-// $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.nhx;
-
-import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
-import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
-import org.forester.io.parsers.util.ParserUtils;
-import org.forester.io.parsers.util.PhylogenyParserException;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Accession;
-import org.forester.phylogeny.data.Confidence;
-import org.forester.phylogeny.data.DomainArchitecture;
-import org.forester.phylogeny.data.Event;
-import org.forester.phylogeny.data.Identifier;
-import org.forester.phylogeny.data.PhylogenyDataUtil;
-import org.forester.phylogeny.data.Sequence;
-import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.ForesterUtil;
-
-public final class NHXParser2 implements PhylogenyParser {
-
- public static final TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT = TAXONOMY_EXTRACTION.NO;
- final static private boolean GUESS_ROOTEDNESS_DEFAULT = true;
- final static private boolean GUESS_IF_SUPPORT_VALUES = true;
- final static private boolean IGNORE_QUOTES_DEFAULT = false;
- final static public boolean REPLACE_UNDERSCORES_DEFAULT = false;
- private boolean _saw_closing_paren;
- final static private byte STRING = 0;
- final static private byte STRING_BUFFER = 1;
- final static private byte CHAR_ARRAY = 2;
- final static private byte BUFFERED_READER = 3;
- final static private byte STRING_BUILDER = 4;
- private boolean _guess_rootedness;
- private boolean _ignore_quotes;
- private byte _input_type;
- private int _source_length;
- private PhylogenyNode _current_node;
- private StringBuilder _current_anotation;
- private Object _nhx_source;
- private int _clade_level;
- private Phylogeny _current_phylogeny;
- private TAXONOMY_EXTRACTION _taxonomy_extraction;
- private boolean _replace_underscores;
- public final static Pattern UC_LETTERS_NUMBERS_PATTERN = Pattern.compile( "^[A-Z0-9]+$" );
- public final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" );
- public final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([^,]+)" );
- public final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob_stddev=([^,]+)" );
- public final static Pattern MB_BL_PATTERN = Pattern.compile( "length_median=([^,]+)" );
- boolean _in_comment = false;
- boolean _saw_colon = false;
- boolean _saw_open_bracket = false;
- boolean _in_open_bracket = false;
- boolean _in_double_quote = false;
- boolean _in_single_quote = false;
- String _my_source_str = null;
- StringBuffer _my_source_sbuff = null;
- StringBuilder _my_source_sbuil = null;
- char[] _my_source_charary = null;
- BufferedReader _my_source_br = null;
- int _i;
- private Phylogeny _next;
- private Object _source;
-
- public NHXParser2() {
- init();
- }
-
- public TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
- }
-
- public boolean hasNext() {
- return _next != null;
- }
-
- public Phylogeny next() throws NHXFormatException, IOException {
- final Phylogeny phy = _next;
- getNext();
- return phy;
- }
-
- @Override
- public Phylogeny[] parse() throws IOException {
- reset();
- List<Phylogeny> l = new ArrayList<Phylogeny>();
- System.out.println( ">> _next=" + _next );
- while ( hasNext() ) {
- Phylogeny n = next();
- System.out.println( ">> going to add " + n );
- l.add( n );
- }
- final Phylogeny[] p = new Phylogeny[ l.size() ];
- for( int i = 0; i < l.size(); ++i ) {
- p[ i ] = l.get( i );
- }
- return p;
- }
-
- public void reset() throws NHXFormatException, IOException {
- _i = 0;
- _next = null;
- _in_comment = false;
- _saw_colon = false;
- _saw_open_bracket = false;
- _in_open_bracket = false;
- _in_double_quote = false;
- _in_single_quote = false;
- setCladeLevel( 0 );
- newCurrentAnotation();
- setCurrentPhylogeny( null );
- setCurrentNode( null );
- _my_source_str = null;
- _my_source_sbuff = null;
- _my_source_sbuil = null;
- _my_source_charary = null;
- _my_source_br = null;
- determineSourceType( _source );
- switch ( getInputType() ) {
- case STRING:
- _my_source_str = ( String ) getNhxSource();
- break;
- case STRING_BUFFER:
- _my_source_sbuff = ( StringBuffer ) getNhxSource();
- break;
- case STRING_BUILDER:
- _my_source_sbuil = ( StringBuilder ) getNhxSource();
- break;
- case CHAR_ARRAY:
- _my_source_charary = ( char[] ) getNhxSource();
