
if ( !it5.next().getName().equals( "A" ) ) {
return false;
}
if ( !it5.next().getName().equals( "B" ) ) {
return false;
}
if ( !it5.next().getName().equals( "C" ) ) {
return false;
}
if ( !it5.next().getName().equals( "D" ) ) {
return false;
}
final Phylogeny t5 = factory.create( "A", new NHXParser() )[ 0 ];
PhylogenyNodeIterator it6;
for( it6 = t5.iteratorLevelOrder(); it6.hasNext(); ) {
it6.next();
}
for( it6.reset(); it6.hasNext(); ) {
it6.next();
}
final PhylogenyNodeIterator it7 = t5.iteratorLevelOrder();
if ( !it7.next().getName().equals( "A" ) ) {
return false;
}
if ( it.hasNext() ) {
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 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;
}
PhylogenyMethods.midpointRoot( t1 );
if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
return false;
}
t1.reRoot( t1.getNode( "A" ) );
PhylogenyMethods.midpointRoot( t1 );
if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 4 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 1 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 3 ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNexusCharactersParsing() {
try {
final NexusCharactersParser parser = new NexusCharactersParser();
parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex" ) );
parser.parse();
String[] labels = parser.getCharStateLabels();
if ( labels.length != 7 ) {
return false;
}
if ( !labels[ 0 ].equals( "14-3-3" ) ) {
return false;
}
if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
return false;
}
if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
return false;
}
if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
return false;
}
if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
return false;
}
if ( !labels[ 5 ].equals( "3-HAO" ) ) {
return false;
}
if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
return false;
}
parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
parser.parse();
labels = parser.getCharStateLabels();
if ( labels.length != 7 ) {
return false;
}
if ( !labels[ 0 ].equals( "14-3-3" ) ) {
return false;
}
if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
return false;
}
if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
return false;
}
if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
return false;
}
if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
return false;
}
if ( !labels[ 5 ].equals( "3-HAO" ) ) {
return false;
}
if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNexusMatrixParsing() {
try {
final NexusBinaryStatesMatrixParser parser = new NexusBinaryStatesMatrixParser();
parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_9.nex" ) );
parser.parse();
final CharacterStateMatrix m = parser.getMatrix();
if ( m.getNumberOfCharacters() != 9 ) {
return false;
}
if ( m.getNumberOfIdentifiers() != 5 ) {
return false;
}
if ( m.getState( 0, 0 ) != BinaryStates.PRESENT ) {
return false;
}
if ( m.getState( 0, 1 ) != BinaryStates.ABSENT ) {
return false;
}
if ( m.getState( 1, 0 ) != BinaryStates.PRESENT ) {
return false;
}
if ( m.getState( 2, 0 ) != BinaryStates.ABSENT ) {
return false;
}
if ( m.getState( 4, 8 ) != BinaryStates.PRESENT ) {
return false;
}
if ( !m.getIdentifier( 0 ).equals( "MOUSE" ) ) {
return false;
}
if ( !m.getIdentifier( 4 ).equals( "ARATH" ) ) {
return false;
}
// if ( labels.length != 7 ) {
// return false;
// }
// if ( !labels[ 0 ].equals( "14-3-3" ) ) {
// return false;
// }
// if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
// return false;
// }
// if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
// return false;
// }
// if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
// return false;
// }
// if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
// return false;
// }
// if ( !labels[ 5 ].equals( "3-HAO" ) ) {
// return false;
// }
// if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
// return false;
// }
// parser.setSource( new File( Test.PATH_TO_TEST_DATA + "nexus_test_8.nex" ) );
// parser.parse();
// labels = parser.getCharStateLabels();
// if ( labels.length != 7 ) {
// return false;
// }
// if ( !labels[ 0 ].equals( "14-3-3" ) ) {
// return false;
// }
// if ( !labels[ 1 ].equals( "2-Hacid_dh" ) ) {
// return false;
// }
// if ( !labels[ 2 ].equals( "2-Hacid_dh_C" ) ) {
// return false;
// }
// if ( !labels[ 3 ].equals( "2-oxoacid_dh" ) ) {
// return false;
// }
// if ( !labels[ 4 ].equals( "2OG-FeII_Oxy" ) ) {
// return false;
// }
// if ( !labels[ 5 ].equals( "3-HAO" ) ) {
// return false;
// }
// if ( !labels[ 6 ].equals( "3_5_exonuc" ) ) {
// return false;
// }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNexusTreeParsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex", parser );
if ( phylogenies.length != 1 ) {
return false;
}
if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 25 ) {
return false;
}
if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
return false;
}
phylogenies = null;
phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex", parser );
if ( phylogenies.length != 1 ) {
return false;
}
if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
return false;
}
if ( !phylogenies[ 0 ].getName().equals( "name" ) ) {
return false;
}
phylogenies = null;
phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex", parser );
if ( phylogenies.length != 1 ) {
return false;
}
if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( !phylogenies[ 0 ].getName().equals( "" ) ) {
return false;
}
if ( phylogenies[ 0 ].isRooted() ) {
return false;
}
phylogenies = null;
phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_4.nex", parser );
if ( phylogenies.length != 18 ) {
return false;
}
if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 10 ) {
return false;
}
if ( !phylogenies[ 0 ].getName().equals( "tree 0" ) ) {
return false;
}
if ( !phylogenies[ 1 ].getName().equals( "tree 1" ) ) {
return false;
}
if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 10 ) {
return false;
}
if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( phylogenies[ 3 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( phylogenies[ 4 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( phylogenies[ 5 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( phylogenies[ 6 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( phylogenies[ 7 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( !phylogenies[ 8 ].getName().equals( "tree 8" ) ) {
return false;
}
if ( phylogenies[ 8 ].isRooted() ) {
return false;
}
if ( phylogenies[ 8 ].getNumberOfExternalNodes() != 3 ) {
return false;
}
if ( !phylogenies[ 9 ].getName().equals( "tree 9" ) ) {
return false;
}
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 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( 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 " ) ) {
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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[ 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[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
new NHXParser() );
if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
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;
}
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 != 1 ) || !p32[ 0 ].isEmpty() ) {
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;
}
final String p34_S = "B;";
final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
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 ) ) {
return false;
}
final String p36_S = "(A)";
final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
return false;
}
final String p37_S = "((A))";
final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
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 ) ) {
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 ) ) {
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 ) ) {
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 ) ) {
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 ) ) {
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 ) ) {
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 ) ) {
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 ) ) {
return false;
}
final String p46_S = "";
final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
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() ) ) {
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() ) ) {
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() ) ) {
return false;
}
final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
if ( p50.getNode( "A" ) == null ) {
return false;
}
if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
.equals( "((A,B)ab:2.0[88],C);" ) ) {
return false;
}
if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
return false;
}
if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
.equals( "((A,B)88:2.0,C);" ) ) {
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 ) {
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 ) {
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 ) {
return false;
}
//
final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
if ( p54.getNode( "A" ) == null ) {
return false;
}
if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
.equals( "((A,B)[88],C);" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNHXconversion() {
try {
final PhylogenyNode n1 = new PhylogenyNode();
final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
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]" );
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]" );
if ( !n1.toNewHampshireX().equals( "" ) ) {
return false;
}
if ( !n2.toNewHampshireX().equals( "" ) ) {
return false;
}
if ( !n3.toNewHampshireX().equals( "n3" ) ) {
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]" ) ) {
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]" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNHXNodeParsing() {
try {
final PhylogenyNode n1 = new PhylogenyNode();
final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "" );
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:B=56:T=1:On=22:SOn=33:SNn=44:W=2:C=10.20.30:XN=S=tag1=value1=unit1:XN=S=tag3=value3=unit3]" );
if ( !n3.getName().equals( "n3" ) ) {
return false;
}
if ( n3.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
return false;
}
if ( n3.isDuplication() ) {
return false;
}
if ( n3.isHasAssignedEvent() ) {
return false;
}
if ( PhylogenyMethods.getBranchWidthValue( n3 ) != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) {
return false;
}
if ( !n4.getName().equals( "n4" ) ) {
return false;
}
if ( n4.getDistanceToParent() != 0.01 ) {
return false;
}
if ( !n5.getName().equals( "n5" ) ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( n5 ) != 56 ) {
return false;
}
if ( n5.getDistanceToParent() != 0.1 ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n5 ).equals( "Ecoli" ) ) {
return false;
}
if ( !n5.isDuplication() ) {
