X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2Futil%2FParserUtils.java;h=e86ed49fbaabf2b7b67a83bc7a6195b71a5954e0;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=4d74229ddb136e831acce4d641cfeeeec3e86205;hpb=9f15c8c3415681ea197bf9d629ee3f2c126fc5b7;p=jalview.git

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 4d74229..e86ed49 100644
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -55,29 +55,52 @@ import org.forester.util.ForesterUtil;
 
 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-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA|CAP\\b" );
-    final private static Pattern TAXOMONY_CODE_PATTERN_2        = Pattern
-                                                                        .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_3        = Pattern
-                                                                        .compile( "_([A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA|CAP)_" );
-    final private static Pattern TAXOMONY_CODE_PATTERN_PF       = Pattern
-                                                                        .compile( "([A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA|CAP)/\\d+-\\d+" );
-    final public static Pattern  TAXOMONY_CODE_PATTERN_4        = Pattern
-                                                                        .compile( "\\[(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP)\\]" );
-    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+" );
+    final private static String  SN_BN                                = "[A-Z][a-z]{2,30}[_ ][a-z]{3,30}";
+    final public static String   TAX_CODE                             = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA";
+    final public static String   TAX_CODE_LO                          = "(?:[A-Z]{5})|RAT|PIG|PEA";
+    final public static Pattern  TAXOMONY_CODE_PATTERN_A              = Pattern.compile( "(?:\\b|_)(" + TAX_CODE
+                                                                                         + ")(?:\\b|_)" );
+    final public static Pattern  TAXOMONY_CODE_PATTERN_A_LO           = Pattern.compile( "_(" + TAX_CODE_LO
+                                                                                         + ")(?:\\b|_)" );
+    final public static Pattern  TAXOMONY_CODE_PATTERN_BRACKETED      = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" );
+    final public static Pattern  TAXOMONY_CODE_PATTERN_PFR            = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_("
+            + TAX_CODE + ")\\b" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_GENUS            = Pattern.compile( "([A-Z][a-z]{2,30})" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_SN               = Pattern.compile( "(?:\\b|_)(" + SN_BN
+                                                                                         + ")(?:(\\s*$)|([_ ][a-z]*[A-Z0-9]))" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_SNS              = Pattern.compile( "(?:\\b|_)(" + SN_BN
+                                                                                         + "[_ ][a-z]{3,30}"
+                                                                                         + ")[_ ][a-z]*[A-Z0-9]" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_SNS2             = Pattern.compile( "[A-Z0-9][a-z]*[_ ](" + SN_BN
+                                                                                         + "[_ ][a-z]{3,30}" + ")\\s*$" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_SP               = Pattern
+            .compile( "(?:\\b|_)([A-Z][a-z]{2,30}[_ ]sp\\.?)(?:\\b|_)?" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_STRAIN_1         = Pattern
+            .compile( "(?:\\b|_)("
+                    + SN_BN
+                    + "[_ ](?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60})(?:\\b|_)" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_STRAIN_2         = Pattern
+            .compile( "(?:\\b|_)("
+                    + SN_BN
+                    + "[_ ]\\((?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60}\\))" );
+    final public static Pattern  TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN = Pattern
+            .compile( "(?:\\b|_)("
+                    + SN_BN
+                    + "[_ ]str[a-z]{0,3}\\.?[_ ]\\S{1,60}[_ ]substr[a-z]{0,3}\\.?[_ ]\\S{1,60})(?:\\b|_)" );
+    final private static Pattern TAXOMONY_CODE_PATTERN_PFS            = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_("
+            + TAX_CODE + ")/\\d+-\\d+\\b" );
+    final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR      = Pattern
+            .compile( "(?:\\b|_)[A-Z0-9]{1,}_(\\d{1,7})\\b" );
+    final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFS      = Pattern
+            .compile( "(?:\\b|_)[A-Z0-9]{4,}_(\\d{1,7})/\\d+-\\d+\\b" );
 
