added AGRESSIVE tax extraction ^^

diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java
index f82779c..164bfee 100644 (file)
--- a/forester/java/src/org/forester/application/phyloxml_converter.java
+++ b/forester/java/src/org/forester/application/phyloxml_converter.java
@@ -209,11 +209,13 @@ public class phyloxml_converter {
                         && ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_COMMON_NAME )
                         && ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
                     if ( extr_taxonomy_pf_only ) {
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                        ( ( NHXParser ) parser )
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         replace_underscores = false;
                     }
                     else if ( extr_taxonomy ) {
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+                        ( ( NHXParser ) parser )
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
                         replace_underscores = false;
                     }
                 }

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index 6ef7350..3ccacf5 100644 (file)
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -308,13 +308,13 @@ public class rio {
                     final NHXParser nhx = ( NHXParser ) p;
                     nhx.setReplaceUnderscores( false );
                     nhx.setIgnoreQuotes( true );
-                    nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+                    nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
                 }
                 else if ( p instanceof NexusPhylogeniesParser ) {
                     final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
                     nex.setReplaceUnderscores( false );
                     nex.setIgnoreQuotes( true );
-                    nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+                    nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
                 }
                 else {
                     throw new RuntimeException( "unknown parser type: " + p );

diff --git a/forester/java/src/org/forester/application/support_transfer.java b/forester/java/src/org/forester/application/support_transfer.java
index 59090c2..927da4f 100644 (file)
--- a/forester/java/src/org/forester/application/support_transfer.java
+++ b/forester/java/src/org/forester/application/support_transfer.java
@@ -95,7 +95,7 @@ public final class support_transfer {
             final PhylogenyParser pp_bl = ParserUtils.createParserDependingOnFileType( infile_bl, true );
             final PhylogenyParser pp_s = ParserUtils.createParserDependingOnFileType( infile_support_vals, true );
             if ( pp_bl instanceof NHXParser ) {
-                ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+                ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             }
             phylogeny_w_bl = factory.create( infile_bl, pp_bl )[ index_of_tree_w_bl ];
             phylogeny_w_support_vals = factory.create( infile_support_vals, pp_s )[ 0 ];

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index f84d8c4..0dd82d7 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -43,6 +43,7 @@ import java.net.URL;
 import java.text.ParseException;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
@@ -474,7 +475,7 @@ public final class AptxUtil {
         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
             if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) {
-                final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( n );
+                final Set<Taxonomy> taxs = obtainDistinctTaxonomies( n );
                 if ( ( taxs != null ) && ( taxs.size() == 1 ) ) {
                     AptxUtil.collapseSubtree( n, true );
                     if ( !n.getNodeData().isHasTaxonomy() ) {
@@ -493,6 +494,40 @@ public final class AptxUtil {
         }
     }
 
+    /**
+     * Returns the set of distinct taxonomies of
+     * all external nodes of node.
+     * If at least one the external nodes has no taxonomy,
+     * null is returned.
+     * 
+     */
+    public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
+        for( final PhylogenyNode n : descs ) {
+            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
+                return null;
+            }
+            tax_set.add( n.getNodeData().getTaxonomy() );
+        }
+        return tax_set;
+    }
+
+    public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
+        for( final PhylogenyNode n : descs ) {
+            if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) {
+                tax_set.add( n.getNodeData().getTaxonomy() );
+                System.out.println( n.getNodeData().getTaxonomy() );
+            }
+        }
+        for( final Taxonomy taxonomy : tax_set ) {
+            System.out.println( taxonomy );
+        }
+        return tax_set;
+    }
+
     final static void collapseSubtree( final PhylogenyNode node, final boolean collapse ) {
         node.setCollapse( collapse );
         if ( node.isExternal() ) {
@@ -636,7 +671,22 @@ public final class AptxUtil {
             }
             if ( phy.getIdentifier() != null ) {
                 desc.append( "Id: " );
-                desc.append( phy.getIdentifier() );
+                desc.append( phy.getIdentifier().toString() );
+                desc.append( "\n" );
+            }
+            if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
+                desc.append( "Description: " );
+                desc.append( phy.getDescription() );
+                desc.append( "\n" );
+            }
+            if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
+                desc.append( "Distance Unit: " );
+                desc.append( phy.getDistanceUnit() );
+                desc.append( "\n" );
+            }
+            if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
+                desc.append( "Type: " );
+                desc.append( phy.getType() );
                 desc.append( "\n" );
             }
             desc.append( "Rooted: " );
@@ -663,7 +713,7 @@ public final class AptxUtil {
             desc.append( "Maximum distance to root: " );
             desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
             desc.append( "\n" );
-            final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+            final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
             if ( taxs != null ) {
                 desc.append( "Distinct external taxonomies: " );
                 desc.append( taxs.size() );

