package org.forester.io.parsers.nhx;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.File;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParser {
- public final static Pattern MB_BL_PATTERN = Pattern.compile( "length.median=([^,]+)" );
- 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 NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" );
- final static public boolean REPLACE_UNDERSCORES_DEFAULT = false;
- private static final boolean ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT = false;
- final static private byte BUFFERED_READER = 3;
- final static private byte CHAR_ARRAY = 2;
- final static private boolean GUESS_IF_SUPPORT_VALUES = true;
- final static private boolean GUESS_ROOTEDNESS_DEFAULT = true;
- final static private boolean IGNORE_QUOTES_DEFAULT = false;
+ private final static Pattern MB_BL_PATTERN = Pattern.compile( "length.median=([-+eE0-9\\.]+)" );
+ private final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([-+eE0-9\\.]+)" );
+ private final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob.stddev=([-+eE0-9\\.]+)" );
+ private final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" );
+
+ private final static Pattern BEAST_STYLE_EXTENDED_BOOTSTRAP_PATTERN = Pattern.compile( "boot?strap=([\\d\\.]+)" );
+ private final static Pattern BEAST_STYLE_EXTENDED_COLOR_PATTERN = Pattern.compile( "colou?r=(#[\\da-fA-F]{6})" );
+ private final static Pattern ENDS_WITH_NUMBER_PATTERN = Pattern.compile( "(:[-+eE0-9\\.]+$)" );
+
+
+ public final static boolean REPLACE_UNDERSCORES_DEFAULT = false;
+ private final static boolean ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT = false;
+ private final static byte BUFFERED_READER = 3;
+ private final static byte CHAR_ARRAY = 2;
+ private final static boolean GUESS_IF_SUPPORT_VALUES = true;
+ private final static boolean GUESS_ROOTEDNESS_DEFAULT = true;
+ private final static boolean IGNORE_QUOTES_DEFAULT = false;
- final static private char BELL = 7;
- public final static String UTF_8 = "UTF-8";
- public final static String ISO_8859_1 = "ISO-8859-1";
- private final static String ENCODING_DEFAULT = UTF_8;
+ private final static char BELL = 7;
+ private final static String ENCODING_DEFAULT = ForesterConstants.UTF_8;
private boolean _allow_errors_in_distance_to_parent;
private int _clade_level;
private StringBuilder _current_anotation;
private Object _source;
private int _source_length;
private TAXONOMY_EXTRACTION _taxonomy_extraction;
+ private boolean _parse_beast_style_extended_tags = false;
private final String _encoding;
public NHXParser() {
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
if ( GUESS_IF_SUPPORT_VALUES ) {
if ( isBranchLengthsLikeBootstrapValues( _current_phylogeny ) ) {
moveBranchLengthsToConfidenceValues( _current_phylogeny );
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
_current_phylogeny = new Phylogeny();
_current_phylogeny.setRoot( new_node );
return _current_phylogeny;
setGuessRootedness( GUESS_ROOTEDNESS_DEFAULT );
setIgnoreQuotes( IGNORE_QUOTES_DEFAULT );
setAllowErrorsInDistanceToParent( ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT );
+ setParseBeastStyleExtendedTags( false );
}
private final boolean isAllowErrorsInDistanceToParent() {
if ( c == ':' ) {
_saw_colon = true;
}
- else if ( !( ( c < 33 ) || ( c > 126 ) ) && _saw_colon
+ else if ( !( ( c < 33 ) || ( c == 127 ) ) && _saw_colon
&& ( ( c != '[' ) && ( c != '.' ) && ( ( c < 48 ) || ( c > 57 ) ) ) ) {
_saw_colon = false;
}
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
_current_anotation = new StringBuilder();
_current_node.addAsChild( new_node );
}
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
_current_anotation = new StringBuilder();
}
if ( !_current_node.isRoot() ) {
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
if ( _current_node == null ) {
throw new NHXFormatException( "format might not be NH or NHX" );
}
getTaxonomyExtraction(),
isReplaceUnderscores(),
isAllowErrorsInDistanceToParent(),
- true );
+ true,
+ isParseBeastStyleExtendedTags());
}
_current_anotation = new StringBuilder();
_saw_closing_paren = false;
final TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean replace_underscores,
final boolean allow_errors_in_distance_to_parent,
- final boolean replace_bell ) throws NHXFormatException,
+ final boolean replace_bell,
+ final boolean parse_beast_style_extended_tags ) 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" );
else if ( s.indexOf( "prob=" ) > -1 ) {
processMrBayes3Data( s, node_to_annotate );
}
+ if ( parse_beast_style_extended_tags ) {
+ processBeastStyleExtendedData( s, node_to_annotate );
+ }
+ final Matcher ewn_matcher = ENDS_WITH_NUMBER_PATTERN.matcher( s );
+ if ( ewn_matcher.find() ) {
+ b = ewn_matcher.group(1);
+ }
}
s = s.substring( 0, ob ) + b;
if ( ( s.indexOf( "[" ) > -1 ) || ( s.indexOf( "]" ) > -1 ) ) {
}
}
final StringTokenizer t = new StringTokenizer( s, ":" );
+
if ( t.countTokens() > 0 ) {
if ( !s.startsWith( ":" ) ) {
if ( ( s.indexOf( BELL ) <= -1 ) || !replace_bell ) {
}
}
+ private final static void processBeastStyleExtendedData( final String s,
+ final PhylogenyNode node_to_annotate )
+ throws NHXFormatException {
+ final Matcher ft_bs_matcher = BEAST_STYLE_EXTENDED_BOOTSTRAP_PATTERN.matcher( s );
+
+ double bs = -1;
+ if ( ft_bs_matcher.find() ) {
+ try {
+ bs = Double.parseDouble( ft_bs_matcher.group( 1 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ throw new NHXFormatException( "failed to parse bootstrap support from \""
+ + s + "\"" );
+ }
+ if ( bs >= 0.0 ) {
+ node_to_annotate.getBranchData()
+ .addConfidence( new Confidence( bs, "bootstrap" ) );
+ }
+ }
+ final Matcher ft_color_matcher = BEAST_STYLE_EXTENDED_COLOR_PATTERN.matcher( s );
+ Color c = null;
+ if ( ft_color_matcher.find() ) {
+ try {
+ c = Color.decode(ft_color_matcher.group( 1 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ throw new NHXFormatException( "failed to parse color from \""
+ + s + "\"" );
+ }
+ }
+ if ( c != null ) {
+ node_to_annotate.getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
+
private final static void processMrBayes3Data( final String s, final PhylogenyNode node_to_annotate )
throws NHXFormatException {
double sd = -1;
return _encoding;
}
+ private final boolean isParseBeastStyleExtendedTags() {
+ return _parse_beast_style_extended_tags;
+ }
+
+ public final void setParseBeastStyleExtendedTags( final boolean parse_beast_style_extended_tags ) {
+ _parse_beast_style_extended_tags = parse_beast_style_extended_tags;
+ }
+
public static enum TAXONOMY_EXTRACTION {
AGGRESSIVE, NO, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT;
}
git://source.jalview.org / jalview.git / blobdiff