     final public static PhylogenyParser createParserDependingFileContents( final File file,
                                                                            final boolean phyloxml_validate_against_xsd )
-            throws FileNotFoundException, IOException {
+                                                                                   throws FileNotFoundException, IOException {
         PhylogenyParser parser = null;
         final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
         if ( first_line.startsWith( "<" ) ) {
-            parser = new PhyloXmlParser();
+            parser = PhyloXmlParser.createPhyloXmlParser();
             if ( phyloxml_validate_against_xsd ) {
                 final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
                 final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
@@ -104,72 +127,32 @@ public final class ParserUtils {
 
     final public static PhylogenyParser createParserDependingOnFileType( final File file,
                                                                          final boolean phyloxml_validate_against_xsd )
-            throws FileNotFoundException, IOException {
+                                                                                 throws FileNotFoundException, IOException {
         PhylogenyParser parser = null;
         parser = ParserUtils.createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd );
         if ( parser == null ) {
             parser = createParserDependingFileContents( file, phyloxml_validate_against_xsd );
         }
-        return parser;
-    }
-
-    /**
-     * Return null if it can not guess the parser to use based on name suffix.
-     * 
-     * @param filename
-     * @return
-     */
-    final public static PhylogenyParser createParserDependingOnSuffix( final String filename,
-                                                                       final boolean phyloxml_validate_against_xsd ) {
-        PhylogenyParser parser = null;
-        final String filename_lc = filename.toLowerCase();
-        if ( filename_lc.endsWith( ".tol" ) || filename_lc.endsWith( ".tolxml" ) || filename_lc.endsWith( ".tol.zip" ) ) {
-            parser = new TolParser();
-        }
-        else if ( filename_lc.endsWith( ".xml" ) || filename_lc.endsWith( ".px" ) || filename_lc.endsWith( "phyloxml" )
-                || filename_lc.endsWith( ".zip" ) ) {
-            parser = new PhyloXmlParser();
-            if ( phyloxml_validate_against_xsd ) {
-                final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
-                final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
-                if ( xsd_url != null ) {
-                    ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
-                }
-                else {
-                    if ( ForesterConstants.RELEASE ) {
-                        throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
-                                + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
-                    }
-                }
+        if ( ( parser != null ) && file.toString().toLowerCase().endsWith( ".zip" ) ) {
+            if ( parser instanceof PhyloXmlParser ) {
+                ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
+            }
+            else if ( parser instanceof TolParser ) {
+                ( ( TolParser ) parser ).setZippedInputstream( true );
             }
-        }
-        else if ( filename_lc.endsWith( ".nexus" ) || filename_lc.endsWith( ".nex" ) || filename_lc.endsWith( ".nx" ) ) {
-            parser = new NexusPhylogeniesParser();
-        }
-        else if ( filename_lc.endsWith( ".nhx" ) || filename_lc.endsWith( ".nh" ) || filename_lc.endsWith( ".newick" )
-                || filename_lc.endsWith( ".nwk" ) ) {
-            parser = new NHXParser();
         }
         return parser;
     }
 
     final public static PhylogenyParser createParserDependingOnUrlContents( final URL url,
                                                                             final boolean phyloxml_validate_against_xsd )
-            throws FileNotFoundException, IOException {
+                                                                                    throws FileNotFoundException, IOException {
         final String lc_filename = url.getFile().toString().toLowerCase();
         PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd );
-        if ( ( parser != null ) && lc_filename.endsWith( ".zip" ) ) {
-            if ( parser instanceof PhyloXmlParser ) {
-                ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
-            }
-            else if ( parser instanceof TolParser ) {
-                ( ( TolParser ) parser ).setZippedInputstream( true );
-            }
-        }
         if ( parser == null ) {
             final String first_line = ForesterUtil.getFirstLine( url ).trim().toLowerCase();
             if ( first_line.startsWith( "<" ) ) {
-                parser = new PhyloXmlParser();
+                parser = PhyloXmlParser.createPhyloXmlParser();
                 if ( phyloxml_validate_against_xsd ) {
                     final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
                     final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
@@ -190,6 +173,14 @@ public final class ParserUtils {
                 parser = new NHXParser();
             }
         }
+        if ( ( parser != null ) && lc_filename.endsWith( ".zip" ) ) {
+            if ( parser instanceof PhyloXmlParser ) {
+                ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
+            }
+            else if ( parser instanceof TolParser ) {
+                ( ( TolParser ) parser ).setZippedInputstream( true );
+            }
+        }
         return parser;
     }
 