- break;
- case BUFFERED_READER:
- if ( _my_source_br != null ) {
- try {
- _my_source_br.close();
- }
- catch ( IOException e ) {
- //do nothing
- }
- }
- _my_source_br = ( BufferedReader ) getNhxSource();
- break;
- default:
- throw new RuntimeException( "unknown input type" );
- }
- getNext();
- }
-
- public void setGuessRootedness( final boolean guess_rootedness ) {
- _guess_rootedness = guess_rootedness;
- }
-
- public void setIgnoreQuotes( final boolean ignore_quotes ) {
- _ignore_quotes = ignore_quotes;
- }
-
- public void setReplaceUnderscores( final boolean replace_underscores ) {
- _replace_underscores = replace_underscores;
- }
-
- /**
- * This sets the source to be parsed. The source can be: String,
- * StringBuffer, char[], File, or InputStream. The source can contain more
- * than one phylogenies in either New Hamphshire (NH) or New Hamphshire
- * Extended (NHX) format. There is no need to separate phylogenies with any
- * special character. White space is always ignored, as are semicolons
- * inbetween phylogenies. Example of a source describing two phylogenies
- * (source is a String, in this example): "(A,(B,(C,(D,E)de)cde)bcde)abcde
- * ((((A,B)ab,C)abc,D)abcd,E)abcde". Everything between a '[' followed by any
- * character other than '&' and ']' is considered a comment and ignored
- * (example: "[this is a comment]"). NHX tags are surrounded by '[&&NHX' and
- * ']' (example: "[&&NHX:S=Varanus_storri]"). A sequence like "[& some
- * info]" is ignored, too (at the PhylogenyNode level, though).
- * Exception: numbers only between [ and ] (e.g. [90]) are interpreted as support values.
- *
- * @see #parse()
- * @see org.forester.io.parsers.PhylogenyParser#setSource(java.lang.Object)
- * @param nhx_source
- * the source to be parsed (String, StringBuffer, char[], File,
- * or InputStream)
- * @throws NHXFormatException
- * @throws IOException
- * @throws PhylogenyParserException
- */
- @Override
- public void setSource( final Object nhx_source ) throws NHXFormatException, IOException {
- _source = nhx_source;
- reset();
- }
-
- private void determineSourceType( final Object nhx_source ) throws PhylogenyParserException, FileNotFoundException {
- if ( nhx_source == null ) {
- throw new PhylogenyParserException( getClass() + ": attempt to parse null object." );
- }
- else if ( nhx_source instanceof String ) {
- setInputType( NHXParser2.STRING );
- setSourceLength( ( ( String ) nhx_source ).length() );
- setNhxSource( nhx_source );
- }
- else if ( nhx_source instanceof StringBuilder ) {
- setInputType( NHXParser2.STRING_BUILDER );
- setSourceLength( ( ( StringBuilder ) nhx_source ).length() );
- setNhxSource( nhx_source );
- }
- else if ( nhx_source instanceof StringBuffer ) {
- setInputType( NHXParser2.STRING_BUFFER );
- setSourceLength( ( ( StringBuffer ) nhx_source ).length() );
- setNhxSource( nhx_source );
- }
- else if ( nhx_source instanceof StringBuilder ) {
- setInputType( NHXParser2.STRING_BUILDER );
- setSourceLength( ( ( StringBuilder ) nhx_source ).length() );
- setNhxSource( nhx_source );
- }
- else if ( nhx_source instanceof char[] ) {
- setInputType( NHXParser2.CHAR_ARRAY );
- setSourceLength( ( ( char[] ) nhx_source ).length );
- setNhxSource( nhx_source );
- }
- else if ( nhx_source instanceof File ) {
- setInputType( NHXParser2.BUFFERED_READER );
- setSourceLength( 0 );
- final File f = ( File ) nhx_source;
- final String error = ForesterUtil.isReadableFile( f );
- if ( !ForesterUtil.isEmpty( error ) ) {
- throw new PhylogenyParserException( error );
- }
- setNhxSource( new BufferedReader( new FileReader( f ) ) );
- }
- else if ( nhx_source instanceof InputStream ) {
- setInputType( NHXParser2.BUFFERED_READER );
- setSourceLength( 0 );
- final InputStreamReader isr = new InputStreamReader( ( InputStream ) nhx_source );
- setNhxSource( new BufferedReader( isr ) );
- }
- else {
- throw new IllegalArgumentException( getClass() + " can only parse objects of type String,"
- + " StringBuffer, StringBuilder, char[], File," + " or InputStream "
- + " [attempt to parse object of " + nhx_source.getClass() + "]." );
- }
- }
-
- public void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;
- }
-
- /**
- * Decreases the clade level by one.
- *
- * @throws PhylogenyParserException
- * if level goes below zero.
- */
- private void decreaseCladeLevel() throws PhylogenyParserException {
- if ( getCladeLevel() < 0 ) {
- throw new PhylogenyParserException( "error in NH (Newick)/NHX formatted data: most likely cause: number of close parens is larger than number of open parens" );
- }
- --_clade_level;
- }
-
- private Phylogeny finishPhylogeny2() throws PhylogenyParserException, NHXFormatException,
- PhyloXmlDataFormatException {
- //setCladeLevel( 0 );
- if ( getCurrentPhylogeny() != null ) {
- System.out.println( "fp: cp=" + getCurrentPhylogeny() );
- if ( getCurrentAnotation() != null ) {
- System.out.println( "fp: ca=" + getCurrentAnotation().toString() );
- }
- else {
- System.out.println( "fp: ca=null" );
- }
- parseNHX( getCurrentAnotation() != null ? getCurrentAnotation().toString() : "", getCurrentPhylogeny()
- .getRoot(), getTaxonomyExtraction(), isReplaceUnderscores() );
- if ( GUESS_IF_SUPPORT_VALUES ) {
- if ( isBranchLengthsLikeBootstrapValues( getCurrentPhylogeny() ) ) {
- moveBranchLengthsToConfidenceValues( getCurrentPhylogeny() );
- }
- }
- if ( isGuessRootedness() ) {
- final PhylogenyNode root = getCurrentPhylogeny().getRoot();
- if ( ( root.getDistanceToParent() >= 0.0 ) || !ForesterUtil.isEmpty( root.getName() )
- || !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( root ) ) || root.isHasAssignedEvent() ) {
- getCurrentPhylogeny().setRooted( true );
- }
- }
- return getCurrentPhylogeny();
- }
- return null;
- }
-
- private Phylogeny finishSingleNodePhylogeny2() throws PhylogenyParserException, NHXFormatException,
- PhyloXmlDataFormatException {
- // setCladeLevel( 0 );
- final PhylogenyNode new_node = new PhylogenyNode();
- parseNHX( getCurrentAnotation().toString(), new_node, getTaxonomyExtraction(), isReplaceUnderscores() );
- setCurrentPhylogeny( new Phylogeny() );
- getCurrentPhylogeny().setRoot( new_node );
- return getCurrentPhylogeny();
- }
-
- private int getCladeLevel() {
- return _clade_level;
- }
-
- private StringBuilder getCurrentAnotation() {
- return _current_anotation;
- }
-
- private PhylogenyNode getCurrentNode() {
- return _current_node;
- }
-
- private Phylogeny getCurrentPhylogeny() {
- return _current_phylogeny;
- }
-
- private byte getInputType() {
- return _input_type;
- }
-
- private void getNext() throws IOException, NHXFormatException {
- while ( true ) {
- char c = '\b';
- if ( getInputType() == BUFFERED_READER ) {
- final int ci = _my_source_br.read();
- if ( ci >= 0 ) {
- c = ( char ) ci;
- }
- else {
- break;
- }
- }
- else {
- if ( _i >= getSourceLength() ) {
