// 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
+// Copyright (C) 2014 Christian M. Zmasek
+// Copyright (C) 2014 Sanford-Burnham Medical Research Institute
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// 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: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.io.StringWriter;
+import java.io.Writer;
import java.net.URL;
import java.util.ArrayList;
import java.util.Date;
import org.forester.application.support_transfer;
import org.forester.archaeopteryx.TreePanelUtil;
+import org.forester.archaeopteryx.webservices.WebserviceUtil;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.io.writers.SequenceWriter;
import org.forester.msa.BasicMsa;
+import org.forester.msa.DeleteableMsa;
import org.forester.msa.Mafft;
import org.forester.msa.Msa;
+import org.forester.msa.Msa.MSA_FORMAT;
import org.forester.msa.MsaInferrer;
import org.forester.msa.MsaMethods;
import org.forester.pccx.TestPccx;
+ ForesterUtil.getFileSeparator() + "test_data"
+ ForesterUtil.getFileSeparator();
private final static boolean PERFORM_DB_TESTS = false;
+ private static final boolean PERFORM_WEB_TREE_ACCESS = true;
private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
+ ForesterConstants.PHYLO_XML_VERSION + "/"
+ ForesterConstants.PHYLO_XML_XSD;
System.out.println( "failed." );
failed++;
}
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Ebi Entry Retrieval: " );
- if ( Test.testEbiEntryRetrieval() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- }
- // System.exit( 0 );
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Sequence DB tools 2: " );
- if ( testSequenceDbWsTools2() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- System.exit( -1 );
- }
- }
- // System.exit( 0 );
System.out.print( "Hmmscan output parser: " );
if ( testHmmscanOutputParser() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- //
System.out.print( "Overlap removal: " );
if ( !org.forester.test.Test.testOverlapRemoval() ) {
System.out.println( "failed." );
succeeded++;
}
System.out.println( "OK." );
- //
System.out.print( "Taxonomy code extraction: " );
if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Uniprot Entry Retrieval: " );
- if ( Test.testUniprotEntryRetrieval() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- }
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Uniprot Taxonomy Search: " );
- if ( Test.testUniprotTaxonomySearch() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- }
- //----
String path = "";
final String os = ForesterUtil.OS_NAME.toLowerCase();
if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
path = "C:\\Program Files\\mafft-win\\mafft.bat";
}
else {
- path = "/home/czmasek/bin/mafft";
- }
- if ( !MsaInferrer.isInstalled( path ) ) {
path = "mafft";
- }
- if ( !MsaInferrer.isInstalled( path ) ) {
- path = "/usr/local/bin/mafft";
- }
- if ( !MsaInferrer.isInstalled( path ) ) {
- path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft";
+ if ( !MsaInferrer.isInstalled( path ) ) {
+ path = "/usr/bin/mafft";
+ }
+ if ( !MsaInferrer.isInstalled( path ) ) {
+ path = "/usr/local/bin/mafft";
+ }
}
if ( MsaInferrer.isInstalled( path ) ) {
System.out.print( "MAFFT (external program): " );
System.out.println( "failed [will not count towards failed tests]" );
}
}
- //----
System.out.print( "Next nodes with collapsed: " );
if ( Test.testNextNodeWithCollapsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- System.out.print( "NHX parsing from URL: " );
- if ( Test.testNHXparsingFromURL() ) {
+ System.out.print( "Deleteable MSA: " );
+ if ( Test.testDeleteableMsa() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "phyloXML parsing from URL: " );
- if ( Test.testPhyloXMLparsingFromURL() ) {
- System.out.println( "OK." );
- succeeded++;
+ if ( PERFORM_DB_TESTS ) {
+ System.out.print( "Uniprot Entry Retrieval: " );
+ if ( Test.testUniprotEntryRetrieval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Ebi Entry Retrieval: " );
+ if ( Test.testEbiEntryRetrieval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Sequence DB tools 2: " );
+ if ( testSequenceDbWsTools2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ System.exit( -1 );
+ }
+ System.out.print( "Uniprot Taxonomy Search: " );
+ if ( Test.testUniprotTaxonomySearch() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
}
- else {
- System.out.println( "failed." );
- failed++;
+ if ( PERFORM_WEB_TREE_ACCESS ) {
+ System.out.print( "NHX parsing from URL: " );
+ if ( Test.testNHXparsingFromURL() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "phyloXML parsing from URL: " );
+ if ( Test.testPhyloXMLparsingFromURL() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "TreeBase acccess: " );
+ if ( Test.testTreeBaseReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ System.out.print( "ToL access: " );