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" ) ) {
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" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
return false;
}
final PhylogenyNode n10 = PhylogenyNode
.createInstanceFromNhxString( "n10.ECOLI", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
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" ) ) {
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" ) ) {
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" ) ) {
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 );
if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n20xxx ).length() > 0 ) {
return false;
}
final PhylogenyNode n20xxxx = PhylogenyNode
.createInstanceFromNhxString( "n20_Ecoli/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
return false;
}
final PhylogenyNode n21 = PhylogenyNode
.createInstanceFromNhxString( "n21_PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
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 );
if ( !n21x.getName().equals( "n21_PIG" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n21x ).length() > 0 ) {
return false;
}
final PhylogenyNode n22 = PhylogenyNode
.createInstanceFromNhxString( "n22/PIG", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
if ( !n22.getName().equals( "n22/PIG" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n22 ).length() > 0 ) {
return false;
}
final PhylogenyNode n23 = PhylogenyNode
.createInstanceFromNhxString( "n23/PIG_1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
if ( !n23.getName().equals( "n23/PIG_1" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) {
return false;
}
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( "ECOLI" ) ) {
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( "RATAF" ) ) {
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 e2 = PhylogenyNode
.createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !e2.getName().equals( "n10_RAT1" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
return false;
}
final PhylogenyNode e3 = PhylogenyNode
.createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !e3.getName().equals( "n10_RAT~" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) {
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" ) ) {
return false;
}
if ( n11.getDistanceToParent() != 0.4 ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
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" ) ) {
return false;
}
if ( n12.getDistanceToParent() != 0.4 ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
return false;
}
final PhylogenyNode m = PhylogenyNode
.createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !m.getName().equals( "n10_MOUSEa" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
return false;
}
final PhylogenyNode o = PhylogenyNode
.createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !o.getName().equals( "n10_MOUSE_" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
return false;
}
final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" );
final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" );
if ( !tvu1.getRef().equals( "tag1" ) ) {
return false;
}
if ( !tvu1.getDataType().equals( "xsd:string" ) ) {
return false;
}
if ( !tvu1.getUnit().equals( "unit1" ) ) {
return false;
}
if ( !tvu1.getValue().equals( "value1" ) ) {
return false;
}
if ( !tvu3.getRef().equals( "tag3" ) ) {
return false;
}
if ( !tvu3.getDataType().equals( "xsd:string" ) ) {
return false;
}
if ( !tvu3.getUnit().equals( "unit3" ) ) {
return false;
}
if ( !tvu3.getValue().equals( "value3" ) ) {
return false;
}
if ( n1.getName().compareTo( "" ) != 0 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( n1 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
return false;
}
if ( n1.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
return false;
}
if ( n2.getName().compareTo( "" ) != 0 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( n2 ) != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
return false;
}
if ( n2.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
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;
}
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 );
if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
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" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
return false;
}
final PhylogenyNode n15 = PhylogenyNode
.createInstanceFromNhxString( "something_wicked[123]",
PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
if ( !n15.getName().equals( "something_wicked" ) ) {
return false;
}
if ( n15.getBranchData().getNumberOfConfidences() != 1 ) {
return false;
}
if ( !isEqual( n15.getBranchData().getConfidence( 0 ).getValue(), 123 ) ) {
return false;
}
final PhylogenyNode n16 = PhylogenyNode
.createInstanceFromNhxString( "something_wicked2[9]",
PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
if ( !n16.getName().equals( "something_wicked2" ) ) {
return false;
}
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]",
PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
if ( !n17.getName().equals( "something_wicked3" ) ) {
return false;
}
if ( n17.getBranchData().getNumberOfConfidences() != 0 ) {
return false;
}
final PhylogenyNode n18 = PhylogenyNode
.createInstanceFromNhxString( ":0.5[91]", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
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;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNHXParsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p1 = factory.create( "(A [&&NHX:S=a_species],B1[&&NHX:S=b_species])", new NHXParser() )[ 0 ];
if ( !p1.toNewHampshireX().equals( "(A[&&NHX:S=a_species],B1[&&NHX:S=b_species])" ) ) {
return false;
}
final String p2_S = "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]";
final Phylogeny[] p2 = factory.create( p2_S, new NHXParser() );
if ( !p2[ 0 ].toNewHampshireX().equals( p2_S ) ) {
return false;
}
final String p2b_S = "(((((((A:0.2[&NHX:S=qw,erty]):0.2[&:S=u(io)p]):0.3[&NHX:S=asdf]):0.4[S=zxc]):0.5[]):0.6[&&NH:S=asd]):0.7[&&HX:S=za]):0.8[&&:S=zaq]";
final Phylogeny[] p2b = factory.create( p2b_S, new NHXParser() );
if ( !p2b[ 0 ].toNewHampshireX().equals( "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8" ) ) {
return false;
}
final Phylogeny[] p3 = factory
.create( "[ comment&&NHX,())))](((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq]",
new NHXParser() );
if ( !p3[ 0 ].toNewHampshireX().equals( p2_S ) ) {
return false;
}
final Phylogeny[] p4 = factory
.create( "(((((((A:0.2[&&NHX:S=qwerty]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=asdf]):0.4[&&NHX:S=zxc]):0.5[&&NHX:S=a]):0.6[&&NHX:S=asd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(]",
new NHXParser() );
if ( !p4[ 0 ].toNewHampshireX().equals( p2_S ) ) {
return false;
}
final Phylogeny[] p5 = factory
.create( "[] ( [][ ][ ] ([((( &&NHXcomment only))]werty][,,,,))]):0.2[&&NHX:S=uiop]):0.3[&&NHX:S=a[comment,,))]sdf])[comment(((]:0.4[&&NHX:S=zxc][comment(((][comment(((]):0.5[&&NHX:S=a]):0.6[&&NHX:S=a[comment(((]sd]):0.7[&&NHX:S=za]):0.8[&&NHX:S=zaq][comment(((]",
new NHXParser() );
if ( !p5[ 0 ].toNewHampshireX().equals( p2_S ) ) {
return false;
}
final String p6_S_C = "(A[][][][1][22][333][4444][55555][666666][&&NHX:S=Aspecies],B[))],C,(AA,BB,CC,(CCC,DDD,EEE,[comment](FFFF,GGGG)x)y,D[comment]D,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 String p6_S_WO_C = "(A[&&NHX:S=Aspecies],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[] p6 = factory.create( p6_S_C, new NHXParser() );
if ( !p6[ 0 ].toNewHampshireX().equals( p6_S_WO_C ) ) {
return false;
}
final String p7_S_C = "(((A [&&NHX:S=species_a], B [&&NHX:S=Vstorri] , C , D),(A,B,C,D[comment])[],[c][]([xxx]A[comment],[comment]B[comment][comment],[comment][comment]C[comment][comment],[comment][comment]D[comment][comment])[comment][comment],[comment] [comment](A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C[comment][comment][comment][comment][comment] [comment],D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),[comment][comment]((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
final String p7_S_WO_C = "(((A[&&NHX:S=species_a],B[&&NHX:S=Vstorri],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[] p7 = factory.create( p7_S_C, new NHXParser() );
if ( !p7[ 0 ].toNewHampshireX().equals( p7_S_WO_C ) ) {
return false;
}
final String p8_S_C = "[cmt](((([]([))))))](((((A[&&NHX:S= [a comment] a])))))))[too many comments!:)])),(((((((((B[&&NHX[ a comment in a bad place]:S =b])))))[] [] )))),(((((((((C[&&NHX:S=c]) ))[,,, ])))))))";
final String p8_S_WO_C = "((((((((((A[&&NHX:S=a]))))))))),(((((((((B[&&NHX:S=b]))))))))),(((((((((C[&&NHX:S=c]))))))))))";
final Phylogeny[] p8 = factory.create( p8_S_C, new NHXParser() );
if ( !p8[ 0 ].toNewHampshireX().equals( p8_S_WO_C ) ) {
return false;
}
final Phylogeny p9 = factory.create( "((A:0.2,B:0.3):0.5[91],C:0.1)root:0.1[100]", new NHXParser() )[ 0 ];
if ( !p9.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
return false;
}
final Phylogeny p10 = factory
.create( " [79] ( (A [co mment] :0 .2[comment],B:0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],C: 0.1)[comment]root:0.1[100] [comment]",
new NHXParser() )[ 0 ];
if ( !p10.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNHXParsingQuotes() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final NHXParser p = new NHXParser();
final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "quotes.nhx" ), p );
if ( phylogenies_0.length != 5 ) {
return false;
}
final Phylogeny phy = phylogenies_0[ 4 ];
if ( phy.getNumberOfExternalNodes() != 7 ) {
return false;
}
if ( phy.getNodes( "a name in double quotes from tree ((a,b),c)" ).size() != 1 ) {
return false;
}
if ( phy.getNodes( "charles darwin 'origin of species'" ).size() != 1 ) {
return false;
}
if ( !phy.getNodes( "charles darwin 'origin of species'" ).get( 0 ).getNodeData().getTaxonomy()
.getScientificName().equals( "hsapiens" ) ) {
return false;
}
if ( phy.getNodes( "shouldbetogether single quotes" ).size() != 1 ) {
return false;
}
if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
return false;
}
if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
return false;
}
if ( phy.getNodes( "noquotes" ).size() != 1 ) {
return false;
}
if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
return false;
}
final NHXParser p1p = new NHXParser();
p1p.setIgnoreQuotes( true );
final Phylogeny p1 = factory.create( "(\"A\",'B1')", p1p )[ 0 ];
if ( !p1.toNewHampshire().equals( "(A,B1);" ) ) {
return false;
}
final NHXParser p2p = new NHXParser();
p1p.setIgnoreQuotes( false );
final Phylogeny p2 = factory.create( "(\"A\",'B1')", p2p )[ 0 ];
if ( !p2.toNewHampshire().equals( "(A,B1);" ) ) {
return false;
}
final NHXParser p3p = new NHXParser();
p3p.setIgnoreQuotes( false );
final Phylogeny p3 = factory.create( "(\"A)\",'B1')", p3p )[ 0 ];