- break;
- }
- else {
- switch ( getInputType() ) {
- case STRING:
- c = _my_source_str.charAt( _i );
- break;
- case STRING_BUFFER:
- c = _my_source_sbuff.charAt( _i );
- break;
- case STRING_BUILDER:
- c = _my_source_sbuil.charAt( _i );
- break;
- case CHAR_ARRAY:
- c = _my_source_charary[ _i ];
- break;
- }
- }
- }
- if ( !_in_single_quote && !_in_double_quote ) {
- if ( c == ':' ) {
- _saw_colon = true;
- }
- else if ( !( ( c < 33 ) || ( c > 126 ) ) && _saw_colon
- && ( ( c != '[' ) && ( c != '.' ) && ( ( c < 48 ) || ( c > 57 ) ) ) ) {
- _saw_colon = false;
- }
- if ( _in_open_bracket && ( c == ']' ) ) {
- _in_open_bracket = false;
- }
- }
- // \n\t is always ignored,
- // as is " (34) and ' (39) (space is 32):
- if ( ( isIgnoreQuotes() && ( ( c < 33 ) || ( c > 126 ) || ( c == 34 ) || ( c == 39 ) || ( ( getCladeLevel() == 0 ) && ( c == ';' ) ) ) )
- || ( !isIgnoreQuotes() && ( ( c < 32 ) || ( c > 126 ) || ( ( getCladeLevel() == 0 ) && ( c == ';' ) ) ) ) ) {
- // Do nothing.
- }
- else if ( ( c == 32 ) && ( !_in_single_quote && !_in_double_quote ) ) {
- // Do nothing.
- }
- else if ( _in_comment ) {
- if ( c == ']' ) {
- _in_comment = false;
- }
- }
- else if ( _in_double_quote ) {
- if ( c == '"' ) {
- _in_double_quote = false;
- }
- else {
- getCurrentAnotation().append( c );
- }
- }
- else if ( c == '"' ) {
- _in_double_quote = true;
- }
- else if ( _in_single_quote ) {
- if ( c == 39 ) {
- _in_single_quote = false;
- }
- else {
- getCurrentAnotation().append( c );
- }
- }
- else if ( c == 39 ) {
- _in_single_quote = true;
- }
- else if ( c == '[' ) {
- _saw_open_bracket = true;
- _in_open_bracket = true;
- }
- else if ( _saw_open_bracket ) {
- if ( c != ']' ) {
- // everything not starting with "[&" is considered a comment
- // unless ":digits and/or . [bootstrap]":
- if ( c == '&' ) {
- getCurrentAnotation().append( "[&" );
- }
- else if ( _saw_colon ) {
- getCurrentAnotation().append( "[" + c );
- }
- else {
- _in_comment = true;
- }
- }
- // comment consisting just of "[]":
- _saw_open_bracket = false;
- }
- else if ( ( c == '(' ) && !_in_open_bracket ) {
- final Phylogeny phy = processOpenParen2();
- if ( phy != null ) {
- ++_i;
- // return phy;
- _next = phy;
- return;
- }
- }
- else if ( ( c == ')' ) && !_in_open_bracket ) {
- processCloseParen();
- }
- else if ( ( c == ',' ) && !_in_open_bracket ) {
- processComma();
- }
- else {
- getCurrentAnotation().append( c );
- }
- ++_i;
- } // while ( true )
- System.out.println( "done with loop" );
- if ( getCurrentPhylogeny() == null ) {
- System.out.println( "... but is null" );
- }