+ if ( Test.testToLReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ System.out.print( "TreeFam access: " );
+ if ( Test.testTreeFamReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ //
+ //
+ System.out.print( "Pfam tree access: " );
+ if ( Test.testPfamTreeReading() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
}
System.out.println();
final Runtime rt = java.lang.Runtime.getRuntime();
return true;
}
- public static final boolean testPhyloXMLparsingFromURL() {
- try {
- final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
- final URL u = new URL( s );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
- if ( ( phys == null ) || ( phys.length != 2 ) ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace();
- }
- return true;
- }
-
public static final boolean testNHXparsingFromURL() {
try {
final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
final URL u = new URL( s );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny[] phys = factory.create( u, new NHXParser() );
- if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ if ( ( phys == null ) || ( phys.length != 5 ) ) {
return false;
}
- if ( !phys[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
+ if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
System.out.println( phys[ 0 ].toNewHampshire() );
return false;
}
+ if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ System.out.println( phys[ 1 ].toNewHampshire() );
+ return false;
+ }
final Phylogeny[] phys2 = factory.create( u.openStream(), new NHXParser() );
- if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
+ if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
return false;
}
- if ( !phys2[ 0 ].toNewHampshire().equals( "((a,b),c);" ) ) {
+ if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
System.out.println( phys2[ 0 ].toNewHampshire() );
return false;
}
if ( !p.hasNext() ) {
return false;
}
- if ( !p.next().toNewHampshire().equals( "((a,b),c);" ) ) {
- return false;
- }
- if ( p.hasNext() ) {
- return false;
- }
- if ( p.next() != null ) {
- return false;
- }
- if ( p.hasNext() ) {
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
return false;
}
- if ( p.next() != null ) {
+ if ( !p.hasNext() ) {
return false;
}
p.reset();
if ( !p.hasNext() ) {
return false;
}
- if ( !p.next().toNewHampshire().equals( "((a,b),c);" ) ) {
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
return false;
}
- if ( p.hasNext() ) {
- return false;
- }
- if ( p.next() != null ) {
+ if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
return false;
}
- if ( p.hasNext() ) {
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- if ( p.next() != null ) {
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
return false;
}
- p.reset();
- if ( !p.hasNext() ) {
+ if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
return false;
}
}
return true;
}
+ public static final boolean testPfamTreeReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
+ final NHXParser parser = new NHXParser();
+ parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ parser.setReplaceUnderscores( false );
+ parser.setGuessRootedness( true );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testPhyloXMLparsingFromURL() {
+ try {
+ final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
+ final URL u = new URL( s );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
+ if ( ( phys == null ) || ( phys.length != 2 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testToLReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "15079" ) ) {
+ return false;
+ }
+ if ( !phys[ 0 ].getRoot().getNodeData().getTaxonomy().getScientificName().equals( "Protacanthopterygii" ) ) {
+ return false;
+ }
+ if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testTreeBaseReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
+ final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
+ parser.setReplaceUnderscores( true );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
+ final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
+ parser2.setReplaceUnderscores( true );
+ final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
+ if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public static final boolean testTreeFamReading() {
+ try {
+ final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
+ final NHXParser parser = new NHXParser();
+ parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
+ parser.setReplaceUnderscores( false );
+ parser.setGuessRootedness( true );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ if ( ( phys == null ) || ( phys.length != 1 ) ) {
+ return false;
+ }
+ if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
return p;
if ( t4.getNumberOfExternalNodes() != 5 ) {
return false;
}
- String s = w.toNewHampshire( t4, false, true ).toString();
+ String s = w.toNewHampshire( t4, true ).toString();
