--- /dev/null
+// $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: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.io.parsers.nexus;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.forester.archaeopteryx.Constants;
+import org.forester.io.parsers.IteratingPhylogenyParser;
+import org.forester.io.parsers.nhx.NHXFormatException;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.io.parsers.util.PhylogenyParserException;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.ForesterUtil;
+
+public class NexusPhylogeniesParser2 implements IteratingPhylogenyParser {
+
+ final private static String begin_trees = NexusConstants.BEGIN_TREES.toLowerCase();
+ final private static String taxlabels = NexusConstants.TAXLABELS.toLowerCase();
+ final private static String translate = NexusConstants.TRANSLATE.toLowerCase();
+ final private static String tree = NexusConstants.TREE.toLowerCase();
+ final private static String utree = NexusConstants.UTREE.toLowerCase();
+ final private static String end = NexusConstants.END.toLowerCase();
+ final private static String endblock = "endblock";
+ final private static Pattern TREE_NAME_PATTERN = Pattern.compile( "\\s*.?Tree\\s+(.+?)\\s*=.+",
+ Pattern.CASE_INSENSITIVE );
+ final private static Pattern ROOTEDNESS_PATTERN = Pattern.compile( ".+=\\s*\\[&([R|U])\\].*" );
+ private Object _nexus_source;
+ private List<Phylogeny> _phylogenies;
+ private List<String> _taxlabels;
+ private Map<String, String> _translate_map;
+ private boolean _replace_underscores = NHXParser.REPLACE_UNDERSCORES_DEFAULT;
+ private boolean _ignore_quotes_in_nh_data = Constants.NH_PARSING_IGNORE_QUOTES_DEFAULT;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction = NHXParser.TAXONOMY_EXTRACTION_DEFAULT;
+ private Phylogeny _next;
+ private BufferedReader reader;
+ private boolean in_trees_block;
+ private StringBuilder nhx;
+ private String name;
+ private StringBuilder translate_sb;
+ private boolean in_taxalabels;
+ private boolean in_translate;
+ private boolean is_rooted;
+ private boolean rooted_info_present;
+ private boolean in_tree;
+
+ @Override
+ public final void reset() throws FileNotFoundException, IOException {
+ setPhylogenies( new ArrayList<Phylogeny>() );
+ setTaxlabels( new ArrayList<String>() );
+ setTranslateMap( new HashMap<String, String>() );
+ nhx = new StringBuilder();
+ name = "";
+ translate_sb = new StringBuilder();
+ _next = null;
+ in_trees_block = false;
+ in_taxalabels = false;
+ in_translate = false;
+ in_tree = false;
+ rooted_info_present = false;
+ is_rooted = false;
+ reader = ParserUtils.createReader( getNexusSource() );
+ getNext();
+ }
+
+ private final void getNext() throws IOException, NHXFormatException {
+ _next = null;
+ String line;
+ while ( ( line = reader.readLine() ) != null ) {
+ line = line.trim();
+ if ( ( line.length() > 0 ) && !line.startsWith( "#" ) && !line.startsWith( ">" ) ) {
+ line = ForesterUtil.collapseWhiteSpace( line );
+ line = removeWhiteSpaceBeforeSemicolon( line );
+ final String line_lc = line.toLowerCase();
+ if ( line_lc.startsWith( begin_trees ) ) {
+ in_trees_block = true;
+ in_taxalabels = false;
+ in_translate = false;
+ }
+ else if ( line_lc.startsWith( taxlabels ) ) {
+ in_trees_block = false;
+ in_taxalabels = true;
+ in_translate = false;
+ }
+ else if ( line_lc.startsWith( translate ) ) {
+ in_taxalabels = false;
+ in_translate = true;
+ }
+ else if ( in_trees_block ) {
+ //FIXME TODO need to work on this "title" and "link"
+ if ( line_lc.startsWith( "title" ) || line_lc.startsWith( "link" ) ) {
+ // Do nothing.