@@ -222,133 +213,162 @@ public final class ParserUtils {
         }
         else {
             throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass()
-                    + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" );
+                                                + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" );
         }
         return reader;
     }
 
-    public final static String extractTaxonomyCodeFromNodeName( final String name,
-                                                                final TAXONOMY_EXTRACTION taxonomy_extraction ) {
-        if ( ( name.indexOf( "_" ) > 0 )
-                && ( ( 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_STRICT ) {
-                        final Matcher m = TAXOMONY_CODE_PATTERN_PF.matcher( str );
-                        if ( m.matches() ) {
-                            return m.group( 1 );
-                        }
-                    }
-                    else {
-                        final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( str );
-                        if ( m1.matches() ) {
-                            return m1.group();
-                        }
-                        final Matcher m2 = TAXOMONY_CODE_PATTERN_2.matcher( str );
-                        if ( m2.matches() ) {
-                            return m2.group( 1 );
-                        }
-                    }
-                }
+    public final static String extractScientificNameFromNodeName( final String name ) {
+        final Matcher m_ss = TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN.matcher( name );
+        if ( m_ss.find() ) {
+            String s = m_ss.group( 1 ).replace( '_', ' ' );
+            if ( s.indexOf( " str " ) > 4 ) {
+                s = s.replaceFirst( " str ", " str. " );
+            }
+            if ( s.indexOf( " substr " ) > 4 ) {
+                s = s.replaceFirst( " substr ", " substr. " );
+            }
+            return s;
+        }
+        final Matcher m_str1 = TAXOMONY_SN_PATTERN_STRAIN_1.matcher( name );
+        if ( m_str1.find() ) {
+            String s = m_str1.group( 1 ).replace( '_', ' ' );
+            if ( s.indexOf( " str " ) > 4 ) {
+                s = s.replaceFirst( " str ", " str. " );
+            }
+            else if ( s.indexOf( " subsp " ) > 4 ) {
+                s = s.replaceFirst( " subsp ", " subsp. " );
+            }
+            else if ( s.indexOf( " ssp " ) > 4 ) {
+                s = s.replaceFirst( " ssp ", " subsp. " );
+            }
+            else if ( s.indexOf( " ssp. " ) > 4 ) {
+                s = s.replaceFirst( " ssp. ", " subsp. " );
+            }
+            else if ( s.indexOf( " var " ) > 4 ) {
+                s = s.replaceFirst( " var ", " var. " );
             }
+            return s;
         }
-        if ( ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
-                || ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGRESSIVE ) ) {
-            final Matcher m1 = TAXOMONY_CODE_PATTERN_1.matcher( name );
-            if ( m1.matches() ) {
-                return name;
+        final Matcher m_str2 = TAXOMONY_SN_PATTERN_STRAIN_2.matcher( name );
+        if ( m_str2.find() ) {
+            String s = m_str2.group( 1 ).replace( '_', ' ' );
+            if ( s.indexOf( " (str " ) > 4 ) {
+                s = s.replaceFirst( " \\(str ", " (str. " );
             }
-            final Matcher m3 = TAXOMONY_CODE_PATTERN_3.matcher( name );
-            if ( m3.matches() ) {
-                return m3.group( 1 );
+            else if ( s.indexOf( " (subsp " ) > 4 ) {
+                s = s.replaceFirst( " \\(subsp ", " (subsp. " );
             }
+            else if ( s.indexOf( " (ssp " ) > 4 ) {
+                s = s.replaceFirst( " \\(ssp ", " (subsp. " );
+            }
+            else if ( s.indexOf( " (ssp. " ) > 4 ) {
+                s = s.replaceFirst( " \\(ssp. ", " (subsp. " );
+            }
+            else if ( s.indexOf( " (var " ) > 4 ) {
+                s = s.replaceFirst( " \\(var ", " (var. " );
+            }
+            return s;
+        }
+        final Matcher m_sns = TAXOMONY_SN_PATTERN_SNS.matcher( name );
+        if ( m_sns.find() ) {
+            return m_sns.group( 1 ).replace( '_', ' ' );
+        }
+        final Matcher m_sns2 = TAXOMONY_SN_PATTERN_SNS2.matcher( name );
+        if ( m_sns2.find() ) {
+            return m_sns2.group( 1 ).replace( '_', ' ' );
+        }
+        final Matcher m_sn = TAXOMONY_SN_PATTERN_SN.matcher( name );
+        if ( m_sn.find() ) {
+            return m_sn.group( 1 ).replace( '_', ' ' );
+        }
+        final Matcher m_sp = TAXOMONY_SN_PATTERN_SP.matcher( name );
+        if ( m_sp.find() ) {
+            String s = m_sp.group( 1 ).replace( '_', ' ' );
+            if ( s.endsWith( " sp" ) ) {
+                s = s + ".";
+            }
+            return s;
         }
         return null;
     }
 