if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
return false;
}
if ( !n.getName().equals( "D" ) ) {
return false;
}
- s = w.toNewHampshire( t4, false, true ).toString();
+ s = w.toNewHampshire( t4, true ).toString();
if ( !s.equals( "((A,B12),D);" ) ) {
return false;
}
if ( t5.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t5, false, true ).toString();
+ s = w.toNewHampshire( t5, true ).toString();
if ( !s.equals( "(((B11,B12),B2),(C,D));" ) ) {
return false;
}
if ( t6.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t6, false, false ).toString();
+ s = w.toNewHampshire( t6, false ).toString();
if ( !s.equals( "((A,(B12,B2)),(C,D));" ) ) {
return false;
}
if ( t7.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t7, false, true ).toString();
+ s = w.toNewHampshire( t7, true ).toString();
if ( !s.equals( "((A,(B11,B2)),(C,D));" ) ) {
return false;
}
if ( t8.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t8, false, false ).toString();
+ s = w.toNewHampshire( t8, false ).toString();
if ( !s.equals( "((A,(B11,B12)),(C,D));" ) ) {
return false;
}
if ( t9.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t9, false, true ).toString();
+ s = w.toNewHampshire( t9, true ).toString();
if ( !s.equals( "((A,((B11,B12),B2)),D);" ) ) {
return false;
}
if ( t10.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t10, false, true ).toString();
+ s = w.toNewHampshire( t10, true ).toString();
if ( !s.equals( "((A,((B11,B12),B2)),C);" ) ) {
return false;
}
if ( t11.getNumberOfExternalNodes() != 2 ) {
return false;
}
- s = w.toNewHampshire( t11, false, true ).toString();
+ s = w.toNewHampshire( t11, true ).toString();
if ( !s.equals( "(B,C);" ) ) {
return false;
}
if ( t11.getNumberOfExternalNodes() != 1 ) {
return false;
}
- s = w.toNewHampshire( t11, false, false ).toString();
+ s = w.toNewHampshire( t11, false ).toString();
if ( !s.equals( "B;" ) ) {
return false;
}
if ( t12.getNumberOfExternalNodes() != 8 ) {
return false;
}
- s = w.toNewHampshire( t12, false, true ).toString();
+ s = w.toNewHampshire( t12, true ).toString();
if ( !s.equals( "((A1,A2,A3),(B1,B3),(C1,C2,C3));" ) ) {
return false;
}
if ( t12.getNumberOfExternalNodes() != 7 ) {
return false;
}
- s = w.toNewHampshire( t12, false, true ).toString();
+ s = w.toNewHampshire( t12, true ).toString();
if ( !s.equals( "((A1,A2,A3),B1,(C1,C2,C3));" ) ) {
return false;
}
if ( t12.getNumberOfExternalNodes() != 6 ) {
return false;
}
- s = w.toNewHampshire( t12, false, true ).toString();
+ s = w.toNewHampshire( t12, true ).toString();
if ( !s.equals( "((A1,A2,A3),B1,(C1,C2));" ) ) {
return false;
}
if ( t12.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t12, false, true ).toString();
+ s = w.toNewHampshire( t12, true ).toString();
if ( !s.equals( "((A2,A3),B1,(C1,C2));" ) ) {
return false;
}
if ( t12.getNumberOfExternalNodes() != 4 ) {
return false;
}
- s = w.toNewHampshire( t12, false, true ).toString();
+ s = w.toNewHampshire( t12, true ).toString();
if ( !s.equals( "((A2,A3),(C1,C2));" ) ) {
return false;
}
if ( t12.getNumberOfExternalNodes() != 3 ) {
return false;
}
- s = w.toNewHampshire( t12, false, true ).toString();
+ s = w.toNewHampshire( t12, true ).toString();
if ( !s.equals( "(A2,(C1,C2));" ) ) {
return false;
}
if ( t12.getNumberOfExternalNodes() != 2 ) {
return false;
}
- s = w.toNewHampshire( t12, false, true ).toString();
+ s = w.toNewHampshire( t12, true ).toString();
if ( !s.equals( "(C1,C2);" ) ) {
return false;
}
if ( t13.getNumberOfExternalNodes() != 4 ) {
return false;
}
- s = w.toNewHampshire( t13, false, true ).toString();
+ s = w.toNewHampshire( t13, true ).toString();
if ( !s.equals( "(A,B,C,E:5.0);" ) ) {
return false;
}
if ( t14.getNumberOfExternalNodes() != 5 ) {
return false;
}
- s = w.toNewHampshire( t14, false, true ).toString();
+ s = w.toNewHampshire( t14, true ).toString();
if ( !s.equals( "((A,B,C,D:1.1),F);" ) ) {
return false;
}
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" ) ) {
+ 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();
+ }
+ final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
+ final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
+ if ( !iter.next().getName().equals( "A" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "B" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "C" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "D" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "E" ) ) {
+ return false;
+ }
+ if ( !iter.next().getName().equals( "F" ) ) {
+ return false;
+ }
+ if ( iter.hasNext() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testExtractSNFromNodeName() {