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index c563795..855ded5 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -86,7 +86,7 @@ public final class Configuration {
     private short                           _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
     private boolean                         _editable                                              = true;
     private boolean                         _nh_parsing_replace_underscores                        = false;
-    private TAXONOMY_EXTRACTION             _taxonomy_extraction                                   = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
+    private TAXONOMY_EXTRACTION             _taxonomy_extraction                                   = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
     private boolean                         _internal_number_are_confidence_for_nh_parsing         = false;
     private boolean                         _display_sequence_relations                            = false;
     private boolean                         _validate_against_phyloxml_xsd_schema                  = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
@@ -1342,10 +1342,10 @@ public final class Configuration {
                 setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
             }
             else if ( s.equalsIgnoreCase( "yes" ) ) {
-                setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+                setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             }
             else if ( s.equalsIgnoreCase( "pfam" ) ) {
-                setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             }
             else {
                 ForesterUtil.printWarningMessage( Constants.PRG_NAME,

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 0cc981e..37f84e4 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -1121,10 +1121,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
                 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
         if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.YES );
+            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
         }
         else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
-            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
         }
         else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
             options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index e2f4737..8a6730a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1040,9 +1040,9 @@ public final class MainFrameApplication extends MainFrame {
         customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
                                       getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
         customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
-                                      getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
+                                      getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
         customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
-                                      getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                      getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
@@ -2026,7 +2026,8 @@ public final class MainFrameApplication extends MainFrame {
                     final PhylogenyNode n = it.next();
                     final String name = n.getName().trim();
                     if ( !ForesterUtil.isEmpty( name ) ) {
-                        final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES );
+                        final String nt = ParserUtils
+                                .extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
                         if ( !ForesterUtil.isEmpty( nt ) ) {
                             if ( counter < 15 ) {
                                 sb.append( name + ": " + nt + "\n" );
@@ -2576,7 +2577,12 @@ public final class MainFrameApplication extends MainFrame {
             final int count = getMainPanel().getTabbedPane().getTabCount();
             final List<Phylogeny> trees = new ArrayList<Phylogeny>();
             for( int i = 0; i < count; ++i ) {
-                trees.add( getMainPanel().getPhylogeny( i ) );
+                final Phylogeny phy = getMainPanel().getPhylogeny( i );
+                if ( ForesterUtil.isEmpty( phy.getName() )
+                        && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {
+                    phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );
+                }
+                trees.add( phy );
                 getMainPanel().getTreePanels().get( i ).setEdited( false );
             }
             final PhylogenyWriter writer = new PhylogenyWriter();

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 9857b51..a0c70f3 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -458,7 +458,7 @@ final public class Options {
         _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
         _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
         _nh_parsing_replace_underscores = false;
-        _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
+        _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
         _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
         _show_domain_labels = true;
         setAbbreviateScientificTaxonNames( false );

diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index ea4bca0..7d88a31 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
@@ -109,13 +109,15 @@ public class UrlTreeReader implements Runnable {
                         break;
                     case NH_EXTRACT_TAXONOMY:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                        ( ( NHXParser ) parser )
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;
                     case PFAM:
                         parser = new NHXParser();
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                        ( ( NHXParser ) parser )
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
                         ( ( NHXParser ) parser ).setGuessRootedness( true );
                         break;