+ }
+ else if ( line_lc.startsWith( end ) || line_lc.startsWith( endblock ) ) {
+ in_trees_block = false;
+ in_tree = false;
+ in_translate = false;
+ if ( nhx.length() > 0 ) {
+ createPhylogeny( name, nhx, rooted_info_present, is_rooted );
+ nhx = new StringBuilder();
+ name = "";
+ rooted_info_present = false;
+ is_rooted = false;
+ if ( _next != null ) {
+ return;
+ }
+ }
+ }
+ else if ( line_lc.startsWith( tree ) || ( line_lc.startsWith( utree ) ) ) {
+ boolean might = false;
+ if ( nhx.length() > 0 ) {
+ might = true;
+ createPhylogeny( name, nhx, rooted_info_present, is_rooted );
+ nhx = new StringBuilder();
+ name = "";
+ rooted_info_present = false;
+ is_rooted = false;
+ }
+ in_tree = true;
+ nhx.append( line.substring( line.indexOf( '=' ) ) );
+ final Matcher name_matcher = TREE_NAME_PATTERN.matcher( line );
+ if ( name_matcher.matches() ) {
+ name = name_matcher.group( 1 );
+ name = name.replaceAll( "['\"]+", "" );
+ }
+ final Matcher rootedness_matcher = ROOTEDNESS_PATTERN.matcher( line );
+ if ( rootedness_matcher.matches() ) {
+ final String s = rootedness_matcher.group( 1 );
+ line = line.replaceAll( "\\[\\&.\\]", "" );
+ rooted_info_present = true;
+ if ( s.toUpperCase().equals( "R" ) ) {
+ is_rooted = true;
+ }
+ }
+ if ( might && ( _next != null ) ) {
+ return;
+ }
+ }
+ else if ( in_tree && !in_translate ) {
+ nhx.append( line );
+ }
+ if ( !line_lc.startsWith( "title" ) && !line_lc.startsWith( "link" ) && !in_translate
+ && !line_lc.startsWith( end ) && !line_lc.startsWith( endblock ) && line_lc.endsWith( ";" ) ) {
+ in_tree = false;
+ in_translate = false;
+ createPhylogeny( name, nhx, rooted_info_present, is_rooted );
+ nhx = new StringBuilder();
+ name = "";
+ rooted_info_present = false;
+ is_rooted = false;
+ if ( _next != null ) {
+ return;
+ }
+ }
+ }
+ if ( in_taxalabels ) {
+ if ( line_lc.startsWith( end ) || line_lc.startsWith( endblock ) ) {
+ in_taxalabels = false;
+ }
+ else {
+ final String[] labels = line.split( "\\s+" );
+ for( String label : labels ) {
+ if ( !label.toLowerCase().equals( taxlabels ) ) {
+ if ( label.endsWith( ";" ) ) {
+ in_taxalabels = false;
+ label = label.substring( 0, label.length() - 1 );
+ }
+ if ( label.length() > 0 ) {
+ getTaxlabels().add( label );
+ }
+ }
+ }
+ }
+ }
+ if ( in_translate ) {
+ if ( line_lc.startsWith( end ) || line_lc.startsWith( endblock ) ) {
+ in_translate = false;
+ }
+ else {
+ translate_sb.append( " " );
+ translate_sb.append( line.trim() );
+ if ( line.endsWith( ";" ) ) {
+ in_translate = false;
+ setTranslateKeyValuePairs( translate_sb );
+ }
+ }
+ }
+ }
+ }
+ if ( nhx.length() > 0 ) {
+ createPhylogeny( name, nhx, rooted_info_present, is_rooted );
+ if ( _next != null ) {
+ return;
+ }
+ }
+ }
+
+ public void setIgnoreQuotes( final boolean ignore_quotes_in_nh_data ) {
+ _ignore_quotes_in_nh_data = ignore_quotes_in_nh_data;
+ }
+
+ public void setReplaceUnderscores( final boolean replace_underscores ) {
+ _replace_underscores = replace_underscores;
+ }
+
+ public void setSource( final Object nexus_source ) throws PhylogenyParserException, IOException {
+ if ( nexus_source == null ) {
+ throw new PhylogenyParserException( "attempt to parse null object" );
+ }
+ _nexus_source = nexus_source;
+ reset();
+ }
+
+ public void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ private void createPhylogeny( final String name,
+ final StringBuilder nhx,
+ final boolean rooted_info_present,
+ final boolean is_rooted ) throws IOException {
+ _next = null;
+ final NHXParser pars = new NHXParser();
+ if ( ( getTaxlabels().size() < 1 ) && ( getTranslateMap().size() < 1 ) ) {
+ pars.setTaxonomyExtraction( getTaxonomyExtraction() );
+ pars.setReplaceUnderscores( isReplaceUnderscores() );
+ pars.setIgnoreQuotes( isIgnoreQuotes() );
+ }
+ else {