+ try {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCDO2" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus musculus BCDO2" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_BCDO2" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2 Mus musculus musculus" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Bcl Mus musculus musculus" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( ParserUtils.extractScientificNameFromNodeName( "vcl Mus musculus musculus" ) != null ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_BCDO2" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_Musculus" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( ParserUtils.extractScientificNameFromNodeName( "could_be_anything_Mus_musculus_musculus_musculus" ) != null ) {
+ return false;
+ }
+ if ( ParserUtils.extractScientificNameFromNodeName( "musculus" ) != null ) {
+ return false;
+ }
+ if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus" ) != null ) {
+ return false;
+ }
+ if ( ParserUtils.extractScientificNameFromNodeName( "mus_musculus_musculus" ) != null ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_1" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_1" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_bcl" ) != null ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_BCL" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( ParserUtils.extractScientificNameFromNodeName( "Mus musculus bcl" ) != null ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus BCL" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus xBCL" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus musculus x1" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus_12" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12 affrre e" )
+ .equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus_12_affrre_e" )
+ .equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_2bcl2" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_musculus_bcl2" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Mus_musculus_123" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Pilostyles mexicana Mexico Breedlove 27233" )
+ .equals( "Pilostyles mexicana" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_strain_K12/DH10B" )
+ .equals( "Escherichia coli strain K12/DH10B" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K12/DH10B" )
+ .equals( "Escherichia coli str. K12/DH10B" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K12/DH10B" )
+ .equals( "Escherichia coli str. K12/DH10B" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis_lyrata_subsp_lyrata" )
+ .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata" )
+ .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata 395" )
+ .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp. lyrata bcl2" )
+ .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subsp lyrata bcl2" )
+ .equals( "Arabidopsis lyrata subsp. lyrata" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Arabidopsis lyrata subspecies lyrata bcl2" )
+ .equals( "Arabidopsis lyrata subspecies lyrata" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Verbascum sinuatum var. adenosepalum bcl2" )
+ .equals( "Verbascum sinuatum var. adenosepalum" ) ) {
return false;
}
- n = n.getNextExternalNode();
- if ( !n.getName().equals( "C" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12)" )
+ .equals( "Escherichia coli (strain K12)" ) ) {
return false;
}
- n = n.getNextExternalNode();
- if ( !n.getName().equals( "D" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (strain K12) bcl2" )
+ .equals( "Escherichia coli (strain K12)" ) ) {
return false;
}
- n = n.getNextExternalNode();
- if ( !n.getName().equals( "E" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12)" )
+ .equals( "Escherichia coli (str. K12)" ) ) {
return false;
}
- n = n.getNextExternalNode();
- if ( !n.getName().equals( "F" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str K12)" )
+ .equals( "Escherichia coli (str. K12)" ) ) {
return false;
}
- n = n.getNextExternalNode();
- if ( !n.getName().equals( "G" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (str. K12) bcl2" )
+ .equals( "Escherichia coli (str. K12)" ) ) {
return false;
}
- n = n.getNextExternalNode();
- if ( !n.getName().equals( "H" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli (var K12) bcl2" )
+ .equals( "Escherichia coli (var. K12)" ) ) {
return false;
}
- n = t3.getNode( "B" );
- while ( !n.isLastExternalNode() ) {
- n = n.getNextExternalNode();
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str. K-12 substr. MG1655star" )
+ .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
+ return false;
}
- 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();
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star" )
+ .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
+ return false;
}
- 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();
+ if ( !ParserUtils
+ .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star" )
+ .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
+ return false;
}
- final Phylogeny t6 = factory.create( "((((((A))),(((B))),((C)),((((D)))),E)),((F)))", new NHXParser() )[ 0 ];
- final PhylogenyNodeIterator iter = t6.iteratorExternalForward();
- if ( !iter.next().getName().equals( "A" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia coli str K-12 substr MG1655star gene1" )
+ .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
return false;
}
- if ( !iter.next().getName().equals( "B" ) ) {
+ if ( !ParserUtils
+ .extractScientificNameFromNodeName( "could be anything Escherichia coli str K-12 substr MG1655star GENE1" )
+ .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
return false;
}
- if ( !iter.next().getName().equals( "C" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
+ .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
return false;
}
- if ( !iter.next().getName().equals( "D" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Escherichia_coli_str_K-12_substr_MG1655star" )
+ .equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
return false;
}
- if ( !iter.next().getName().equals( "E" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
return false;
}
- if ( !iter.next().getName().equals( "F" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. 123" ).equals( "Macrocera sp." ) ) {
return false;
}
- if ( iter.hasNext() ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp. K12" ).equals( "Macrocera sp." ) ) {
return false;
}
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
- private static boolean testExtractSNFromNodeName() {
- try {
- if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "something Macrocera sp. K12" )
+ .equals( "Macrocera sp." ) ) {
return false;
}
- if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" )
- .equals( "Mus musculus musculus" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
return false;
}
- if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" )
- .equals( "Mus musculus musculus" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
+ .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
return false;
}
- if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
+ .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
return false;
}
- if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" )
- .equals( "Mus musculus" ) ) {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" )
+ .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" )
+ .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
return false;
}
}
private static boolean testMsaQualityMethod() {
try {
- final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
- final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
- final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
- final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
+ final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
+ final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
+ final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
+ final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
final List<Sequence> l = new ArrayList<Sequence>();
l.add( s0 );
l.add( s1 );
if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
return false;
}
+ if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testDeleteableMsa() {
+ try {
+ final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
+ final Sequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
+ final Sequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
+ final Sequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
+ final Sequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
+ final Sequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
+ final List<Sequence> l0 = new ArrayList<Sequence>();
+ l0.add( s0 );
+ l0.add( s1 );
+ l0.add( s2 );
+ l0.add( s3 );
+ l0.add( s4 );
+ l0.add( s5 );
+ final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
+ dmsa0.deleteRow( "b" );
+ if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
+ return false;
+ }
+ dmsa0.deleteRow( "e" );
+ dmsa0.deleteRow( "a" );
+ dmsa0.deleteRow( "f" );
+ if ( dmsa0.getLength() != 4 ) {
+ return false;
+ }
+ if ( dmsa0.getNumberOfSequences() != 2 ) {
+ return false;
+ }
+ if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
+ return false;
+ }
+ if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
+ return false;
+ }
+ if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) {
+ return false;
+ }
+ if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) {
+ return false;
+ }
+ if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
+ return false;
+ }
+ dmsa0.deleteRow( "c" );
+ dmsa0.deleteRow( "d" );
+ if ( dmsa0.getNumberOfSequences() != 0 ) {
+ return false;
+ }
+ //
+ final Sequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
+ final Sequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