if ( !p3.toNewHampshire().equals( "('A)',B1);" ) ) {
return false;
}
final NHXParser p4p = new NHXParser();
p4p.setIgnoreQuotes( false );
final Phylogeny p4 = factory.create( "(\"A)\",'B(),; x')", p4p )[ 0 ];
if ( !p4.toNewHampshire().equals( "('A)','B(),; x');" ) ) {
return false;
}
final Phylogeny p10 = factory
.create( " [79] ( (\"A \n\tB \" [co mment] :0 .2[comment],'B':0.3[com])[com ment]: 0. 5 \t[ 9 1 ][ comment],'C (or D?\\//;,))': 0.1)[comment]'\nroot is here (cool, was! ) ':0.1[100] [comment]",
new NHXParser() )[ 0 ];
final String p10_clean_str = "(('A B':0.2,B:0.3):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
if ( !p10.toNewHampshireX().equals( p10_clean_str ) ) {
return false;
}
final Phylogeny p11 = factory.create( p10.toNewHampshireX(), new NHXParser() )[ 0 ];
if ( !p11.toNewHampshireX().equals( p10_clean_str ) ) {
return false;
}
//
final Phylogeny p12 = factory
.create( " [79] ( (\"A \n\tB \" [[][] :0 .2[comment][\t&\t&\n N\tH\tX:S=mo\tnkey !],'\tB\t\b\t\n\f\rB B ':0.0\b3[])\t[com ment]: 0. 5 \t[ 9 1 ][ \ncomment],'C\t (or D?\\//;,))': 0.\b1)[comment]'\nroot \tis here (cool, \b\t\n\f\r was! ) ':0.1[100] [comment]",
new NHXParser() )[ 0 ];
final String p12_clean_str = "(('A B':0.2[&&NHX:S=monkey!],'BB B':0.03):0.5[&&NHX:B=91],'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1[&&NHX:B=100]";
if ( !p12.toNewHampshireX().equals( p12_clean_str ) ) {
return false;
}
final Phylogeny p13 = factory.create( p12.toNewHampshireX(), new NHXParser() )[ 0 ];
if ( !p13.toNewHampshireX().equals( p12_clean_str ) ) {
return false;
}
final String p12_clean_str_nh = "(('A B':0.2,'BB B':0.03):0.5,'C (or D?\\//;,))':0.1)'root is here (cool, was! )':0.1;";
if ( !p13.toNewHampshire().equals( p12_clean_str_nh ) ) {
return false;
}
final Phylogeny p14 = factory.create( p13.toNewHampshire(), new NHXParser() )[ 0 ];
if ( !p14.toNewHampshire().equals( p12_clean_str_nh ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNHXParsingMB() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p1 = factory.create( "(1[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00,"
+ "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
+ "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
+ "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
+ "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
+ "7.369400000000000e-02}])", new NHXParser() )[ 0 ];
if ( !isEqual( p1.getNode( "1" ).getDistanceToParent(), 4.129e-02 ) ) {
return false;
}
if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getValue(), 0.9500000000000000e+00 ) ) {
return false;
}
if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(),
0.1100000000000000e+00 ) ) {
return false;
}
if ( !isEqual( p1.getNode( "2" ).getDistanceToParent(), 6.375699999999999e-02 ) ) {
return false;
}
if ( !isEqual( p1.getNode( "2" ).getBranchData().getConfidence( 0 ).getValue(), 0.810000000000000e+00 ) ) {
return false;
}
final Phylogeny p2 = factory
.create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
+ "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
+ "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
+ "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
+ "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
+ "7.369400000000000e-02}])",
new NHXParser() )[ 0 ];
if ( p2.getNode( "1" ) == null ) {
return false;
}
if ( p2.getNode( "2" ) == null ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
System.exit( -1 );
return false;
}
return true;
}
private static boolean testPhylogenyBranch() {
try {
final PhylogenyNode a1 = PhylogenyNode.createInstanceFromNhxString( "a" );
final PhylogenyNode b1 = PhylogenyNode.createInstanceFromNhxString( "b" );
final PhylogenyBranch a1b1 = new PhylogenyBranch( a1, b1 );
final PhylogenyBranch b1a1 = new PhylogenyBranch( b1, a1 );
if ( !a1b1.equals( a1b1 ) ) {
return false;
}
if ( !a1b1.equals( b1a1 ) ) {
return false;
}
if ( !b1a1.equals( a1b1 ) ) {
return false;
}
final PhylogenyBranch a1_b1 = new PhylogenyBranch( a1, b1, true );
final PhylogenyBranch b1_a1 = new PhylogenyBranch( b1, a1, true );
final PhylogenyBranch a1_b1_ = new PhylogenyBranch( a1, b1, false );
if ( a1_b1.equals( b1_a1 ) ) {
return false;
}
if ( a1_b1.equals( a1_b1_ ) ) {
return false;
}
final PhylogenyBranch b1_a1_ = new PhylogenyBranch( b1, a1, false );
if ( !a1_b1.equals( b1_a1_ ) ) {
return false;
}
if ( a1_b1_.equals( b1_a1_ ) ) {
return false;
}
if ( !a1_b1_.equals( b1_a1 ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testPhyloXMLparsingOfDistributionElement() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
PhyloXmlParser xml_parser = null;
try {
xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
}
catch ( final Exception e ) {
// Do nothing -- means were not running from jar.
}
if ( xml_parser == null ) {
xml_parser = new PhyloXmlParser();
if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
}
else {
xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
}
}
final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
if ( phylogenies_0.length != 1 ) {
return false;
}
final Phylogeny t1 = phylogenies_0[ 0 ];
PhylogenyNode n = null;
Distribution d = null;
n = t1.getNode( "root node" );
if ( !n.getNodeData().isHasDistribution() ) {
return false;
}
if ( n.getNodeData().getDistributions().size() != 1 ) {
return false;
}
d = n.getNodeData().getDistribution();
if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
return false;
}
if ( d.getPoints().size() != 1 ) {
return false;
}
if ( d.getPolygons() != null ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
return false;
}
n = t1.getNode( "node a" );
if ( !n.getNodeData().isHasDistribution() ) {
return false;
}
if ( n.getNodeData().getDistributions().size() != 2 ) {
return false;
}
d = n.getNodeData().getDistribution( 1 );
if ( !d.getDesc().equals( "San Diego" ) ) {
return false;
}
if ( d.getPoints().size() != 1 ) {
return false;
}
if ( d.getPolygons() != null ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
return false;
}
n = t1.getNode( "node bb" );
if ( !n.getNodeData().isHasDistribution() ) {
return false;
}
if ( n.getNodeData().getDistributions().size() != 1 ) {
return false;
}
d = n.getNodeData().getDistribution( 0 );
if ( d.getPoints().size() != 3 ) {
return false;
}
if ( d.getPolygons().size() != 2 ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
return false;
}
if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
return false;
}
if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
return false;
}
if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
return false;
}
if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
return false;
}
Polygon p = d.getPolygons().get( 0 );
if ( p.getPoints().size() != 3 ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
return false;
}
if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
return false;
}
if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
return false;
}
if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
return false;
}
p = d.getPolygons().get( 1 );
if ( p.getPoints().size() != 3 ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
return false;
}
// Roundtrip:
final StringBuffer t1_sb = new StringBuffer( t1.toPhyloXML( 0 ) );
final Phylogeny[] rt = factory.create( t1_sb, xml_parser );
if ( rt.length != 1 ) {
return false;
}
final Phylogeny t1_rt = rt[ 0 ];
n = t1_rt.getNode( "root node" );
if ( !n.getNodeData().isHasDistribution() ) {
return false;
}
if ( n.getNodeData().getDistributions().size() != 1 ) {
return false;
}
d = n.getNodeData().getDistribution();
if ( !d.getDesc().equals( "Hirschweg 38" ) ) {
return false;
}
if ( d.getPoints().size() != 1 ) {
return false;
}
if ( d.getPolygons() != null ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "472" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "47.48148427110029" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "8.768951296806335" ) ) {
return false;
}
n = t1_rt.getNode( "node a" );
if ( !n.getNodeData().isHasDistribution() ) {
return false;
}
if ( n.getNodeData().getDistributions().size() != 2 ) {
return false;
}
d = n.getNodeData().getDistribution( 1 );
if ( !d.getDesc().equals( "San Diego" ) ) {
return false;
}
if ( d.getPoints().size() != 1 ) {
return false;
}
if ( d.getPolygons() != null ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltitude().toString().equals( "104" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getAltiudeUnit().equals( "m" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getGeodeticDatum().equals( "WGS84" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "32.880933" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "-117.217543" ) ) {
return false;
}
n = t1_rt.getNode( "node bb" );
if ( !n.getNodeData().isHasDistribution() ) {
return false;
}
if ( n.getNodeData().getDistributions().size() != 1 ) {
return false;
}
d = n.getNodeData().getDistribution( 0 );
if ( d.getPoints().size() != 3 ) {
return false;
}
if ( d.getPolygons().size() != 2 ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLatitude().toString().equals( "1" ) ) {
return false;
}
if ( !d.getPoints().get( 0 ).getLongitude().toString().equals( "2" ) ) {
return false;
}
if ( !d.getPoints().get( 1 ).getLatitude().toString().equals( "3" ) ) {
return false;
}
if ( !d.getPoints().get( 1 ).getLongitude().toString().equals( "4" ) ) {
return false;
}
if ( !d.getPoints().get( 2 ).getLatitude().toString().equals( "5" ) ) {
return false;
}
if ( !d.getPoints().get( 2 ).getLongitude().toString().equals( "6" ) ) {
return false;
}
p = d.getPolygons().get( 0 );
if ( p.getPoints().size() != 3 ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "0.1" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "0.2" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
return false;
}
if ( !p.getPoints().get( 2 ).getLatitude().toString().equals( "0.5" ) ) {
return false;
}
if ( !p.getPoints().get( 2 ).getLongitude().toString().equals( "0.6" ) ) {
return false;
}
if ( !p.getPoints().get( 2 ).getAltitude().toString().equals( "30" ) ) {
return false;
}
p = d.getPolygons().get( 1 );
if ( p.getPoints().size() != 3 ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLatitude().toString().equals( "1.49348902489947473" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getLongitude().toString().equals( "2.567489393947847492" ) ) {
return false;
}
if ( !p.getPoints().get( 0 ).getAltitude().toString().equals( "10" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testPostOrderIterator() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
PhylogenyNodeIterator it0;
for( it0 = t0.iteratorPostorder(); it0.hasNext(); ) {
it0.next();
}
for( it0.reset(); it0.hasNext(); ) {
it0.next();
}
final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
final PhylogenyNodeIterator it = t1.iteratorPostorder();
if ( !it.next().getName().equals( "A" ) ) {