-    public final static String extractScientificNameFromNodeName( final String name ) {
-        final Matcher m1 = TAXOMONY_SN_PATTERN.matcher( name );
-        if ( m1.matches() ) {
-            return m1.group( 1 ).replace( '_', ' ' );
+    public final static String extractTaxonomyCodeFromNodeName( final String name,
+                                                                final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+        Matcher m = TAXOMONY_CODE_PATTERN_PFS.matcher( name );
+        if ( m.find() ) {
+            return m.group( 1 );
+        }
+        else if ( ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+                || ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) ) {
+            m = TAXOMONY_CODE_PATTERN_PFR.matcher( name );
+            if ( m.find() ) {
+                return m.group( 1 );
+            }
+            else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
+                m = TAXOMONY_CODE_PATTERN_A.matcher( name );
+                if ( m.find() ) {
+                    return m.group( 1 );
+                }
+            }
         }
         return null;
     }
 
     public final static String extractTaxonomyDataFromNodeName( final PhylogenyNode node,
                                                                 final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction )
-            throws PhyloXmlDataFormatException {
+                                                                        throws PhyloXmlDataFormatException {
+        if ( taxonomy_extraction == TAXONOMY_EXTRACTION.NO ) {
+            throw new IllegalArgumentException();
+        }
         final String id = extractUniprotTaxonomyIdFromNodeName( node.getName(), taxonomy_extraction );
         if ( !ForesterUtil.isEmpty( id ) ) {
             if ( !node.getNodeData().isHasTaxonomy() ) {
                 node.getNodeData().setTaxonomy( new Taxonomy() );
             }
-            if ( ( node.getNodeData().getTaxonomy().getIdentifier() == null )
-                    || ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {
-                node.getNodeData().getTaxonomy().setIdentifier( new Identifier( id, "uniprot" ) );
-                return id;
-            }
+            node.getNodeData().getTaxonomy().setIdentifier( new Identifier( id, "uniprot" ) );
+            return id;
         }
         else {
-            final String code = extractTaxonomyCodeFromNodeName( node.getName(), taxonomy_extraction );
-            if ( !ForesterUtil.isEmpty( code ) ) {
-                if ( !node.getNodeData().isHasTaxonomy() ) {
-                    node.getNodeData().setTaxonomy( new Taxonomy() );
-                }
-                if ( ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
-                    node.getNodeData().getTaxonomy().setTaxonomyCode( code );
-                    return code;
-                }
-            }
-            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() ) {
-                        node.getNodeData().setTaxonomy( new Taxonomy() );
-                    }
-                    if ( ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
+            String code = null;
+            if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
+                code = extractTaxonomyCodeFromNodeNameLettersOnly( node.getName() );
+                if ( ForesterUtil.isEmpty( code ) ) {
+                    final String sn = extractScientificNameFromNodeName( node.getName() );
+                    if ( !ForesterUtil.isEmpty( sn ) ) {
+                        if ( !node.getNodeData().isHasTaxonomy() ) {
+                            node.getNodeData().setTaxonomy( new Taxonomy() );
+                        }
                         node.getNodeData().getTaxonomy().setScientificName( sn );
                         return sn;
                     }
                 }
             }
+            if ( ForesterUtil.isEmpty( code ) ) {
+                code = extractTaxonomyCodeFromNodeName( node.getName(), taxonomy_extraction );
+            }
+            if ( !ForesterUtil.isEmpty( code ) ) {
+                if ( !node.getNodeData().isHasTaxonomy() ) {
+                    node.getNodeData().setTaxonomy( new Taxonomy() );
+                }
+                node.getNodeData().getTaxonomy().setTaxonomyCode( code );
+                return code;
+            }
         }
         return null;
     }
 