+ final Sequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
+ final Sequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
+ final Sequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
+ final Sequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
+ final List<Sequence> l1 = new ArrayList<Sequence>();
+ l1.add( s_0 );
+ l1.add( s_1 );
+ l1.add( s_2 );
+ l1.add( s_3 );
+ l1.add( s_4 );
+ l1.add( s_5 );
+ final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
+ dmsa1.deleteGapOnlyColumns();
+ dmsa1.deleteRow( "a" );
+ dmsa1.deleteRow( "f" );
+ dmsa1.deleteRow( "d" );
+ dmsa1.deleteGapOnlyColumns();
+ if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
+ return false;
+ }
+ if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) {
+ return false;
+ }
+ if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
+ return false;
+ }
+ dmsa1.deleteRow( "c" );
+ dmsa1.deleteGapOnlyColumns();
+ final Writer w0 = new StringWriter();
+ dmsa1.write( w0, MSA_FORMAT.FASTA );
+ final Writer w1 = new StringWriter();
+ dmsa1.write( w1, MSA_FORMAT.PHYLIP );
+ if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
+ return false;
+ }
+ if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
+ return false;
+ }
+ //
+ final Sequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
+ final Sequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
+ final Sequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
+ final Sequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
+ final Sequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
+ final Sequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
+ final List<Sequence> l2 = new ArrayList<Sequence>();
+ l2.add( s__0 );
+ l2.add( s__1 );
+ l2.add( s__2 );
+ l2.add( s__3 );
+ l2.add( s__4 );
+ l2.add( s__5 );
+ final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
+ dmsa2.deleteGapColumns( 0.5 );
+ if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
+ return false;
+ }
+ dmsa2.deleteGapColumns( 0.2 );
+ if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
+ return false;
+ }
+ dmsa2.deleteGapColumns( 0 );
+ dmsa2.deleteRow( "a" );
+ dmsa2.deleteRow( "b" );
+ dmsa2.deleteRow( "f" );
+ dmsa2.deleteRow( "e" );
+ dmsa2.setIdentifier( 0, "new_c" );
+ dmsa2.setIdentifier( 1, "new_d" );
+ dmsa2.setResidueAt( 0, 0, 'x' );
+ dmsa2.deleteRow( "new_d" );
+ final Writer w = new StringWriter();
+ dmsa2.write( w, MSA_FORMAT.PHYLIP );
+ final String phylip = w.toString();
+ if ( !phylip.equals( "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
+ return false;
+ }
+ final Writer w2 = new StringWriter();
+ dmsa2.write( w2, MSA_FORMAT.FASTA );
+ final String fasta = w2.toString();
+ if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
if ( phylogenies[ 17 ].getNumberOfExternalNodes() != 10 ) {
return false;
}
+ final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
+ phylogenies = null;
+ phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S15613.nex", p2 );
+ if ( phylogenies.length != 9 ) {
+ return false;
+ }
+ if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
+ .getDistanceToParent() ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
+ .getDistanceToParent() ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getName().equals( "Family Diadocidiidae BAT (con_50_majrule)" ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.065284, phylogenies[ 7 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.065284, phylogenies[ 8 ].getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
if ( phy != null ) {
return false;
}
- ////
+ //
p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
if ( !p.hasNext() ) {
return false;
if ( phy != null ) {
return false;
}
- ////
+ //
p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
- // if ( phylogenies.length != 18 ) {
- // return false;
- // }
- //0
if ( !p.hasNext() ) {
return false;
}
+ //0
phy = p.next();
if ( phy == null ) {
return false;
return false;
}
if ( phy.getNumberOfExternalNodes() != 3 ) {
+ System.out.println( phy.toString() );
return false;
}
if ( !phy.getName().equals( "" ) ) {
if ( phy.isRooted() ) {
return false;
}
+ //
+ final NexusPhylogeniesParser p2 = new NexusPhylogeniesParser();
+ p2.setSource( Test.PATH_TO_TEST_DATA + "S15613.nex" );
+ // 0
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
+ return false;
+ }
+ // 1
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ // 2
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ // 3
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ // 4
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ // 5
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ // 6
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ // 7
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ // 8
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ if ( !isEqual( 0.065284, phy.getNode( "Bradysia_amoena" ).getDistanceToParent() ) ) {