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
index 89a7d8f..397c14a 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -712,6 +712,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
     }
 
     public static enum TAXONOMY_EXTRACTION {
-        NO, YES, PFAM_STYLE_ONLY;
+        NO, AGRESSIVE, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT;
     }
 }

diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
index 51f7f89..4ba38fa 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -57,11 +57,12 @@ public final class ParserUtils {
 
     final public static Pattern  TAXOMONY_SN_PATTERN            = Pattern
                                                                         .compile( "[^_]{2,}_([A-Z][a-z]+_[a-z]{2,}(_[A-Za-z]\\w+|))\\b" );
-    final public static Pattern  TAXOMONY_CODE_PATTERN_1        = Pattern.compile( "\\b[A-Z0-9]{5}|RAT|PIG|PEA|CAP\\b" );
+    final public static Pattern  TAXOMONY_CODE_PATTERN_1        = Pattern
+                                                                        .compile( "\\b[A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA|CAP\\b" );
     final private static Pattern TAXOMONY_CODE_PATTERN_2        = Pattern
-                                                                        .compile( "([A-Z0-9]{5}|RAT|PIG|PEA|CAP)[^0-9A-Za-z].*" );
+                                                                        .compile( "([A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA|CAP)[^0-9A-Za-z].*" );
     final private static Pattern TAXOMONY_CODE_PATTERN_PF       = Pattern
-                                                                        .compile( "([A-Z0-9]{5}|RAT|PIG|PEA|CAP)/\\d+-\\d+" );
+                                                                        .compile( "([A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA|CAP)/\\d+-\\d+" );
     final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_1  = Pattern.compile( "\\b\\d{1,7}\\b" );
     final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_2  = Pattern.compile( "(\\d{1,7})[^0-9A-Za-z].*" );
     final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PF = Pattern.compile( "(\\d{1,7})/\\d+-\\d+" );
@@ -225,12 +226,12 @@ public final class ParserUtils {
     public final static String extractTaxonomyCodeFromNodeName( final String name,
                                                                 final TAXONOMY_EXTRACTION taxonomy_extraction ) {
         if ( ( name.indexOf( "_" ) > 0 )
-                && ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name.indexOf( "/" ) > 4 ) ) ) {
+                && ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) || ( name.indexOf( "/" ) > 4 ) ) ) {
             final String[] s = name.split( "[_\\s]" );
             if ( s.length > 1 ) {
                 final String str = s[ 1 ];
                 if ( !ForesterUtil.isEmpty( str ) ) {
-                    if ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) {
+                    if ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) {
                         final Matcher m = TAXOMONY_CODE_PATTERN_PF.matcher( str );
                         if ( m.matches() ) {
                             return m.group( 1 );
@@ -249,7 +250,7 @@ public final class ParserUtils {
                 }
             }
         }
-        else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.YES ) {
+        else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) {
             final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( name );
             if ( m1.matches() ) {
                 return name;
@@ -291,7 +292,8 @@ public final class ParserUtils {
                     return code;
                 }
             }
-            else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.YES ) {
+            else if ( ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+                    || ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGRESSIVE ) ) {
                 final String sn = extractScientificNameFromNodeName( node.getName() );
                 if ( !ForesterUtil.isEmpty( sn ) ) {
                     if ( !node.getNodeData().isHasTaxonomy() ) {
@@ -310,12 +312,12 @@ public final class ParserUtils {
     public final static String extractUniprotTaxonomyIdFromNodeName( final String name,
                                                                      final TAXONOMY_EXTRACTION taxonomy_extraction ) {
         if ( ( name.indexOf( "_" ) > 0 )
-                && ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name.indexOf( "/" ) > 4 ) ) ) {
+                && ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) || ( name.indexOf( "/" ) > 4 ) ) ) {
             final String[] s = name.split( "[_\\s]" );
             if ( s.length > 1 ) {
                 final String str = s[ 1 ];
                 if ( !ForesterUtil.isEmpty( str ) ) {
-                    if ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) {
+                    if ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) {
                         final Matcher m = TAXOMONY_UNIPROT_ID_PATTERN_PF.matcher( str );
                         if ( m.matches() ) {
                             return m.group( 1 );
@@ -334,7 +336,7 @@ public final class ParserUtils {
                 }
             }
         }
-        else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.YES ) {
+        if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGRESSIVE ) {
             final Matcher m1 = TAXOMONY_UNIPROT_ID_PATTERN_1.matcher( name );
             if ( m1.matches() ) {
                 return name;

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index a3efa67..27f2a33 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -768,25 +768,6 @@ public class PhylogenyMethods {
     }
 
     /**
-     * Returns the set of distinct taxonomies of
-     * all external nodes of node.
-     * If at least one the external nodes has no taxonomy,
-     * null is returned.
-     * 
-     */
-    public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
-        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
-        final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
-        for( final PhylogenyNode n : descs ) {
-            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
-                return null;
-            }
-            tax_set.add( n.getNodeData().getTaxonomy() );
-        }
-        return tax_set;
-    }
-
-    /**
      * Returns a map of distinct taxonomies of
      * all external nodes of node.
      * If at least one of the external nodes has no taxonomy,

diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java
index d360a1f..cde7804 100644 (file)
--- a/forester/java/src/org/forester/rio/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -826,13 +826,13 @@ public final class RIO {
             final NHXParser nhx = ( NHXParser ) p;
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+            nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
         }
         else if ( p instanceof NexusPhylogeniesParser ) {
             final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
             nex.setReplaceUnderscores( false );
             nex.setIgnoreQuotes( true );
-            nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+            nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
         }
         return factory.create( gene_trees_file, p );
     }

diff --git a/forester/java/src/org/forester/rio/TestRIO.java b/forester/java/src/org/forester/rio/TestRIO.java
index a0604d6..8160446 100644 (file)
--- a/forester/java/src/org/forester/rio/TestRIO.java
+++ b/forester/java/src/org/forester/rio/TestRIO.java
@@ -48,7 +48,7 @@ public final class TestRIO {
             final NHXParser nhx = new NHXParser();
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
@@ -134,7 +134,7 @@ public final class TestRIO {
             final NHXParser nhx = new NHXParser();
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             //
             final String gene_trees_00_str = "(MOUSE,RAT);(MOUSE,RAT);(MOUSE,RAT);(RAT,MOUSE);";
             final Phylogeny[] gene_trees_00 = factory.create( gene_trees_00_str, nhx );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index e2e93c7..f04b445 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -817,63 +817,74 @@ public final class Test {
 
     private static boolean testExtractTaxonomyCodeFromNodeName() {
         try {
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+                    .equals( "MOUSE" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+                    .equals( "RAT" ) ) {
                 return false;
             }
-            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
+            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
+                                                               TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
                     .equals( "MOUSE" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445",
+                                                               TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
                     .equals( "MOUSE" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
+                                                               TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
                     .equals( "MOUSE" ) ) {
                 return false;
             }
-            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
+                                                              TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
                 return false;
             }
-            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
+                                                              TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
-                    .equals( "RAT" ) ) {
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
+                                                               TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
-                    .equals( "RAT" ) ) {
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445",
+                                                               TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
-                    .equals( "RAT" ) ) {
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
+                                                               TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
                 return false;
             }
-            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
+                                                              TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
                 return false;
             }
-            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+            if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
+                                                              TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+                    .equals( "RAT" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
                     .equals( "PIG" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
+            if ( !ParserUtils
+                    .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
                     .equals( "MOUSE" ) ) {
                 return false;
             }
-            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
+            if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
                     .equals( "MOUSE" ) ) {
                 return false;
             }
@@ -892,11 +903,11 @@ public final class Test {
             }
             final PhylogenyNode n1 = new PhylogenyNode();
             final PhylogenyNode n2 = PhylogenyNode
-                    .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             final PhylogenyNode n3 = PhylogenyNode
-                    .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             final PhylogenyNode n4 = PhylogenyNode
-                    .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( n1.isHasAssignedEvent() ) {
                 return false;
             }
@@ -5912,109 +5923,132 @@ public final class Test {
 
     private static boolean testTaxonomyExtraction() {
         try {
-            final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n0 = PhylogenyNode
+                    .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n0.getNodeData().isHasTaxonomy() ) {
                 return false;
             }
-            final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n1 = PhylogenyNode
+                    .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n1.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n1.toString() );
                 return false;
             }
-            final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n2 = PhylogenyNode
+                    .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
             if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
                 System.out.println( n2.toString() );
                 return false;
             }
-            final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n2x = PhylogenyNode
+                    .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            if ( n2x.getNodeData().isHasTaxonomy() ) {
+                return false;
+            }
+            final PhylogenyNode n3 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
                 System.out.println( n3.toString() );
                 return false;
             }
-            final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n4 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n4.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n4.toString() );
                 return false;
             }
-            final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n5 = PhylogenyNode
+                    .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n5.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n5.toString() );
                 return false;
             }
-            final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n6 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n6.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n6.toString() );
                 return false;
             }
-            final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n7 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n7.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n7.toString() );
                 return false;
             }
-            final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n8 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
                 System.out.println( n8.toString() );
                 return false;
             }
-            final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n9 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
                 System.out.println( n9.toString() );
                 return false;
             }
-            final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
-            if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
+            final PhylogenyNode n10x = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            if ( n10x.getNodeData().isHasTaxonomy() ) {
+                System.out.println( n10x.toString() );
+                return false;
+            }
+            final PhylogenyNode n10xx = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            if ( n10xx.getNodeData().isHasTaxonomy() ) {
+                System.out.println( n10xx.toString() );
+                return false;
+            }
+            final PhylogenyNode n10 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
                 System.out.println( n10.toString() );
                 return false;
             }
-            final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n11 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
                 System.out.println( n11.toString() );
                 return false;
             }
-            final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n12 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_Mus_musculus_musculus",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
                 System.out.println( n12.toString() );
                 return false;
             }
-            final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n13 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_Mus_musculus1",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n13.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n13.toString() );
                 return false;
             }
-            final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n14 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_Mus_musculus_11",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n14.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n14.toString() );
                 return false;
             }
-            final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n15 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_Mus_musculus_v11",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
                 System.out.println( n15.toString() );
                 return false;
             }
-            final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n16 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_Mus_musculus_/11",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n16.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n16.toString() );
                 return false;
             }
-            final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n17 = PhylogenyNode
+                    .createInstanceFromNhxString( "blag_Mus_musculus_v",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n17.getNodeData().isHasTaxonomy() ) {
                 System.out.println( n17.toString() );
                 return false;
@@ -6075,7 +6109,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n8 = PhylogenyNode
-                    .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
                 return false;
             }
@@ -6083,7 +6117,8 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n9 = PhylogenyNode
-                    .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
                 return false;
             }
@@ -6091,20 +6126,20 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n10 = PhylogenyNode
-                    .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n10.getName().equals( "n10.ECOLI" ) ) {
                 return false;
             }
             final PhylogenyNode n20 = PhylogenyNode
-                    .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
                 return false;
             }
             if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
                 return false;
             }
-            final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
-                                                                                  NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n20x = PhylogenyNode
+                    .createInstanceFromNhxString( "n20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
                 return false;
             }
@@ -6112,7 +6147,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n20xx = PhylogenyNode
-                    .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
                 return false;
             }
@@ -6120,7 +6155,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n20xxx = PhylogenyNode
-                    .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
                 return false;
             }
@@ -6128,15 +6163,15 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n20xxxx = PhylogenyNode
-                    .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
                 return false;
             }
             if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
                 return false;
             }
-            final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n21 = PhylogenyNode
+                    .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n21.getName().equals( "n21_PIG" ) ) {
                 return false;
             }
@@ -6144,7 +6179,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n21x = PhylogenyNode
-                    .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n21x.getName().equals( "n21_PIG" ) ) {
                 return false;
             }
@@ -6152,7 +6187,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n22 = PhylogenyNode
-                    .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n22.getName().equals( "n22/PIG" ) ) {
