--- /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.nhx;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+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.Annotation;
+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.PropertiesMap;
+import org.forester.phylogeny.data.Property;
+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 _has_next;
+ 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;
+
+ public NHXParser2() {
+ init();
+ }
+
+ public Phylogeny 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 ) {
+ Phylogeny phy = processOpenParen2();
+ if ( phy != null ) {
+ ++_i;
+ return phy;
+ }
+ }
+ 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 ( getCladeLevel() != 0 ) {
+ // setPhylogenies( null );
+ // throw new PhylogenyParserException( "error in NH (Newick)/NHX formatted data: most likely cause: number of open parens does not equal number of close parens" );
+ }
+ if ( getCurrentPhylogeny() != null ) {
+ return finishPhylogeny2();
+ }
+ else if ( getCurrentAnotation().length() > 0 ) {
+ System.out.println( "1node=" + getCurrentAnotation() );
+ return finishSingleNodePhylogeny2();
+ }
+ else {
+ return null;
+ }
+ } // parse()
+
+ public TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
+ }
+
+ public boolean hasNext() {
+ return _has_next;
+ }
+
+ 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 IOException
+ * @throws PhylogenyParserException
+ */
+ @Override
+ public void setSource( final Object nhx_source ) throws PhylogenyParserException, IOException {
+ 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, char[], File," + " or InputStream " + " [attempt to parse object of "
+ + nhx_source.getClass() + "]." );
+ }
+ setHasNext( true );
+ reset();
+ }
+
+ public void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ public void reset() {
+ setHasNext( false );
+ _i = 0;
+ _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;
+ 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:
+ _my_source_br = ( BufferedReader ) getNhxSource();
+ break;
+ default:
+ throw new RuntimeException( "unknown input type" );
+ }
+ }
+
+ /**
+ * 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( "cp=" + getCurrentPhylogeny() );
+ System.out.println( "ca=" + getCurrentAnotation().toString() );
+ parseNHX( 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 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 );
+ setHasNext( false );
+ }
+
+ 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();
+ 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 );
+ 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 setHasNext( final boolean has_next ) {
+ _has_next = has_next;
+ }
+
+ 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.ANNOTATION ) ) {
+ if ( !node_to_annotate.getNodeData().isHasSequence() ) {
+ node_to_annotate.getNodeData().setSequence( new Sequence() );
+ }
+ final Annotation annotation = new Annotation( "_:_" );
+ annotation.setDesc( s.substring( 3 ) );
+ node_to_annotate.getNodeData().getSequence().addAnnotation( annotation );
+ }
+ 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.CUSTOM_DATA_ON_NODE ) ) {
+ if ( !node_to_annotate.getNodeData().isHasProperties() ) {
+ node_to_annotate.getNodeData().setProperties( new PropertiesMap() );
+ }
+ node_to_annotate.getNodeData().getProperties().addProperty( Property.createFromNhxString( s ) );
+ }
+ 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 );
+ }
+
+ @Override
+ public Phylogeny[] parse() throws IOException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff