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.regex.Pattern;
import org.forester.archaeopteryx.Constants;
+import org.forester.io.parsers.IteratingPhylogenyParser;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nhx.NHXFormatException;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.util.PhylogenyParserException;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
-public class NexusPhylogeniesParser implements PhylogenyParser {
+public final class NexusPhylogeniesParser implements IteratingPhylogenyParser, PhylogenyParser {
final private static String begin_trees = NexusConstants.BEGIN_TREES.toLowerCase();
final private static String taxlabels = NexusConstants.TAXLABELS.toLowerCase();
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 _br;
+ private boolean _in_trees_block;
+ private StringBuilder _nh;
+ 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 Phylogeny[] parse() throws IOException, NHXFormatException {
+ public final boolean hasNext() {
+ return _next != null;
+ }
+
+ @Override
+ public final Phylogeny next() throws NHXFormatException, IOException {
+ final Phylogeny phy = _next;
+ getNext();
+ return phy;
+ }
+
+ @Override
+ public final Phylogeny[] parse() throws IOException {
reset();
- final BufferedReader reader = ParserUtils.createReader( getNexusSource() );
+ final List<Phylogeny> l = new ArrayList<Phylogeny>();
+ while ( hasNext() ) {
+ l.add( next() );
+ }
+ final Phylogeny[] p = new Phylogeny[ l.size() ];
+ for( int i = 0; i < l.size(); ++i ) {
+ p[ i ] = l.get( i );
+ }
+ return p;
+ }
+
+ @Override
+ public final void reset() throws FileNotFoundException, IOException {
+ _taxlabels = new ArrayList<String>();
+ _translate_map = new HashMap<String, String>();
+ _nh = 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;
+ _br = ParserUtils.createReader( _nexus_source );
+ getNext();
+ }
+
+ public final void setIgnoreQuotes( final boolean ignore_quotes_in_nh_data ) {
+ _ignore_quotes_in_nh_data = ignore_quotes_in_nh_data;
+ }
+
+ public final void setReplaceUnderscores( final boolean replace_underscores ) {
+ _replace_underscores = replace_underscores;
+ }
+
+ @Override
+ public final 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 final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ private final 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 ( ( _taxlabels.size() < 1 ) && ( _translate_map.size() < 1 ) ) {
+ pars.setTaxonomyExtraction( _taxonomy_extraction );
+ pars.setReplaceUnderscores( _replace_underscores );
+ pars.setIgnoreQuotes( _ignore_quotes_in_nh_data );
+ }
+ 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 ( ( _taxlabels.size() > 0 ) || ( _translate_map.size() > 0 ) ) {
+ final PhylogenyNodeIterator it = p.iteratorExternalForward();
+ while ( it.hasNext() ) {
+ final PhylogenyNode node = it.next();
+ if ( ( _translate_map.size() > 0 ) && _translate_map.containsKey( node.getName() ) ) {
+ node.setName( _translate_map.get( node.getName() ).replaceAll( "['\"]+", "" ) );
+ }
+ else if ( _taxlabels.size() > 0 ) {
+ int i = -1;
+ try {
+ i = Integer.parseInt( node.getName() );
+ }
+ catch ( final NumberFormatException e ) {
+ // Ignore.
+ }
+ if ( i > 0 ) {
+ node.setName( _taxlabels.get( i - 1 ).replaceAll( "['\"]+", "" ) );
+ }
+ }
+ if ( !_replace_underscores && ( ( _taxonomy_extraction != TAXONOMY_EXTRACTION.NO ) ) ) {
+ ParserUtils.extractTaxonomyDataFromNodeName( node, _taxonomy_extraction );
+ // 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;
+ }
+
+ private final void getNext() throws IOException, NHXFormatException {
+ _next = null;
String line;
- String name = "";
- StringBuilder nhx = new StringBuilder();
- final StringBuilder translate_sb = new StringBuilder();
- boolean in_trees_block = false;
- boolean in_taxalabels = false;
- boolean in_translate = false;
- boolean in_tree = false;
- boolean rooted_info_present = false;
- boolean is_rooted = false;
- while ( ( line = reader.readLine() ) != null ) {
+ while ( ( line = _br.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;
+ _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;
+ _in_trees_block = false;
+ _in_taxalabels = true;
+ _in_translate = false;
}
else if ( line_lc.startsWith( translate ) ) {
- in_taxalabels = false;
- in_translate = true;
+ _in_taxalabels = false;
+ _in_translate = true;
}
- else if ( in_trees_block ) {