     public final static String extractUniprotTaxonomyIdFromNodeName( final String name,
                                                                      final TAXONOMY_EXTRACTION taxonomy_extraction ) {
-        if ( ( name.indexOf( "_" ) > 0 )
-                && ( ( 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_STRICT ) {
-                        final Matcher m = TAXOMONY_UNIPROT_ID_PATTERN_PF.matcher( str );
-                        if ( m.matches() ) {
-                            return m.group( 1 );
-                        }
-                    }
-                    else {
-                        final Matcher m1 = TAXOMONY_UNIPROT_ID_PATTERN_1.matcher( str );
-                        if ( m1.matches() ) {
-                            return m1.group();
-                        }
-                        final Matcher m2 = TAXOMONY_UNIPROT_ID_PATTERN_2.matcher( str );
-                        if ( m2.matches() ) {
-                            return m2.group( 1 );
-                        }
-                    }
-                }
-            }
+        Matcher m = TAXOMONY_UNIPROT_ID_PATTERN_PFS.matcher( name );
+        if ( m.find() ) {
+            return m.group( 1 );
         }
-        if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGRESSIVE ) {
-            final Matcher m1 = TAXOMONY_UNIPROT_ID_PATTERN_1.matcher( name );
-            if ( m1.matches() ) {
-                return name;
+        else if ( ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+                || ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) ) {
+            m = TAXOMONY_UNIPROT_ID_PATTERN_PFR.matcher( name );
+            if ( m.find() ) {
+                return m.group( 1 );
             }
         }
         return null;
@@ -361,4 +381,51 @@ public final class ParserUtils {
     public final static Phylogeny[] readPhylogenies( final String file_name ) throws FileNotFoundException, IOException {
         return readPhylogenies( new File( file_name ) );
     }
+
+    /**
+     * Return null if it can not guess the parser to use based on name suffix.
+     *
+     * @param filename
+     * @return
+     */
+    final private static PhylogenyParser createParserDependingOnSuffix( final String filename,
+                                                                        final boolean phyloxml_validate_against_xsd ) {
+        PhylogenyParser parser = null;
+        final String filename_lc = filename.toLowerCase();
+        if ( filename_lc.endsWith( ".tol" ) || filename_lc.endsWith( ".tolxml" ) || filename_lc.endsWith( ".tol.zip" ) ) {
+            parser = new TolParser();
+        }
+        else if ( filename_lc.endsWith( ".xml" ) || filename_lc.endsWith( "phyloxml" ) || filename_lc.endsWith( ".zip" ) ) {
+            parser = PhyloXmlParser.createPhyloXmlParser();
+            if ( phyloxml_validate_against_xsd ) {
+                final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
+                final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
+                if ( xsd_url != null ) {
+                    ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
+                }
+                else {
+                    if ( ForesterConstants.RELEASE ) {
+                        throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
+                                + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
+                    }
+                }
+            }
+        }
+        else if ( filename_lc.endsWith( ".nexus" ) || filename_lc.endsWith( ".nex" ) || filename_lc.endsWith( ".nx" ) ) {
+            parser = new NexusPhylogeniesParser();
+        }
+        else if ( filename_lc.endsWith( ".nhx" ) || filename_lc.endsWith( ".nh" ) || filename_lc.endsWith( ".newick" )
+                || filename_lc.endsWith( ".nwk" ) ) {
+            parser = new NHXParser();
+        }
+        return parser;
+    }
+
+    private final static String extractTaxonomyCodeFromNodeNameLettersOnly( final String name ) {
+        final Matcher m = TAXOMONY_CODE_PATTERN_A_LO.matcher( name );
+        if ( m.find() ) {
+            return m.group( 1 );
+        }
+        return null;
+    }
 }