return false;
}
if ( !it.next().getName().equals( "B" ) ) {
return false;
}
if ( !it.next().getName().equals( "ab" ) ) {
return false;
}
if ( !it.next().getName().equals( "C" ) ) {
return false;
}
if ( !it.next().getName().equals( "D" ) ) {
return false;
}
if ( !it.next().getName().equals( "cd" ) ) {
return false;
}
if ( !it.next().getName().equals( "abcd" ) ) {
return false;
}
if ( !it.next().getName().equals( "E" ) ) {
return false;
}
if ( !it.next().getName().equals( "F" ) ) {
return false;
}
if ( !it.next().getName().equals( "ef" ) ) {
return false;
}
if ( !it.next().getName().equals( "G" ) ) {
return false;
}
if ( !it.next().getName().equals( "H" ) ) {
return false;
}
if ( !it.next().getName().equals( "gh" ) ) {
return false;
}
if ( !it.next().getName().equals( "efgh" ) ) {
return false;
}
if ( !it.next().getName().equals( "r" ) ) {
return false;
}
if ( it.hasNext() ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testPreOrderIterator() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0 = factory.create( "((A,B)ab,(C,D)cd)r", new NHXParser() )[ 0 ];
PhylogenyNodeIterator it0;
for( it0 = t0.iteratorPreorder(); it0.hasNext(); ) {
it0.next();
}
for( it0.reset(); it0.hasNext(); ) {
it0.next();
}
PhylogenyNodeIterator it = t0.iteratorPreorder();
if ( !it.next().getName().equals( "r" ) ) {
return false;
}
if ( !it.next().getName().equals( "ab" ) ) {
return false;
}
if ( !it.next().getName().equals( "A" ) ) {
return false;
}
if ( !it.next().getName().equals( "B" ) ) {
return false;
}
if ( !it.next().getName().equals( "cd" ) ) {
return false;
}
if ( !it.next().getName().equals( "C" ) ) {
return false;
}
if ( !it.next().getName().equals( "D" ) ) {
return false;
}
if ( it.hasNext() ) {
return false;
}
final Phylogeny t1 = factory.create( "(((A,B)ab,(C,D)cd)abcd,((E,F)ef,(G,H)gh)efgh)r", new NHXParser() )[ 0 ];
it = t1.iteratorPreorder();
if ( !it.next().getName().equals( "r" ) ) {
return false;
}
if ( !it.next().getName().equals( "abcd" ) ) {
return false;
}
if ( !it.next().getName().equals( "ab" ) ) {
return false;
}
if ( !it.next().getName().equals( "A" ) ) {
return false;
}
if ( !it.next().getName().equals( "B" ) ) {
return false;
}
if ( !it.next().getName().equals( "cd" ) ) {
return false;
}
if ( !it.next().getName().equals( "C" ) ) {
return false;
}
if ( !it.next().getName().equals( "D" ) ) {
return false;
}
if ( !it.next().getName().equals( "efgh" ) ) {
return false;
}
if ( !it.next().getName().equals( "ef" ) ) {
return false;
}
if ( !it.next().getName().equals( "E" ) ) {
return false;
}
if ( !it.next().getName().equals( "F" ) ) {
return false;
}
if ( !it.next().getName().equals( "gh" ) ) {
return false;
}
if ( !it.next().getName().equals( "G" ) ) {
return false;
}
if ( !it.next().getName().equals( "H" ) ) {
return false;
}
if ( it.hasNext() ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testPropertiesMap() {
try {
final PropertiesMap pm = new PropertiesMap();
final Property p0 = new Property( "dimensions:diameter", "1", "metric:mm", "xsd:decimal", AppliesTo.NODE );
final Property p1 = new Property( "dimensions:length", "2", "metric:mm", "xsd:decimal", AppliesTo.NODE );
final Property p2 = new Property( "something:else",
"?",
"improbable:research",
"xsd:decimal",
AppliesTo.NODE );
pm.addProperty( p0 );
pm.addProperty( p1 );
pm.addProperty( p2 );
if ( !pm.getProperty( "dimensions:diameter" ).getValue().equals( "1" ) ) {
return false;
}
if ( !pm.getProperty( "dimensions:length" ).getValue().equals( "2" ) ) {
return false;
}
if ( pm.getProperties().size() != 3 ) {
return false;
}
if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 2 ) {
return false;
}
if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
return false;
}
if ( pm.getProperties().size() != 3 ) {
return false;
}
pm.removeProperty( "dimensions:diameter" );
if ( pm.getProperties().size() != 2 ) {
return false;
}
if ( pm.getPropertiesWithGivenReferencePrefix( "dimensions" ).size() != 1 ) {
return false;
}
if ( pm.getPropertiesWithGivenReferencePrefix( "something" ).size() != 1 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testReIdMethods() {
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();
p.levelOrderReID();
if ( p.getNode( "r" ).getId() != count ) {
return false;
}
if ( p.getNode( "A" ).getId() != count + 1 ) {
return false;
}
if ( p.getNode( "B" ).getId() != count + 1 ) {
return false;
}
if ( p.getNode( "C" ).getId() != count + 1 ) {
return false;
}
if ( p.getNode( "1" ).getId() != count + 2 ) {
return false;
}
if ( p.getNode( "2" ).getId() != count + 2 ) {
return false;
}
if ( p.getNode( "3" ).getId() != count + 2 ) {
return false;
}
if ( p.getNode( "4" ).getId() != count + 2 ) {
return false;
}
if ( p.getNode( "5" ).getId() != count + 2 ) {
return false;
}
if ( p.getNode( "6" ).getId() != count + 2 ) {
return false;
}
if ( p.getNode( "a" ).getId() != count + 3 ) {
return false;
}
if ( p.getNode( "b" ).getId() != count + 3 ) {
return false;
}
if ( p.getNode( "X" ).getId() != count + 4 ) {
return false;
}
if ( p.getNode( "Y" ).getId() != count + 4 ) {
return false;
}
if ( p.getNode( "Z" ).getId() != count + 4 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testRerooting() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t1 = factory.create( "((A:1,B:2)AB:1[&&NHX:B=55],(C:3,D:5)CD:3[&&NHX:B=10])ABCD:0.5",
new NHXParser() )[ 0 ];
if ( !t1.isRooted() ) {
return false;
}
t1.reRoot( t1.getNode( "D" ) );
t1.reRoot( t1.getNode( "CD" ) );
t1.reRoot( t1.getNode( "A" ) );
t1.reRoot( t1.getNode( "B" ) );
t1.reRoot( t1.getNode( "AB" ) );
t1.reRoot( t1.getNode( "D" ) );
t1.reRoot( t1.getNode( "C" ) );
t1.reRoot( t1.getNode( "CD" ) );
t1.reRoot( t1.getNode( "A" ) );
t1.reRoot( t1.getNode( "B" ) );
t1.reRoot( t1.getNode( "AB" ) );
t1.reRoot( t1.getNode( "D" ) );
t1.reRoot( t1.getNode( "D" ) );
t1.reRoot( t1.getNode( "C" ) );
t1.reRoot( t1.getNode( "A" ) );
t1.reRoot( t1.getNode( "B" ) );
t1.reRoot( t1.getNode( "AB" ) );
t1.reRoot( t1.getNode( "C" ) );
t1.reRoot( t1.getNode( "D" ) );
t1.reRoot( t1.getNode( "CD" ) );
t1.reRoot( t1.getNode( "D" ) );
t1.reRoot( t1.getNode( "A" ) );
t1.reRoot( t1.getNode( "B" ) );
t1.reRoot( t1.getNode( "AB" ) );
t1.reRoot( t1.getNode( "C" ) );
t1.reRoot( t1.getNode( "D" ) );
t1.reRoot( t1.getNode( "CD" ) );
t1.reRoot( t1.getNode( "D" ) );
if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 1 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 2 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 3 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "D" ).getDistanceToParent(), 2.5 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "CD" ).getDistanceToParent(), 2.5 ) ) {
return false;
}
if ( !isEqual( t1.getNode( "AB" ).getDistanceToParent(), 4 ) ) {
return false;
}
final Phylogeny t2 = factory.create( "(((A:1,B:2)AB:10[&&NHX:B=55],C)ABC:3[&&NHX:B=33],D:5)ABCD:0.5",
new NHXParser() )[ 0 ];
t2.reRoot( t2.getNode( "A" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "ABC" ) );
t2.reRoot( t2.getNode( "A" ) );
t2.reRoot( t2.getNode( "B" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "C" ) );
t2.reRoot( t2.getNode( "ABC" ) );
t2.reRoot( t2.getNode( "A" ) );
t2.reRoot( t2.getNode( "B" ) );
t2.reRoot( t2.getNode( "AB" ) );
t2.reRoot( t2.getNode( "AB" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "C" ) );
t2.reRoot( t2.getNode( "B" ) );
t2.reRoot( t2.getNode( "AB" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "ABC" ) );
t2.reRoot( t2.getNode( "A" ) );
t2.reRoot( t2.getNode( "B" ) );
t2.reRoot( t2.getNode( "AB" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "C" ) );
t2.reRoot( t2.getNode( "ABC" ) );
t2.reRoot( t2.getNode( "A" ) );
t2.reRoot( t2.getNode( "B" ) );
t2.reRoot( t2.getNode( "AB" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "C" ) );
t2.reRoot( t2.getNode( "A" ) );
t2.reRoot( t2.getNode( "B" ) );
t2.reRoot( t2.getNode( "AB" ) );
t2.reRoot( t2.getNode( "C" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "ABC" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "A" ) );
t2.reRoot( t2.getNode( "B" ) );
t2.reRoot( t2.getNode( "AB" ) );
t2.reRoot( t2.getNode( "C" ) );
t2.reRoot( t2.getNode( "D" ) );
t2.reRoot( t2.getNode( "ABC" ) );
t2.reRoot( t2.getNode( "D" ) );
if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
return false;
}
t2.reRoot( t2.getNode( "ABC" ) );
if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
return false;
}
t2.reRoot( t2.getNode( "AB" ) );
if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
return false;
}
t2.reRoot( t2.getNode( "AB" ) );
if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "D" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
return false;
}
t2.reRoot( t2.getNode( "D" ) );
if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
return false;
}
t2.reRoot( t2.getNode( "ABC" ) );
if ( !isEqual( t2.getNode( "AB" ).getBranchData().getConfidence( 0 ).getValue(), 55 ) ) {
return false;
}
if ( !isEqual( t2.getNode( "ABC" ).getBranchData().getConfidence( 0 ).getValue(), 33 ) ) {
return false;
}
final Phylogeny t3 = factory.create( "(A[&&NHX:B=10],B[&&NHX:B=20],C[&&NHX:B=30],D[&&NHX:B=40])",
new NHXParser() )[ 0 ];
t3.reRoot( t3.getNode( "B" ) );
if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
return false;
}
if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
return false;
}
if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
return false;
}
t3.reRoot( t3.getNode( "B" ) );
if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
return false;
}
if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
return false;
}
if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
return false;
}
t3.reRoot( t3.getRoot() );
if ( t3.getNode( "B" ).getBranchData().getConfidence( 0 ).getValue() != 20 ) {
return false;
}
if ( t3.getNode( "A" ).getParent().getBranchData().getConfidence( 0 ).getValue() != 20 ) {
return false;
}
if ( t3.getNode( "A" ).getParent().getNumberOfDescendants() != 3 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testSDIse() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny species1 = factory.create( "[&&NHX:S=yeast]", new NHXParser() )[ 0 ];
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 );
if ( !gene1.getRoot().isDuplication() ) {
return false;
}
final Phylogeny species2 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
new NHXParser() )[ 0 ];
final Phylogeny gene2 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=B])ab,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
new NHXParser() )[ 0 ];
species2.setRooted( true );
gene2.setRooted( true );
final SDI sdi2 = new SDIse( gene2, species2 );
if ( sdi2.getDuplicationsSum() != 0 ) {
return false;
}
if ( !gene2.getNode( "ab" ).isSpeciation() ) {
return false;
}
if ( !gene2.getNode( "ab" ).isHasAssignedEvent() ) {
return false;
}
if ( !gene2.getNode( "abc" ).isSpeciation() ) {
return false;
}
if ( !gene2.getNode( "abc" ).isHasAssignedEvent() ) {