+ pars.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ pars.setReplaceUnderscores( false );
+ pars.setIgnoreQuotes( false );
+ }
+ if ( rooted_info_present ) {
+ pars.setGuessRootedness( false );
+ }
+ pars.setSource( nhx );
+ final Phylogeny p = pars.next();
+ if ( p == null ) {
+ throw new PhylogenyParserException( "failed to create phylogeny" );
+ }
+ p.setName( name );
+ if ( rooted_info_present ) {
+ p.setRooted( is_rooted );
+ }
+ if ( ( getTaxlabels().size() > 0 ) || ( getTranslateMap().size() > 0 ) ) {
+ final PhylogenyNodeIterator it = p.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final PhylogenyNode node = it.next();
+ if ( ( getTranslateMap().size() > 0 ) && getTranslateMap().containsKey( node.getName() ) ) {
+ node.setName( getTranslateMap().get( node.getName() ).replaceAll( "['\"]+", "" ) );
+ }
+ else if ( getTaxlabels().size() > 0 ) {
+ int i = -1;
+ try {
+ i = Integer.parseInt( node.getName() );
+ }
+ catch ( final NumberFormatException e ) {
+ // Ignore.
+ }
+ if ( i > 0 ) {
+ node.setName( getTaxlabels().get( i - 1 ).replaceAll( "['\"]+", "" ) );
+ }
+ }
+ if ( !isReplaceUnderscores() && ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) ) {
+ ParserUtils.extractTaxonomyDataFromNodeName( node, getTaxonomyExtraction() );
+ // final String tax = ParserUtils.extractTaxonomyCodeFromNodeName( node.getName(),
+ // getTaxonomyExtraction() );
+ // if ( !ForesterUtil.isEmpty( tax ) ) {
+ // if ( !node.getNodeData().isHasTaxonomy() ) {
+ // node.getNodeData().setTaxonomy( new Taxonomy() );
+ // }
+ // node.getNodeData().getTaxonomy().setTaxonomyCode( tax );
+ // }
+ }
+ }
+ }
+ _next = p;
+ }
+
+ @Override
+ public final boolean hasNext() {
+ return _next != null;
+ }
+
+ @Override
+ public final Phylogeny next() throws NHXFormatException, IOException {
+ final Phylogeny phy = _next;
+ getNext();
+ return phy;
+ }
+
+ private Object getNexusSource() {
+ return _nexus_source;
+ }
+
+ private List<Phylogeny> getPhylogenies() {
+ return _phylogenies;
+ }
+
+ private Phylogeny[] getPhylogeniesAsArray() {
+ final Phylogeny[] p = new Phylogeny[ getPhylogenies().size() ];
+ for( int i = 0; i < getPhylogenies().size(); ++i ) {
+ p[ i ] = getPhylogenies().get( i );
+ }
+ return p;
+ }
+
+ private List<String> getTaxlabels() {
+ return _taxlabels;
+ }
+
+ private TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
+ }
+
+ private Map<String, String> getTranslateMap() {
+ return _translate_map;
+ }
+
+ private boolean isIgnoreQuotes() {
+ return _ignore_quotes_in_nh_data;
+ }
+
+ private boolean isReplaceUnderscores() {
+ return _replace_underscores;
+ }
+
+ private void init() {
+ setPhylogenies( new ArrayList<Phylogeny>() );
+ setTaxlabels( new ArrayList<String>() );
+ setTranslateMap( new HashMap<String, String>() );
+ }
+
+ private void setPhylogenies( final ArrayList<Phylogeny> phylogenies ) {
+ _phylogenies = phylogenies;
+ }
+
+ private void setTaxlabels( final List<String> taxlabels ) {
+ _taxlabels = taxlabels;
+ }
+
+ private void setTranslateKeyValuePairs( final StringBuilder translate_sb ) throws IOException {
+ String s = translate_sb.toString().trim();
+ if ( s.endsWith( ";" ) ) {
+ s = s.substring( 0, s.length() - 1 ).trim();
+ }
+ for( final String pair : s.split( "," ) ) {
+ final String[] kv = pair.trim().split( "\\s+" );
+ if ( ( kv.length < 2 ) || ( kv.length > 3 ) ) {
+ throw new IOException( "ill-formatted translate values: " + translate_sb );
+ }
+ if ( ( kv.length == 3 ) && !kv[ 0 ].toLowerCase().trim().equals( translate ) ) {
+ throw new IOException( "ill-formatted translate values: " + translate_sb );
+ }
+ String key = "";
+ String value = "";
+ if ( kv.length == 3 ) {
+ key = kv[ 1 ];
+ value = kv[ 2 ];
+ }
+ else {
+ key = kv[ 0 ];
+ value = kv[ 1 ];
+ }
+ if ( value.endsWith( ";" ) ) {
+ value = value.substring( 0, value.length() - 1 );