- if ( getCladeLevel() != 0 ) {
- throw new PhylogenyParserException( "error in NH (Newick) formatted data: most likely cause: number of open parens does not equal number of close parens" );
- }
- if ( getCurrentPhylogeny() != null ) {
- System.out.println( "... and current=" + getCurrentPhylogeny() );
- _next = finishPhylogeny2();
- System.out.println( "... _next=" + _next );
- setCurrentPhylogeny( null );
- setCurrentAnotation( null );
- //return finishPhylogeny2();
- }
- else if ( ( getCurrentAnotation() != null ) && ( getCurrentAnotation().length() > 0 ) ) {
- System.out.println( "1node=" + getCurrentAnotation() );
- _next = finishSingleNodePhylogeny2();
- setCurrentAnotation( null );
- //return finishSingleNodePhylogeny2();
- }
- else {
- _next = null;
- //return null;
- }
- }
-
- private Object getNhxSource() {
- return _nhx_source;
- }
-
- private int getSourceLength() {
- return _source_length;
- }
-
- private void increaseCladeLevel() {
- ++_clade_level;
- }
-
- private void init() {
- setTaxonomyExtraction( TAXONOMY_EXTRACTION_DEFAULT );
- setReplaceUnderscores( REPLACE_UNDERSCORES_DEFAULT );
- setGuessRootedness( GUESS_ROOTEDNESS_DEFAULT );
- setIgnoreQuotes( IGNORE_QUOTES_DEFAULT );
- }
-
- private boolean isGuessRootedness() {
- return _guess_rootedness;
- }
-
- private boolean isIgnoreQuotes() {
- return _ignore_quotes;
- }
-
- private boolean isReplaceUnderscores() {
- return _replace_underscores;
- }
-
- private boolean isSawClosingParen() {
- return _saw_closing_paren;
- }
-
- /**
- * Replaces the current annotation with a new StringBuffer.
- */
- private void newCurrentAnotation() {
- setCurrentAnotation( new StringBuilder() );
- }
-
- /**
- * Called if a closing paren is encountered.
- *
- * @throws PhylogenyParserException
- * @throws NHXFormatException
- * @throws PhyloXmlDataFormatException
- */
- private void processCloseParen() throws PhylogenyParserException, NHXFormatException, PhyloXmlDataFormatException {
- decreaseCladeLevel();
- if ( !isSawClosingParen() ) {
- final PhylogenyNode new_node = new PhylogenyNode();
- parseNHX( getCurrentAnotation().toString(), new_node, getTaxonomyExtraction(), isReplaceUnderscores() );
- newCurrentAnotation();
- getCurrentNode().addAsChild( new_node );
- }
- else {
- parseNHX( getCurrentAnotation().toString(),
- getCurrentNode().getLastChildNode(),
- getTaxonomyExtraction(),
- isReplaceUnderscores() );
- newCurrentAnotation();
- }
- if ( !getCurrentNode().isRoot() ) {
- setCurrentNode( getCurrentNode().getParent() );
- }
- setSawClosingParen( true );
- }
-
- /**
- * Called if a comma is encountered.