return false;
}
if ( !gene2.getNode( "r" ).isSpeciation() ) {
return false;
}
if ( !gene2.getNode( "r" ).isHasAssignedEvent() ) {
return false;
}
final Phylogeny species3 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
new NHXParser() )[ 0 ];
final Phylogeny gene3 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=A])aa,[&&NHX:S=C])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
new NHXParser() )[ 0 ];
species3.setRooted( true );
gene3.setRooted( true );
final SDI sdi3 = new SDIse( gene3, species3 );
if ( sdi3.getDuplicationsSum() != 1 ) {
return false;
}
if ( !gene3.getNode( "aa" ).isDuplication() ) {
return false;
}
if ( !gene3.getNode( "aa" ).isHasAssignedEvent() ) {
return false;
}
final Phylogeny species4 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
new NHXParser() )[ 0 ];
final Phylogeny gene4 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=C])ac,[&&NHX:S=B])abc,[&&NHX:S=D])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
new NHXParser() )[ 0 ];
species4.setRooted( true );
gene4.setRooted( true );
final SDI sdi4 = new SDIse( gene4, species4 );
if ( sdi4.getDuplicationsSum() != 1 ) {
return false;
}
if ( !gene4.getNode( "ac" ).isSpeciation() ) {
return false;
}
if ( !gene4.getNode( "abc" ).isDuplication() ) {
return false;
}
if ( gene4.getNode( "abcd" ).isDuplication() ) {
return false;
}
if ( species4.getNumberOfExternalNodes() != 6 ) {
return false;
}
if ( gene4.getNumberOfExternalNodes() != 6 ) {
return false;
}
final Phylogeny species5 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
new NHXParser() )[ 0 ];
final Phylogeny gene5 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=D])ad,[&&NHX:S=C])adc,[&&NHX:S=B])abcd,([&&NHX:S=E],[&&NHX:S=F])ef)r",
new NHXParser() )[ 0 ];
species5.setRooted( true );
gene5.setRooted( true );
final SDI sdi5 = new SDIse( gene5, species5 );
if ( sdi5.getDuplicationsSum() != 2 ) {
return false;
}
if ( !gene5.getNode( "ad" ).isSpeciation() ) {
return false;
}
if ( !gene5.getNode( "adc" ).isDuplication() ) {
return false;
}
if ( !gene5.getNode( "abcd" ).isDuplication() ) {
return false;
}
if ( species5.getNumberOfExternalNodes() != 6 ) {
return false;
}
if ( gene5.getNumberOfExternalNodes() != 6 ) {
return false;
}
// Trees from Louxin Zhang 1997 "On a Mirkin-Muchnik-Smith
// Conjecture for Comparing Molecular Phylogenies"
// J. of Comput Bio. Vol. 4, No 2, pp.177-187
final Phylogeny species6 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
+ "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
new NHXParser() )[ 0 ];
final Phylogeny gene6 = factory
.create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1,"
+ "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
+ "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
new NHXParser() )[ 0 ];
species6.setRooted( true );
gene6.setRooted( true );
final SDI sdi6 = new SDIse( gene6, species6 );
if ( sdi6.getDuplicationsSum() != 3 ) {
return false;
}
if ( !gene6.getNode( "r" ).isDuplication() ) {
return false;
}
if ( !gene6.getNode( "4-5-6" ).isDuplication() ) {
return false;
}
if ( !gene6.getNode( "7-8-9" ).isDuplication() ) {
return false;
}
if ( !gene6.getNode( "1-2" ).isSpeciation() ) {
return false;
}
if ( !gene6.getNode( "1-2-3" ).isSpeciation() ) {
return false;
}
if ( !gene6.getNode( "5-6" ).isSpeciation() ) {
return false;
}
if ( !gene6.getNode( "8-9" ).isSpeciation() ) {
return false;
}
if ( !gene6.getNode( "4-5-6-7-8-9" ).isSpeciation() ) {
return false;
}
sdi6.computeMappingCostL();
if ( sdi6.computeMappingCostL() != 17 ) {
return false;
}
if ( species6.getNumberOfExternalNodes() != 9 ) {
return false;
}
if ( gene6.getNumberOfExternalNodes() != 9 ) {
return false;
}
final Phylogeny species7 = Test.createPhylogeny( "(((((((" + "([&&NHX:S=a1],[&&NHX:S=a2]),"
+ "([&&NHX:S=b1],[&&NHX:S=b2])" + "),[&&NHX:S=x]),(" + "([&&NHX:S=m1],[&&NHX:S=m2]),"
+ "([&&NHX:S=n1],[&&NHX:S=n2])" + ")),(" + "([&&NHX:S=i1],[&&NHX:S=i2]),"
+ "([&&NHX:S=j1],[&&NHX:S=j2])" + ")),(" + "([&&NHX:S=e1],[&&NHX:S=e2]),"
+ "([&&NHX:S=f1],[&&NHX:S=f2])" + ")),[&&NHX:S=y]),[&&NHX:S=z])" );
species7.setRooted( true );
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 );
if ( sdi7.getDuplicationsSum() != 0 ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "a2" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "b1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "x" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "m1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "i1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "e1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "y" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_1, "a1", "z" ).isSpeciation() ) {
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 );
if ( sdi7_2.getDuplicationsSum() != 1 ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
return false;
}
if ( !Test.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
return false;
}
}
catch ( final Exception e ) {
return false;
}
return true;
}
private static boolean testSDIunrooted() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p0 = factory.create( "((((A,B)ab,(C1,C2)cc)abc,D)abcd,(E,F)ef)abcdef", new NHXParser() )[ 0 ];
final List l = SDIR.getBranchesInPreorder( p0 );
final Iterator iter = l.iterator();
PhylogenyBranch br = iter.next();
if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "ef" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "ef" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "ab" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "ab" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "abc" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "abc" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "C1" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "C1" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "C2" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "C2" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "cc" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "cc" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "abc" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "abc" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "abcd" ) && !br.getFirstNode().getName().equals( "D" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "abcd" ) && !br.getSecondNode().getName().equals( "D" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "abcd" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "abcd" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "E" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "E" ) ) {
return false;
}
br = iter.next();
if ( !br.getFirstNode().getName().equals( "ef" ) && !br.getFirstNode().getName().equals( "F" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ef" ) && !br.getSecondNode().getName().equals( "F" ) ) {
return false;
}
if ( iter.hasNext() ) {
return false;
}
final Phylogeny p1 = factory.create( "(C,(A,B)ab)abc", new NHXParser() )[ 0 ];
final List l1 = SDIR.getBranchesInPreorder( p1 );
final Iterator iter1 = l1.iterator();
br = iter1.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
return false;
}
br = iter1.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
return false;
}
br = iter1.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
return false;
}
if ( iter1.hasNext() ) {
return false;
}
final Phylogeny p2 = factory.create( "((A,B)ab,C)abc", new NHXParser() )[ 0 ];
final List l2 = SDIR.getBranchesInPreorder( p2 );
final Iterator iter2 = l2.iterator();
br = iter2.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "C" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "C" ) ) {
return false;
}
br = iter2.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "A" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "A" ) ) {
return false;
}
br = iter2.next();
if ( !br.getFirstNode().getName().equals( "ab" ) && !br.getFirstNode().getName().equals( "B" ) ) {
return false;
}
if ( !br.getSecondNode().getName().equals( "ab" ) && !br.getSecondNode().getName().equals( "B" ) ) {
return false;
}
if ( iter2.hasNext() ) {
return false;
}
final Phylogeny species0 = factory
.create( "(((([&&NHX:S=A],[&&NHX:S=B]),[&&NHX:S=C]),[&&NHX:S=D]),([&&NHX:S=E],[&&NHX:S=F]))",
new NHXParser() )[ 0 ];
final Phylogeny gene1 = factory
.create( "(((((A:0.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])",
new NHXParser() )[ 0 ];
species0.setRooted( true );
gene1.setRooted( true );
final SDIR sdi_unrooted = new SDIR();
sdi_unrooted.infer( gene1, species0, false, true, true, true, 10 );
if ( sdi_unrooted.getCount() != 1 ) {
return false;
}
if ( sdi_unrooted.getMinimalDuplications() != 0 ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.4 ) ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 1.0 ) ) {
return false;
}
if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
return false;
}
final Phylogeny gene2 = factory
.create( "(((((A:2.6[&&NHX:S=A],B:0.1[&&NHX:S=B])ab:0.1,C:0.1[&&NHX:S=C])abc:0.3,D:1.0[&&NHX:S=D])abcd:0.2,E:0.1[&&NHX:S=E])abcde:0.2,F:0.2[&&NHX:S=F])",
new NHXParser() )[ 0 ];
gene2.setRooted( true );
sdi_unrooted.infer( gene2, species0, false, false, true, true, 10 );
if ( sdi_unrooted.getCount() != 1 ) {
return false;
}
if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 2.0 ) ) {
return false;
}
if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
return false;
}
final Phylogeny species6 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
+ "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
new NHXParser() )[ 0 ];
final Phylogeny gene6 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
+ "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
new NHXParser() )[ 0 ];
species6.setRooted( true );
gene6.setRooted( true );
Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
if ( sdi_unrooted.getCount() != 1 ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
return false;
}
if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
return false;
}
if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
return false;
}
if ( !p6[ 0 ].getRoot().isDuplication() ) {
return false;
}
if ( !p6[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
return false;
}
if ( !p6[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
return false;
}
if ( p6[ 0 ].getNode( "1-2" ).isDuplication() ) {
return false;
}
if ( p6[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
return false;
}
if ( p6[ 0 ].getNode( "5-6" ).isDuplication() ) {
return false;
}
if ( p6[ 0 ].getNode( "8-9" ).isDuplication() ) {
return false;
}
if ( p6[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
return false;
}
p6 = null;
final Phylogeny species7 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
+ "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
new NHXParser() )[ 0 ];
final Phylogeny gene7 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