+ return false;
+ }
+ if ( p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ if ( phy != null ) {
+ return false;
+ }
+ // 0
+ p2.reset();
+ if ( !p2.hasNext() ) {
+ return false;
+ }
+ phy = p2.next();
+ if ( !isEqual( 0.48039661496919533, phy.getNode( "Diadocidia_spinosula" ).getDistanceToParent() ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.3959796191512233, phy.getNode( "Diadocidia_stanfordensis" ).getDistanceToParent() ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
.equals( "Aranaeus" ) ) {
return false;
}
+ phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
+ if ( phylogenies.length != 3 ) {
+ return false;
+ }
+ if ( !isEqual( phylogenies[ 2 ].getNode( "Aloysia lycioides 251-76-02169" ).getDistanceToParent(),
+ 0.00100049 ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
nhxp.setReplaceUnderscores( true );
final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
- if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
+ if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A" ) ) {
return false;
}
- if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
+ if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( "B B" ) ) {
return false;
}
final Phylogeny p1b = factory
if ( p50.getNode( "A" ) == null ) {
return false;
}
- if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ if ( !p50.toNewHampshire( 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);" ) ) {
+ if ( !p50.toNewHampshire( 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 )
+ if ( !p50.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
.equals( "((A,B)88:2.0,C);" ) ) {
return false;
}
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);" ) ) {
+ if ( !p54.toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ).equals( "((A,B)[88],C);" ) ) {
+ return false;
+ }
+ final Phylogeny p55 = factory
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ),
+ new NHXParser() )[ 0 ];
+ if ( !p55
+ .toNewHampshire()
+ .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,lcl|HPV66_L1.1x:0.0798012);" ) ) {
+ System.out.println( p55.toNewHampshire() );
+ return false;
+ }
+ final Phylogeny p56 = factory
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+ new NHXParser() )[ 0 ];
+ if ( !p56
+ .toNewHampshire()
+ .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
+ System.out.println( p56.toNewHampshire() );
+ return false;
+ }
+ final Phylogeny p57 = factory
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+ new NHXParser() )[ 0 ];
+ if ( !p57
+ .toNewHampshire()
+ .equals( "(('lcl|HPV32_L1.:1 s':0.195593,'lcl|HPV30_L1.1|;a':0.114237):0.0359322,'lcl|HPV56_L1.1|,d':0.0727412,'lcl|HPV66_L1.1:x':0.0798012);" ) ) {
+ System.out.println( p56.toNewHampshire() );
+ return false;
+ }
+ final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
+ final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
+ if ( !p58.toNewHampshire().equals( s58 ) ) {
+ System.out.println( p58.toNewHampshire() );
+ return false;
+ }
+ final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
+ final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
+ if ( !p59.toNewHampshire().equals( s59 ) ) {
+ System.out.println( p59.toNewHampshire() );
+ return false;
+ }
+ final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
+ final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
+ if ( !p60.toNewHampshire().equals( s60 ) ) {
+ System.out.println( p60.toNewHampshire() );
+ return false;
+ }
+ final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
+ final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
+ if ( !p61.toNewHampshire()
+ .equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
+ System.out.println( p61.toNewHampshire() );
return false;
}
}
System.out.println( n6.toNewHampshireX() );
return false;
}
+ final PhylogenyNode n7 = new PhylogenyNode();
+ n7.setName( " gks:dr-m4 \" ' `@:[]sadq04 " );
+ if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
+ System.out.println( n7
+ .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
final PhylogenyNode n13 = PhylogenyNode
- .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
- if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
+ .createInstanceFromNhxString( "BLAH_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n13.getName().equals( "BLAH_12345/1-2" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) {
return false;
}
final PhylogenyNode n19 = PhylogenyNode
- .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAH_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
return false;
}
return false;
}
final PhylogenyNode n30 = PhylogenyNode
- .createInstanceFromNhxString( "blah_1234567-roejojoej",
+ .createInstanceFromNhxString( "BLAH_1234567-roejojoej",
NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
return false;
return false;
}
final PhylogenyNode n31 = PhylogenyNode