- *
- * @throws PhylogenyParserException
- * @throws NHXFormatException
- * @throws PhyloXmlDataFormatException
- */
- private void processComma() throws PhylogenyParserException, NHXFormatException, PhyloXmlDataFormatException {
- if ( !isSawClosingParen() ) {
- final PhylogenyNode new_node = new PhylogenyNode();
- parseNHX( getCurrentAnotation().toString(), new_node, getTaxonomyExtraction(), isReplaceUnderscores() );
- if ( getCurrentNode() == null ) {
- throw new NHXFormatException( "format might not be NH or NHX" );
- }
- getCurrentNode().addAsChild( new_node );
- }
- else {
- parseNHX( getCurrentAnotation().toString(),
- getCurrentNode().getLastChildNode(),
- getTaxonomyExtraction(),
- isReplaceUnderscores() );
- }
- newCurrentAnotation();
- setSawClosingParen( false );
- }
-
- private Phylogeny processOpenParen2() throws PhylogenyParserException, NHXFormatException,
- PhyloXmlDataFormatException {
- Phylogeny phy = null;
- final PhylogenyNode new_node = new PhylogenyNode();
- System.out.println( "level=" + getCladeLevel() );
- if ( getCladeLevel() == 0 ) {
- if ( getCurrentPhylogeny() != null ) {
- phy = finishPhylogeny2();
- }
- setCladeLevel( 1 );
- newCurrentAnotation();
- setCurrentPhylogeny( new Phylogeny() );
- getCurrentPhylogeny().setRoot( new_node );
- }
- else {
- increaseCladeLevel();
- getCurrentNode().addAsChild( new_node );
- }
- setCurrentNode( new_node );
- setSawClosingParen( false );
- if ( phy != null ) {
- System.out.println( "processOpenParen2 returns " + phy.toString() );
- }
- else {
- System.out.println( "processOpenParen2 returns null" );
- }
- return phy;
- }
-
- private void setCladeLevel( final int clade_level ) {
- if ( clade_level < 0 ) {
- throw new IllegalArgumentException( "attempt to set clade level to a number smaller than zero" );
- }
- _clade_level = clade_level;
- }
-
- private void setCurrentAnotation( final StringBuilder current_anotation ) {
- _current_anotation = current_anotation;
- }
-
- private void setCurrentNode( final PhylogenyNode current_node ) {
- _current_node = current_node;
- }
-
- private void setCurrentPhylogeny( final Phylogeny current_phylogeny ) {
- _current_phylogeny = current_phylogeny;
- }
-
- private void setInputType( final byte input_type ) {
- _input_type = input_type;
- }
-
- private void setNhxSource( final Object nhx_source ) {
- _nhx_source = nhx_source;
- }
-
- private void setSawClosingParen( final boolean saw_closing_paren ) {
- _saw_closing_paren = saw_closing_paren;
- }
-
- private void setSourceLength( final int source_length ) {
- _source_length = source_length;
- }
-
- public static void parseNHX( String s,
- final PhylogenyNode node_to_annotate,
- final TAXONOMY_EXTRACTION taxonomy_extraction,
- final boolean replace_underscores ) throws NHXFormatException,
- PhyloXmlDataFormatException {
- if ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.NO ) && replace_underscores ) {
- throw new IllegalArgumentException( "cannot extract taxonomies and replace under scores at the same time" );
- }
- if ( ( s != null ) && ( s.length() > 0 ) ) {
- if ( replace_underscores ) {
- s = s.replaceAll( "_+", " " );
- }
- boolean is_nhx = false;
- final int ob = s.indexOf( "[" );
- if ( ob > -1 ) {
- String b = "";
- is_nhx = true;
- final int cb = s.indexOf( "]" );
- if ( cb < 0 ) {
- throw new NHXFormatException( "error in NHX formatted data: no closing \"]\" in \"" + s + "\"" );
- }
- if ( s.indexOf( "&&NHX" ) == ( ob + 1 ) ) {
- b = s.substring( ob + 6, cb );
- }
- else {
- // No &&NHX and digits only: is likely to be a support value.