+ "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
new NHXParser() )[ 0 ];
species7.setRooted( true );
gene7.setRooted( true );
Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
if ( sdi_unrooted.getCount() != 1 ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
return false;
}
if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
return false;
}
if ( sdi_unrooted.getMinimalMappingCost() != 17 ) {
return false;
}
if ( !p7[ 0 ].getRoot().isDuplication() ) {
return false;
}
if ( !p7[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
return false;
}
if ( !p7[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
return false;
}
if ( p7[ 0 ].getNode( "1-2" ).isDuplication() ) {
return false;
}
if ( p7[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
return false;
}
if ( p7[ 0 ].getNode( "5-6" ).isDuplication() ) {
return false;
}
if ( p7[ 0 ].getNode( "8-9" ).isDuplication() ) {
return false;
}
if ( p7[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
return false;
}
p7 = null;
final Phylogeny species8 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
+ "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
new NHXParser() )[ 0 ];
final Phylogeny gene8 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
+ "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
new NHXParser() )[ 0 ];
species8.setRooted( true );
gene8.setRooted( true );
Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
if ( sdi_unrooted.getCount() != 1 ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalDiffInSubTreeHeights(), 0.0 ) ) {
return false;
}
if ( !Test.isEqual( sdi_unrooted.getMinimalTreeHeight(), 0.375 ) ) {
return false;
}
if ( sdi_unrooted.getMinimalDuplications() != 3 ) {
return false;
}
if ( sdi_unrooted.getMinimalMappingCost() != Integer.MAX_VALUE ) {
return false;
}
if ( !p8[ 0 ].getRoot().isDuplication() ) {
return false;
}
if ( !p8[ 0 ].getNode( "4-5-6" ).isDuplication() ) {
return false;
}
if ( !p8[ 0 ].getNode( "7-8-9" ).isDuplication() ) {
return false;
}
if ( p8[ 0 ].getNode( "1-2" ).isDuplication() ) {
return false;
}
if ( p8[ 0 ].getNode( "1-2-3" ).isDuplication() ) {
return false;
}
if ( p8[ 0 ].getNode( "5-6" ).isDuplication() ) {
return false;
}
if ( p8[ 0 ].getNode( "8-9" ).isDuplication() ) {
return false;
}
if ( p8[ 0 ].getNode( "4-5-6-7-8-9" ).isDuplication() ) {
return false;
}
p8 = null;
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testSplit() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
//Archaeopteryx.createApplication( p0 );
final Set ex = new HashSet();
ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
// System.out.println( s0.toString() );
//
Set query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
/////////
// query_nodes = new HashSet();
// query_nodes.add( new PhylogenyNode( "X" ) );
// query_nodes.add( new PhylogenyNode( "Y" ) );
// query_nodes.add( new PhylogenyNode( "A" ) );
// query_nodes.add( new PhylogenyNode( "B" ) );
// query_nodes.add( new PhylogenyNode( "C" ) );
// query_nodes.add( new PhylogenyNode( "D" ) );
// query_nodes.add( new PhylogenyNode( "E" ) );
// query_nodes.add( new PhylogenyNode( "F" ) );
// query_nodes.add( new PhylogenyNode( "G" ) );
// if ( !s0.match( query_nodes ) ) {
// return false;
// }
// query_nodes = new HashSet();
// query_nodes.add( new PhylogenyNode( "X" ) );
// query_nodes.add( new PhylogenyNode( "Y" ) );
// query_nodes.add( new PhylogenyNode( "A" ) );
// query_nodes.add( new PhylogenyNode( "B" ) );
// query_nodes.add( new PhylogenyNode( "C" ) );
// if ( !s0.match( query_nodes ) ) {
// return false;
// }
// //
// query_nodes = new HashSet();
// query_nodes.add( new PhylogenyNode( "X" ) );
// query_nodes.add( new PhylogenyNode( "Y" ) );
// query_nodes.add( new PhylogenyNode( "D" ) );
// query_nodes.add( new PhylogenyNode( "E" ) );
// query_nodes.add( new PhylogenyNode( "F" ) );
// query_nodes.add( new PhylogenyNode( "G" ) );
// if ( !s0.match( query_nodes ) ) {
// return false;
// }
// //
// query_nodes = new HashSet();
// query_nodes.add( new PhylogenyNode( "X" ) );
// query_nodes.add( new PhylogenyNode( "Y" ) );
// query_nodes.add( new PhylogenyNode( "A" ) );
// query_nodes.add( new PhylogenyNode( "B" ) );
// query_nodes.add( new PhylogenyNode( "C" ) );
// query_nodes.add( new PhylogenyNode( "D" ) );
// if ( !s0.match( query_nodes ) ) {
// return false;
// }
// //
// query_nodes = new HashSet();
// query_nodes.add( new PhylogenyNode( "X" ) );
// query_nodes.add( new PhylogenyNode( "Y" ) );
// query_nodes.add( new PhylogenyNode( "E" ) );
// query_nodes.add( new PhylogenyNode( "F" ) );
// query_nodes.add( new PhylogenyNode( "G" ) );
// if ( !s0.match( query_nodes ) ) {
// return false;
// }
// //
// query_nodes = new HashSet();
// query_nodes.add( new PhylogenyNode( "X" ) );
// query_nodes.add( new PhylogenyNode( "Y" ) );
// query_nodes.add( new PhylogenyNode( "F" ) );
// query_nodes.add( new PhylogenyNode( "G" ) );
// if ( !s0.match( query_nodes ) ) {
// return false;
// }
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
///////////////////////////
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testSplitStrict() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
final Set ex = new HashSet();
ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
Set query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
//
query_nodes = new HashSet();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testSubtreeDeletion() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t1 = factory.create( "((A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
t1.deleteSubtree( t1.getNode( "A" ), false );
if ( t1.getNumberOfExternalNodes() != 5 ) {
return false;
}
t1.toNewHampshireX();
t1.deleteSubtree( t1.getNode( "E" ), false );
if ( t1.getNumberOfExternalNodes() != 4 ) {
return false;
}
t1.toNewHampshireX();
t1.deleteSubtree( t1.getNode( "F" ), false );
if ( t1.getNumberOfExternalNodes() != 3 ) {
return false;
}
t1.toNewHampshireX();
t1.deleteSubtree( t1.getNode( "D" ), false );
t1.toNewHampshireX();
if ( t1.getNumberOfExternalNodes() != 3 ) {
return false;
}
t1.deleteSubtree( t1.getNode( "def" ), false );
t1.toNewHampshireX();
if ( t1.getNumberOfExternalNodes() != 2 ) {
return false;
}
t1.deleteSubtree( t1.getNode( "B" ), false );
t1.toNewHampshireX();
if ( t1.getNumberOfExternalNodes() != 1 ) {
return false;
}
t1.deleteSubtree( t1.getNode( "C" ), false );
t1.toNewHampshireX();
if ( t1.getNumberOfExternalNodes() != 1 ) {
return false;
}
t1.deleteSubtree( t1.getNode( "abc" ), false );
t1.toNewHampshireX();
if ( t1.getNumberOfExternalNodes() != 1 ) {
return false;
}
t1.deleteSubtree( t1.getNode( "r" ), false );
if ( t1.getNumberOfExternalNodes() != 0 ) {
return false;
}
if ( !t1.isEmpty() ) {
return false;
}
final Phylogeny t2 = factory.create( "(((1,2,3)A,B,C)abc,(D,E,F)def)r", new NHXParser() )[ 0 ];
t2.deleteSubtree( t2.getNode( "A" ), false );
t2.toNewHampshireX();
if ( t2.getNumberOfExternalNodes() != 5 ) {
return false;
}
t2.deleteSubtree( t2.getNode( "abc" ), false );
t2.toNewHampshireX();
if ( t2.getNumberOfExternalNodes() != 3 ) {
return false;
}
t2.deleteSubtree( t2.getNode( "def" ), false );
t2.toNewHampshireX();
if ( t2.getNumberOfExternalNodes() != 1 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testSupportCount() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
+ "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
+ "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
+ "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
+ "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
new NHXParser() );
SupportCount.count( t0_1, phylogenies_1, true, false );
final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
+ "(((((A,B),C),D),E),((F,G),X))"
+ "(((((A,Y),B),C),D),((F,G),E))"
+ "(((((A,B),C),D),E),(F,G))"
+ "(((((A,B),C),D),E),(F,G))"
+ "(((((A,B),C),D),E),(F,G))"
+ "(((((A,B),C),D),E),(F,G),Z)"
+ "(((((A,B),C),D),E),(F,G))"
+ "((((((A,B),C),D),E),F),G)"
+ "(((((X,Y),F,G),E),((A,B),C)),D)",
new NHXParser() );
SupportCount.count( t0_2, phylogenies_2, true, false );
final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
if ( !n.isExternal() && ( PhylogenyMethods.getConfidenceValue( n ) != 10 ) ) {
return false;
}
}
final Phylogeny t0_3 = factory.create( "(((A,B)ab,C)abc,((D,E)de,F)def)", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_3 = factory.create( "(((A,B),C),((D,E),F))" + "(((A,C),B),((D,F),E))"
+ "(((C,A),B),((F,D),E))" + "(((A,B),F),((D,E),C))" + "(((((A,B),C),D),E),F)", new NHXParser() );
SupportCount.count( t0_3, phylogenies_3, true, false );
t0_3.reRoot( t0_3.getNode( "def" ).getId() );
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "ab" ) ) != 3 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "abc" ) ) != 4 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "def" ) ) != 4 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "de" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "A" ) ) != 5 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "B" ) ) != 5 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "C" ) ) != 5 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "D" ) ) != 5 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "E" ) ) != 5 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_3.getNode( "F" ) ) != 5 ) {
return false;
}
final Phylogeny t0_4 = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_4 = factory.create( "((((((A,X),C),B),D),E),F) "
+ "(((A,B,Z),C,Q),(((D,Y),E),F))", new NHXParser() );
SupportCount.count( t0_4, phylogenies_4, true, false );
t0_4.reRoot( t0_4.getNode( "F" ).getId() );
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "1" ) ) != 1 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "2" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "3" ) ) != 1 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "4" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "A" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "B" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "C" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "D" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "E" ) ) != 2 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( t0_4.getNode( "F" ) ) != 2 ) {
return false;
}
Phylogeny a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
final Phylogeny b1 = factory.create( "(((((B,A)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
double d = SupportCount.compare( b1, a, true, true, true );
if ( !Test.isEqual( d, 5.0 / 5.0 ) ) {
return false;
}
a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
final Phylogeny b2 = factory.create( "(((((C,B)1,A)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
d = SupportCount.compare( b2, a, true, true, true );
if ( !Test.isEqual( d, 4.0 / 5.0 ) ) {
return false;
}
a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)", new NHXParser() )[ 0 ];
final Phylogeny b3 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)", new NHXParser() )[ 0 ];
d = SupportCount.compare( b3, a, true, true, true );
if ( !Test.isEqual( d, 2.0 / 5.0 ) ) {
return false;
}
a = factory.create( "(((((A,B)1,C)2,D)3,E)4,F)r", new NHXParser() )[ 0 ];
final Phylogeny b4 = factory.create( "(((((F,C)1,A)2,B)3,D)4,E)r", new NHXParser() )[ 0 ];
d = SupportCount.compare( b4, a, true, true, false );
if ( !Test.isEqual( d, 1.0 / 5.0 ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testSupportTransfer() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p1 = factory.create( "(((A,B)ab:97,C)abc:57,((D,E)de:10,(F,G)fg:50,(H,I)hi:64)defghi)",
new NHXParser() )[ 0 ];
final Phylogeny p2 = factory
.create( "(((A:0.1,B:0.3)ab:0.4,C)abc:0.5,((D,E)de,(F,G)fg,(H,I)hi:0.59)defghi)", new NHXParser() )[ 0 ];
if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) >= 0.0 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) >= 0.0 ) {
return false;
}
support_transfer.moveBranchLengthsToBootstrap( p1 );
support_transfer.transferSupportValues( p1, p2 );
if ( p2.getNode( "ab" ).getDistanceToParent() != 0.4 ) {
return false;
}
if ( p2.getNode( "abc" ).getDistanceToParent() != 0.5 ) {
return false;
}
if ( p2.getNode( "hi" ).getDistanceToParent() != 0.59 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "ab" ) ) != 97 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "abc" ) ) != 57 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "de" ) ) != 10 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "fg" ) ) != 50 ) {
return false;
}
if ( PhylogenyMethods.getConfidenceValue( p2.getNode( "hi" ) ) != 64 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testUniprotTaxonomySearch() {
try {
List results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
10 );
if ( results.size() != 1 ) {
return false;
}
if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
return false;
}
if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
return false;
}
if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
return false;
}
if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
return false;
}
if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
return false;
}
results = null;
results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
if ( results.size() != 1 ) {
return false;
}
if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
return false;
}
if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
return false;
}
if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
return false;
}
if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
return false;
}
if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
return false;
}
results = null;
results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
if ( results.size() != 1 ) {
return false;
}
if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
return false;
}
if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
return false;
}
if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
return false;
}
if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
return false;
}
if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
return false;
}
results = null;
results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
if ( results.size() != 1 ) {
return false;
}
if ( !results.get( 0 ).getCode().equals( "NEMVE" ) ) {
return false;
}
if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "starlet sea anemone" ) ) {
return false;
}
if ( !results.get( 0 ).getId().equalsIgnoreCase( "45351" ) ) {
return false;
}
if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
return false;
}
if ( !results.get( 0 ).getScientificName().equals( "Nematostella vectensis" ) ) {
return false;
}
if ( !results.get( 0 ).getLineage().get( 1 ).equals( "Eukaryota" ) ) {
return false;
}
if ( !results.get( 0 ).getLineage().get( 2 ).equals( "Metazoa" ) ) {
return false;
}
if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
.equals( "Nematostella vectensis" ) ) {
System.out.println( results.get( 0 ).getLineage() );
return false;
}
}
catch ( final IOException e ) {
System.out.println();
System.out.println( "the following might be due to absence internet connection:" );
e.printStackTrace( System.out );
return true;
}
catch ( final Exception e ) {
return false;
}
return true;
}
private static boolean testEmblEntryRetrieval() {
//The format for GenBank Accession numbers are:
//Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
//Protein: 3 letters + 5 numerals
//http://www.ncbi.nlm.nih.gov/Sequin/acc.html
if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
return false;
}
if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
return false;
}
if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
return false;
}
if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
return false;
}
if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
return false;
}
if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
return false;
}
return true;
}
private static boolean testUniprotEntryRetrieval() {
if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
return false;
}
if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
return false;
}
if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
return false;
}
if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
return false;
}
if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
return false;
}
if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
return false;
}
if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
return false;
}
if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
return false;
}
if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
return false;
}
if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
return false;
}
if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
return false;
}
if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
return false;
}
if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
return false;
}
try {
final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
if ( !entry.getAccession().equals( "P12345" ) ) {
return false;
}
if ( !entry.getTaxonomyScientificName().equals( "Oryctolagus cuniculus" ) ) {
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;
}
}
catch ( final IOException e ) {
System.out.println();
System.out.println( "the following might be due to absence internet connection:" );
e.printStackTrace( System.out );
return true;
}
catch ( final Exception e ) {
return false;
}
return true;
}
private static boolean testWabiTxSearch() {
try {
String result = "";
result = TxSearch.searchSimple( "nematostella" );
result = TxSearch.getTxId( "nematostella" );
if ( !result.equals( "45350" ) ) {
return false;
}
result = TxSearch.getTxName( "45350" );
if ( !result.equals( "Nematostella" ) ) {
return false;
}
result = TxSearch.getTxId( "nematostella vectensis" );
if ( !result.equals( "45351" ) ) {
return false;
}
result = TxSearch.getTxName( "45351" );
if ( !result.equals( "Nematostella vectensis" ) ) {
return false;
}
result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
if ( !result.equals( "536089" ) ) {
return false;
}
result = TxSearch.getTxName( "536089" );
if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
return false;
}
final List queries = new ArrayList();
queries.add( "Campylobacter coli" );
queries.add( "Escherichia coli" );
queries.add( "Arabidopsis" );
queries.add( "Trichoplax" );
queries.add( "Samanea saman" );
queries.add( "Kluyveromyces marxianus" );
queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
queries.add( "Bornavirus parrot/PDD/2008" );
final List ranks = new ArrayList();
ranks.add( RANKS.SUPERKINGDOM );
ranks.add( RANKS.KINGDOM );
ranks.add( RANKS.FAMILY );
ranks.add( RANKS.GENUS );
ranks.add( RANKS.TRIBE );
result = TxSearch.searchLineage( queries, ranks );
result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
}
catch ( final Exception e ) {
System.out.println();
System.out.println( "the following might be due to absence internet connection:" );
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testAminoAcidSequence() {
try {
final Sequence aa1 = BasicSequence.createAaSequence( "aa1", "aAklm-?xX*z$#" );
if ( aa1.getLength() != 13 ) {
return false;
}
if ( aa1.getResidueAt( 0 ) != 'A' ) {
return false;
}
if ( aa1.getResidueAt( 2 ) != 'K' ) {
return false;
}
if ( !new String( aa1.getMolecularSequence() ).equals( "AAKLM-XXX*ZXX" ) ) {
return false;
}
final Sequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" );
if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) {
return false;
}
final Sequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" );
if ( !new String( dna1.getMolecularSequence() ).equals( "ACGTNN*-NRYMKWSN" ) ) {
return false;
}
final Sequence rna1 = BasicSequence.createRnaSequence( "rna1", "..ACGUTX*-?RYMKWSN" );
if ( !new String( rna1.getMolecularSequence() ).equals( "--ACGUNN*-NRYMKWSN" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testCreateBalancedPhylogeny() {
try {
final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
if ( p0.getRoot().getNumberOfDescendants() != 5 ) {
return false;
}
if ( p0.getNumberOfExternalNodes() != 15625 ) {
return false;
}
final Phylogeny p1 = DevelopmentTools.createBalancedPhylogeny( 2, 10 );
if ( p1.getRoot().getNumberOfDescendants() != 10 ) {
return false;
}
if ( p1.getNumberOfExternalNodes() != 100 ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testFastaParser() {
try {
if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
return false;
}
if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
return false;
}
final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
return false;
}
if ( !msa_0.getIdentifier( 0 ).equals( "one dumb" ) ) {
return false;
}
if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) {
return false;
}
if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) {
return false;
}
if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) {
return false;
}
if ( !msa_0.getSequenceAsString( 4 ).toString().equalsIgnoreCase( "DDDDDDDDDDDDDDDDDDDDAXF" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testGeneralMsaParser() {
try {
final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) );
final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n";
final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) );
final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n";
final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) );
final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n";
final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) );
if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
return false;
}
if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
return false;
}
if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
return false;
}
if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
return false;