+ }
+ getTranslateMap().put( key, value );
+ }
+ }
+
+ private void setTranslateMap( final Map<String, String> translate_map ) {
+ _translate_map = translate_map;
+ }
+
+ private static String removeWhiteSpaceBeforeSemicolon( final String s ) {
+ return s.replaceAll( "\\s+;", ";" );
+ }
+}
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.nexus.NexusPhylogeniesParser2;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
System.exit( -1 );
}
final long start_time = new Date().getTime();
+ System.out.print( "Nexus tree parsing iterating: " );
+ if ( Test.testNexusTreeParsingIterating() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.exit( 0 );
System.out.print( "Sequence id parsing: " );
if ( testSequenceIdParsing() ) {
System.out.println( "OK." );
return true;
}
+ private static boolean testNexusTreeParsingIterating() {
+ try {
+ final NexusPhylogeniesParser2 p = new NexusPhylogeniesParser2();
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ Phylogeny phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 25 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 25 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "name" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "name" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
+ // if ( phylogenies.length != 18 ) {
+ // return false;
+ // }
+ //0
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 0" ) ) {
+ return false;
+ }
+ //1
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 1" ) ) {
+ return false;
+ }
+ //2
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //3
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 4 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //4
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 5 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //5
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //6
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 2 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //7
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //8
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 8" ) ) {
+ return false;
+ }
+ //9
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 9" ) ) {
+ return false;
+ }
+ //10
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 10" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //11
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 11" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //12
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 12" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //13
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 13" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //14
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 14" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //15
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 15" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //16
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 16" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //17
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 17" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ p.reset();
+ //0
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 0" ) ) {
+ return false;
+ }
+ //1
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 1" ) ) {
+ return false;
+ }
+ //2
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //3
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 4 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //4
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 5 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //5
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testNexusTreeParsingTranslating() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
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