- final String bracketed = s.substring( ob + 1, cb );
- final Matcher numbers_only = NUMBERS_ONLY_PATTERN.matcher( bracketed );
- if ( numbers_only.matches() ) {
- b = ":" + NHXtags.SUPPORT + bracketed;
- }
- else if ( s.indexOf( "prob=" ) > -1 ) {
- processMrBayes3Data( s, node_to_annotate );
- }
- }
- s = s.substring( 0, ob ) + b;
- if ( ( s.indexOf( "[" ) > -1 ) || ( s.indexOf( "]" ) > -1 ) ) {
- throw new NHXFormatException( "error in NHX formatted data: more than one \"]\" or \"[\"" );
- }
- }
- final StringTokenizer t = new StringTokenizer( s, ":" );
- if ( t.countTokens() > 0 ) {
- if ( !s.startsWith( ":" ) ) {
- node_to_annotate.setName( t.nextToken() );
- if ( !replace_underscores && ( !is_nhx && ( taxonomy_extraction != TAXONOMY_EXTRACTION.NO ) ) ) {
- ParserUtils.extractTaxonomyDataFromNodeName( node_to_annotate, taxonomy_extraction );
- }
- }
- while ( t.hasMoreTokens() ) {
- s = t.nextToken();
- if ( s.startsWith( org.forester.io.parsers.nhx.NHXtags.SPECIES_NAME ) ) {
- if ( !node_to_annotate.getNodeData().isHasTaxonomy() ) {
- node_to_annotate.getNodeData().setTaxonomy( new Taxonomy() );
- }
- node_to_annotate.getNodeData().getTaxonomy().setScientificName( s.substring( 2 ) );
- }
- else if ( s.startsWith( org.forester.io.parsers.nhx.NHXtags.IS_DUPLICATION ) ) {
- if ( ( s.charAt( 2 ) == 'Y' ) || ( s.charAt( 2 ) == 'T' ) ) {
- node_to_annotate.getNodeData().setEvent( Event.createSingleDuplicationEvent() );
- }
- else if ( ( s.charAt( 2 ) == 'N' ) || ( s.charAt( 2 ) == 'F' ) ) {
- node_to_annotate.getNodeData().setEvent( Event.createSingleSpeciationEvent() );
- }
- else if ( s.charAt( 2 ) == '?' ) {
- node_to_annotate.getNodeData().setEvent( Event.createSingleSpeciationOrDuplicationEvent() );
- }
- else {
- throw new NHXFormatException( "error in NHX formatted data: :D=Y or :D=N or :D=?" );
- }
- }
- else if ( s.startsWith( NHXtags.SUPPORT ) ) {
- PhylogenyMethods.setConfidence( node_to_annotate, doubleValue( s.substring( 2 ) ) );
- }
- else if ( s.startsWith( NHXtags.TAXONOMY_ID ) ) {
- if ( !node_to_annotate.getNodeData().isHasTaxonomy() ) {
- node_to_annotate.getNodeData().setTaxonomy( new Taxonomy() );
- }
- node_to_annotate.getNodeData().getTaxonomy().setIdentifier( new Identifier( s.substring( 2 ) ) );
- }
- else if ( s.startsWith( NHXtags.PARENT_BRANCH_WIDTH ) ) {
- PhylogenyMethods.setBranchWidthValue( node_to_annotate, Integer.parseInt( s.substring( 2 ) ) );
- }
- else if ( s.startsWith( NHXtags.COLOR ) ) {
- final Color c = NHXParser2.stringToColor( s.substring( 2 ) );
- if ( c != null ) {
- PhylogenyMethods.setBranchColorValue( node_to_annotate, c );
- }
- }
- else if ( s.startsWith( NHXtags.DOMAIN_STRUCTURE ) ) {
- if ( !node_to_annotate.getNodeData().isHasSequence() ) {
- node_to_annotate.getNodeData().setSequence( new Sequence() );
- }
- node_to_annotate.getNodeData().getSequence()
- .setDomainArchitecture( new DomainArchitecture( s.substring( 3 ) ) );
- }
- else if ( s.startsWith( NHXtags.SEQUENCE_ACCESSION ) ) {
- if ( !node_to_annotate.getNodeData().isHasSequence() ) {
- node_to_annotate.getNodeData().setSequence( new Sequence() );
- }
- node_to_annotate.getNodeData().getSequence()
- .setAccession( new Accession( s.substring( 3 ), "?" ) );
- }
- else if ( s.startsWith( NHXtags.GENE_NAME ) ) {
- if ( !node_to_annotate.getNodeData().isHasSequence() ) {
- node_to_annotate.getNodeData().setSequence( new Sequence() );
- }
- node_to_annotate.getNodeData().getSequence().setName( s.substring( 3 ) );
- }
- else if ( s.indexOf( '=' ) < 0 ) {