}
if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
return false;
}
if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
return false;
}
if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
return false;
}
if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
return false;
}
if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
return false;
}
if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) {
return false;
}
if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) {
return false;
}
if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) {
return false;
}
final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}
if ( !msa_4.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
return false;
}
if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
return false;
}
final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
return false;
}
if ( !msa_5.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixyy" ) ) {
return false;
}
if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
return false;
}
final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}
if ( !msa_6.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "efghixffffffffyy" ) ) {
return false;
}
if ( !msa_6.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
return false;
}
return true;
}
private static boolean testMafft() {
try {
final List opts = new ArrayList();
opts.add( "--maxiterate" );
opts.add( "1000" );
opts.add( "--localpair" );
opts.add( "--quiet" );
Msa msa = null;
final MsaInferrer mafft = Mafft.createInstance();
msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
return false;
}
if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
private static boolean testNextNodeWithCollapsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
PhylogenyNode n;
List ext = new ArrayList();
final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
t0.getNode( "cd" ).setCollapse( true );
t0.getNode( "cde" ).setCollapse( true );
n = t0.getFirstExternalNode();
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "g" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "h" ) ) {
return false;
}
ext.clear();
final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
t1.getNode( "ab" ).setCollapse( true );
t1.getNode( "cd" ).setCollapse( true );
t1.getNode( "cde" ).setCollapse( true );
n = t1.getNode( "ab" );
ext = new ArrayList();
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "g" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "h" ) ) {
return false;
}
//
//
ext.clear();
final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
t2.getNode( "ab" ).setCollapse( true );
t2.getNode( "cd" ).setCollapse( true );
t2.getNode( "cde" ).setCollapse( true );
t2.getNode( "c" ).setCollapse( true );
t2.getNode( "d" ).setCollapse( true );
t2.getNode( "e" ).setCollapse( true );
t2.getNode( "gh" ).setCollapse( true );
n = t2.getNode( "ab" );
ext = new ArrayList();
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
return false;
}
//
//
ext.clear();
final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
t3.getNode( "ab" ).setCollapse( true );
t3.getNode( "cd" ).setCollapse( true );
t3.getNode( "cde" ).setCollapse( true );
t3.getNode( "c" ).setCollapse( true );
t3.getNode( "d" ).setCollapse( true );
t3.getNode( "e" ).setCollapse( true );
t3.getNode( "gh" ).setCollapse( true );
t3.getNode( "fgh" ).setCollapse( true );
n = t3.getNode( "ab" );
ext = new ArrayList();
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
return false;
}
//
//
ext.clear();
final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
t4.getNode( "ab" ).setCollapse( true );
t4.getNode( "cd" ).setCollapse( true );
t4.getNode( "cde" ).setCollapse( true );
t4.getNode( "c" ).setCollapse( true );
t4.getNode( "d" ).setCollapse( true );
t4.getNode( "e" ).setCollapse( true );
t4.getNode( "gh" ).setCollapse( true );
t4.getNode( "fgh" ).setCollapse( true );
t4.getNode( "abcdefgh" ).setCollapse( true );
n = t4.getNode( "abcdefgh" );
if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
return false;
}
//
//
final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
ext.clear();
n = t5.getFirstExternalNode();
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 8 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 6 ).getName().equals( "g" ) ) {
return false;
}
if ( !ext.get( 7 ).getName().equals( "h" ) ) {
return false;
}
//
//
final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
ext.clear();
t6.getNode( "ab" ).setCollapse( true );
n = t6.getNode( "ab" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 7 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "g" ) ) {
return false;
}
if ( !ext.get( 6 ).getName().equals( "h" ) ) {
return false;
}
//
//
final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
ext.clear();
t7.getNode( "cd" ).setCollapse( true );
n = t7.getNode( "a" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 7 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "g" ) ) {
return false;
}
if ( !ext.get( 6 ).getName().equals( "h" ) ) {
return false;
}
//
//
final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
ext.clear();
t8.getNode( "cd" ).setCollapse( true );
t8.getNode( "c" ).setCollapse( true );
t8.getNode( "d" ).setCollapse( true );
n = t8.getNode( "a" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 7 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
System.out.println( "2 fail" );
return false;
}
if ( !ext.get( 3 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "g" ) ) {
return false;
}
if ( !ext.get( 6 ).getName().equals( "h" ) ) {
return false;
}
//
//
final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
ext.clear();
t9.getNode( "gh" ).setCollapse( true );
n = t9.getNode( "a" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 7 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
return false;
}
//
//
final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
ext.clear();
t10.getNode( "gh" ).setCollapse( true );
t10.getNode( "g" ).setCollapse( true );
t10.getNode( "h" ).setCollapse( true );
n = t10.getNode( "a" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 7 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "f" ) ) {
return false;
}
if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
return false;
}
//
//
final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
ext.clear();
t11.getNode( "gh" ).setCollapse( true );
t11.getNode( "fgh" ).setCollapse( true );
n = t11.getNode( "a" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 6 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
return false;
}
//
//
final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
ext.clear();
t12.getNode( "gh" ).setCollapse( true );
t12.getNode( "fgh" ).setCollapse( true );
t12.getNode( "g" ).setCollapse( true );
t12.getNode( "h" ).setCollapse( true );
t12.getNode( "f" ).setCollapse( true );
n = t12.getNode( "a" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 6 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "a" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "b" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
return false;
}
//
//
final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
ext.clear();
t13.getNode( "ab" ).setCollapse( true );
t13.getNode( "b" ).setCollapse( true );
t13.getNode( "fgh" ).setCollapse( true );
t13.getNode( "gh" ).setCollapse( true );
n = t13.getNode( "ab" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 5 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
return false;
}
//
//
final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
ext.clear();
t14.getNode( "ab" ).setCollapse( true );
t14.getNode( "a" ).setCollapse( true );
t14.getNode( "fgh" ).setCollapse( true );
t14.getNode( "gh" ).setCollapse( true );
n = t14.getNode( "ab" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 5 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
return false;
}
//
//
final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
ext.clear();
t15.getNode( "ab" ).setCollapse( true );
t15.getNode( "a" ).setCollapse( true );
t15.getNode( "fgh" ).setCollapse( true );
t15.getNode( "gh" ).setCollapse( true );
n = t15.getNode( "ab" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 6 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "c" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "d" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "e" ) ) {
return false;
}
if ( !ext.get( 4 ).getName().equals( "x" ) ) {
return false;
}
if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
return false;
}
//
//
final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
ext.clear();
t16.getNode( "ab" ).setCollapse( true );
t16.getNode( "a" ).setCollapse( true );
t16.getNode( "fgh" ).setCollapse( true );
t16.getNode( "gh" ).setCollapse( true );
t16.getNode( "cd" ).setCollapse( true );
t16.getNode( "cde" ).setCollapse( true );
t16.getNode( "d" ).setCollapse( true );
t16.getNode( "x" ).setCollapse( true );
n = t16.getNode( "ab" );
while ( n != null ) {
ext.add( n );
n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
}
if ( ext.size() != 4 ) {
return false;
}
if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
return false;
}
if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
return false;
}
if ( !ext.get( 2 ).getName().equals( "x" ) ) {
return false;
}
if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
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 List l = new ArrayList();
l.add( s0 );
l.add( s1 );
l.add( s2 );
l.add( s3 );
final Msa msa = BasicMsa.createInstance( l );
if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) {
return false;
}
if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) {
return false;
}
if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) {
return false;
}
if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
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 ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
return false;
}
//
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 ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
return false;
}
//
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 ) {
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 ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
return false;
}
//
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 ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
return false;
}
//
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 ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getProvider() );
}
return false;
}
//
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 ) {
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( "XP_12345" );
if ( id != null ) {
return false;
}
// lcl_91970_unknown_
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
return true;
}
}
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