                 return false;
             }
@@ -6160,7 +6195,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n23 = PhylogenyNode
-                    .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n23.getName().equals( "n23/PIG_1" ) ) {
                 return false;
             }
@@ -6168,7 +6203,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode a = PhylogenyNode
-                    .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
                 return false;
             }
@@ -6176,7 +6211,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode b = PhylogenyNode
-                    .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
                 return false;
             }
@@ -6185,7 +6220,7 @@ public final class Test {
             }
             final PhylogenyNode c = PhylogenyNode
                     .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
-                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
                 return false;
             }
@@ -6194,7 +6229,7 @@ public final class Test {
             }
             final PhylogenyNode c1 = PhylogenyNode
                     .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
-                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
                 return false;
             }
@@ -6203,7 +6238,7 @@ public final class Test {
             }
             final PhylogenyNode c2 = PhylogenyNode
                     .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
-                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
                 return false;
             }
@@ -6211,7 +6246,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode d = PhylogenyNode
-                    .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
                 return false;
             }
@@ -6219,23 +6254,23 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode e = PhylogenyNode
-                    .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !e.getName().equals( "n10_RAT1" ) ) {
                 return false;
             }
             if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
                 return false;
             }
-            final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode e2 = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !e2.getName().equals( "n10_RAT1" ) ) {
                 return false;
             }
             if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
                 return false;
             }
-            final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
-                                                                                NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode e3 = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !e3.getName().equals( "n10_RAT~" ) ) {
                 return false;
             }
@@ -6244,7 +6279,7 @@ public final class Test {
             }
             final PhylogenyNode n11 = PhylogenyNode
                     .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
-                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
                 return false;
             }
@@ -6256,7 +6291,7 @@ public final class Test {
             }
             final PhylogenyNode n12 = PhylogenyNode
                     .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
-                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
                 return false;
             }
@@ -6266,16 +6301,16 @@ public final class Test {
             if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
                 return false;
             }
-            final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
-                                                                               NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode m = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_MOUSEa", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !m.getName().equals( "n10_MOUSEa" ) ) {
                 return false;
             }
             if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
                 return false;
             }
-            final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
-                                                                               NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode o = PhylogenyNode
+                    .createInstanceFromNhxString( "n10_MOUSE_", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !o.getName().equals( "n10_MOUSE_" ) ) {
                 return false;
             }
@@ -6313,7 +6348,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n13 = PhylogenyNode
-                    .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
             if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
                 return false;
             }
@@ -6327,16 +6362,16 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n14 = PhylogenyNode
-                    .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
-            if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
+                    .createInstanceFromNhxString( "blah_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+            if ( !n14.getName().equals( "blah_9QX45/1-2" ) ) {
                 return false;
             }
-            if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
+            if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
                 return false;
             }
             final PhylogenyNode n15 = PhylogenyNode
                     .createInstanceFromNhxString( "something_wicked[123]",
-                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n15.getName().equals( "something_wicked" ) ) {
                 return false;
             }
@@ -6347,7 +6382,8 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n16 = PhylogenyNode
-                    .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "something_wicked2[9]",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n16.getName().equals( "something_wicked2" ) ) {
                 return false;
             }
@@ -6358,7 +6394,8 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n17 = PhylogenyNode
-                    .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( "something_wicked3[a]",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !n17.getName().equals( "something_wicked3" ) ) {
                 return false;
             }
@@ -6366,7 +6403,7 @@ public final class Test {
                 return false;
             }
             final PhylogenyNode n18 = PhylogenyNode
-                    .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                    .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
             if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
                 return false;
             }
@@ -6376,29 +6413,31 @@ public final class Test {
             if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
                 return false;
             }
-            final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n19 = PhylogenyNode
+                    .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
                 return false;
             }
             if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
                 return false;
             }
-            final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n30 = PhylogenyNode
+                    .createInstanceFromNhxString( "blah_1234567-roejojoej",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
                 return false;
             }
             if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
                 return false;
             }
-            final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n31 = PhylogenyNode
+                    .createInstanceFromNhxString( "blah_12345678-roejojoej",
+                                                  NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n31.getNodeData().isHasTaxonomy() ) {
                 return false;
             }
-            final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
-                                                                                 NHXParser.TAXONOMY_EXTRACTION.YES );
+            final PhylogenyNode n32 = PhylogenyNode
+                    .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
             if ( n32.getNodeData().isHasTaxonomy() ) {
                 return false;
             }