+ 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;
+ _in_trees_block = false;
+ _in_tree = false;
+ _in_translate = false;
+ if ( _nh.length() > 0 ) {
+ createPhylogeny( _name, _nh, _rooted_info_present, _is_rooted );
+ _nh = new StringBuilder();
+ _name = "";
+ _rooted_info_present = false;
+ _is_rooted = false;
+ if ( _next != null ) {
+ return;
+ }
}
}
else if ( line_lc.startsWith( tree ) || ( line_lc.startsWith( utree ) ) ) {
- if ( nhx.length() > 0 ) {
- createPhylogeny( name, nhx, rooted_info_present, is_rooted );
- nhx = new StringBuilder();
- name = "";
- rooted_info_present = false;
- is_rooted = false;
+ boolean might = false;
+ if ( _nh.length() > 0 ) {
+ might = true;
+ createPhylogeny( _name, _nh, _rooted_info_present, _is_rooted );
+ _nh = new StringBuilder();
+ _name = "";
+ _rooted_info_present = false;
+ _is_rooted = false;
}
- in_tree = true;
- nhx.append( line.substring( line.indexOf( '=' ) ) );
+ _in_tree = true;
+ _nh.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( "['\"]+", "" );
+ _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;
+ _rooted_info_present = true;
if ( s.toUpperCase().equals( "R" ) ) {
- is_rooted = true;
+ _is_rooted = true;
}
}
+ if ( might && ( _next != null ) ) {
+ return;
+ }
}
- else if ( in_tree && !in_translate ) {
- nhx.append( line );
+ else if ( _in_tree && !_in_translate ) {
+ _nh.append( line );
}
- if ( !line_lc.startsWith( "title" ) && !line_lc.startsWith( "link" ) && !in_translate
+ 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;
+ _in_tree = false;
+ _in_translate = false;
+ createPhylogeny( _name, _nh, _rooted_info_present, _is_rooted );
+ _nh = new StringBuilder();
+ _name = "";
+ _rooted_info_present = false;
+ _is_rooted = false;
+ if ( _next != null ) {
+ return;
+ }
}
}
- if ( in_taxalabels ) {
+ if ( _in_taxalabels ) {
if ( line_lc.startsWith( end ) || line_lc.startsWith( endblock ) ) {
- in_taxalabels = false;
+ _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;
+ _in_taxalabels = false;
label = label.substring( 0, label.length() - 1 );
}
if ( label.length() > 0 ) {
- getTaxlabels().add( label );
+ _taxlabels.add( label );
}
}
}
}
}
- if ( in_translate ) {
+ if ( _in_translate ) {
if ( line_lc.startsWith( end ) || line_lc.startsWith( endblock ) ) {
- in_translate = false;
+ _in_translate = false;
}
else {
- translate_sb.append( " " );
- translate_sb.append( line.trim() );
+ _translate_sb.append( " " );
+ _translate_sb.append( line.trim() );
if ( line.endsWith( ";" ) ) {
- in_translate = false;
- setTranslateKeyValuePairs( translate_sb );
+ _in_translate = false;
+ setTranslateKeyValuePairs( _translate_sb );
}
}
}
}
}
- if ( nhx.length() > 0 ) {
- createPhylogeny( name, nhx, rooted_info_present, is_rooted );
- }
- return getPhylogeniesAsArray();
- }
-
- 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;
- }
-
- @Override
- public void setSource( final Object nexus_source ) throws PhylogenyParserException, IOException {
- if ( nexus_source == null ) {
- throw new PhylogenyParserException( getClass() + ": attempt to parse null object." );
- }
- _nexus_source = nexus_source;
- }
-
- 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 {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- 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 );
- }
- final Phylogeny p = factory.create( nhx, pars )[ 0 ];
- 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 );
- // }
- }
+ if ( _nh.length() > 0 ) {
+ createPhylogeny( _name, _nh, _rooted_info_present, _is_rooted );
+ if ( _next != null ) {
+ return;
}
}
- getPhylogenies().add( p );
- }
-
- 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 reset() {
- 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 {
+ private final 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();
if ( value.endsWith( ";" ) ) {
value = value.substring( 0, value.length() - 1 );
}
- getTranslateMap().put( key, value );
+ _translate_map.put( key, value );
}
}
- private void setTranslateMap( final Map<String, String> translate_map ) {
- _translate_map = translate_map;
- }
-
- private static String removeWhiteSpaceBeforeSemicolon( final String s ) {
+ private final static String removeWhiteSpaceBeforeSemicolon( final String s ) {
return s.replaceAll( "\\s+;", ";" );
}
}
+++ /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+;", ";" );
- }
-}
git://source.jalview.org / jalview.git / commitdiff