- if ( node_to_annotate.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
- throw new NHXFormatException( "error in NHX formatted data: more than one distance to parent:"
- + "\"" + s + "\"" );
- }
- node_to_annotate.setDistanceToParent( doubleValue( s ) );
- }
- } // while ( t.hasMoreTokens() )
- }
- }
- }
-
- private static double doubleValue( final String str ) throws NHXFormatException {
- try {
- return Double.valueOf( str ).doubleValue();
- }
- catch ( final NumberFormatException ex ) {
- throw new NHXFormatException( "error in NH/NHX formatted data: failed to parse number from " + "\"" + str
- + "\"" );
- }
- }
-
- private static boolean isBranchLengthsLikeBootstrapValues( final Phylogeny p ) {
- final PhylogenyNodeIterator it = p.iteratorExternalForward();
- final double d0 = it.next().getDistanceToParent();
- if ( ( d0 < 10 ) || !it.hasNext() ) {
- return false;
- }
- while ( it.hasNext() ) {
- final double d = it.next().getDistanceToParent();
- if ( ( d != d0 ) || ( d < 10 ) ) {
- return false;
- }
- }
- return true;
- }
-
- private static void moveBranchLengthsToConfidenceValues( final Phylogeny p ) {
- final PhylogenyNodeIterator it = p.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- PhylogenyMethods.setBootstrapConfidence( n, n.getDistanceToParent() );
- n.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
- }
- }
-
- private static void processMrBayes3Data( final String s, final PhylogenyNode node_to_annotate )
- throws NHXFormatException {
- double sd = -1;
- final Matcher mb_prob_sd_matcher = MB_PROB_SD_PATTERN.matcher( s );
- if ( mb_prob_sd_matcher.find() ) {
- try {
- sd = Double.parseDouble( mb_prob_sd_matcher.group( 1 ) );
- }
- catch ( final NumberFormatException e ) {
- throw new NHXFormatException( "failed to parse probability standard deviation (Mr Bayes output) from \""
- + s + "\"" );
- }
- }
- final Matcher mb_prob_matcher = MB_PROB_PATTERN.matcher( s );
- if ( mb_prob_matcher.find() ) {
- double prob = -1;
- try {
- prob = Double.parseDouble( mb_prob_matcher.group( 1 ) );
- }
- catch ( final NumberFormatException e ) {
- throw new NHXFormatException( "failed to parse probability (Mr Bayes output) from \"" + s + "\"" );
- }
- if ( prob >= 0.0 ) {
- if ( sd >= 0.0 ) {
- node_to_annotate.getBranchData()
- .addConfidence( new Confidence( prob, "posterior probability", sd ) );
- }
- else {
- node_to_annotate.getBranchData().addConfidence( new Confidence( prob, "posterior probability" ) );
- }
- }
- }
- final Matcher mb_bl_matcher = MB_BL_PATTERN.matcher( s );
- if ( mb_bl_matcher.find() ) {
- double bl = -1;
- try {
- bl = Double.parseDouble( mb_bl_matcher.group( 1 ) );
- }
- catch ( final NumberFormatException e ) {
- throw new NHXFormatException( "failed to parse median branch length (Mr Bayes output) from \"" + s
- + "\"" );
- }
- if ( bl >= 0.0 ) {
- node_to_annotate.setDistanceToParent( bl );
- }
- }
- }
-
- /**
- * Parses String s in the format r.g.b (e.g. "12.34.234" ) into red, green,
- * and blue and returns the corresponding Color.
- */
- private static Color stringToColor( final String s ) {
- final StringTokenizer st = new StringTokenizer( s, "." );
- if ( st.countTokens() != 3 ) {
- throw new IllegalArgumentException( "illegal format for color: " + s );
- }
- final int red = ForesterUtil.limitRangeForColor( Integer.parseInt( st.nextToken() ) );
- final int green = ForesterUtil.limitRangeForColor( Integer.parseInt( st.nextToken() ) );
- final int blu = ForesterUtil.limitRangeForColor( Integer.parseInt( st.nextToken() ) );
- return new Color( red, green, blu );
- }
-}