- .createInstanceFromNhxString( "blah_12345678-roejojoej",
+ .createInstanceFromNhxString( "BLAH_12345678-roejojoej",
NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n31.getNodeData().isHasTaxonomy() ) {
return false;
return false;
}
final PhylogenyNode n40 = PhylogenyNode
- .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BCL2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
return false;
}
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;
}
+ final Phylogeny p11 = 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 ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
if ( phy.getNodes( "'single quotes' inside double quotes" ).size() != 1 ) {
return false;
}
- if ( phy.getNodes( "double quotes inside single quotes" ).size() != 1 ) {
+ 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 ) {
+ if ( phy.getNodes( "A ( B C '" ).size() != 1 ) {
return false;
}
final NHXParser p1p = new NHXParser();
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]";
+ 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;
}
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]";
+ 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;
}
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;";
+ 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;
}
return false;
}
final PhylogenyNode n3 = PhylogenyNode
- .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n3.toString() );
return false;
return false;
}
final PhylogenyNode n6 = PhylogenyNode
- .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n6.getNodeData().isHasTaxonomy() ) {
System.out.println( n6.toString() );
return false;
}
final PhylogenyNode n7 = PhylogenyNode
- .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n7.getNodeData().isHasTaxonomy() ) {
System.out.println( n7.toString() );
return false;
}
final PhylogenyNode n8 = PhylogenyNode
- .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n8.toString() );
return false;
}
final PhylogenyNode n9 = PhylogenyNode
- .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n9.toString() );
return false;
}
final PhylogenyNode n10x = PhylogenyNode
- .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n10x.getNodeData().isHasTaxonomy() ) {
System.out.println( n10x.toString() );
return false;
}
final PhylogenyNode n10xx = PhylogenyNode
- .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n10xx.getNodeData().isHasTaxonomy() ) {
System.out.println( n10xx.toString() );
return false;
}
final PhylogenyNode n10 = PhylogenyNode
- .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
System.out.println( n10.toString() );
return false;
System.out.println( n13.toString() );
return false;
}
+ final PhylogenyNode n14 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n14.toString() );
+ return false;
+ }
+ final PhylogenyNode n15 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n15.toString() );
+ return false;
+ }
+ final PhylogenyNode n16 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n16.toString() );
+ return false;
+ }
+ final PhylogenyNode n17 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n17.toString() );
+ return false;
+ }
+ //
+ final PhylogenyNode n18 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n18.toString() );
+ return false;
+ }
+ final PhylogenyNode n19 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n19.toString() );
+ return false;
+ }
+ final PhylogenyNode n20 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n20.toString() );
+ return false;
+ }
+ final PhylogenyNode n21 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus musculus K392",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n21.toString() );
+ return false;
+ }
+ final PhylogenyNode n22 = PhylogenyNode
+ .createInstanceFromNhxString( "NEMVE_Nematostella_vectensis",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n22.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
+ System.out.println( n22.toString() );
+ return false;
+ }
+ final PhylogenyNode n23 = PhylogenyNode
+ .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
+ System.out.println( n23.toString() );
+ return false;
+ }
+ final PhylogenyNode n24 = PhylogenyNode
+ .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
+ System.out.println( n24.toString() );
+ return false;
+ }
+ //
+ final PhylogenyNode n25 = PhylogenyNode
+ .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
+ System.out.println( n25.toString() );
+ return false;
+ }
+ final PhylogenyNode n26 = PhylogenyNode
+ .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
+ System.out.println( n26.toString() );
+ return false;
+ }
+ final PhylogenyNode n27 = PhylogenyNode
+ .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
+ System.out.println( n27.toString() );
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
git://source.jalview.org / jalview.git / blobdiff