X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2Futil%2FParserUtils.java;h=a1f842ee0df8353be6a37a3606bda2296cfd42d9;hb=44fddb76faa8975295b8b0ad38609256b5011ced;hp=09d5b247ebc1cb4d64c37d5b91c1722fa2041422;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;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 09d5b24..a1f842e 100644
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -16,7 +16,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -34,9 +34,142 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.StringReader;
+import java.net.URL;
+import java.util.regex.Matcher;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.tol.TolParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
 
 public final class ParserUtils {
 
+    final public static PhylogenyParser createParserDependingFileContents( final File file,
+                                                                           final boolean phyloxml_validate_against_xsd )
+            throws FileNotFoundException, IOException {
+        PhylogenyParser parser = null;
+        final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
+        if ( first_line.startsWith( "<" ) ) {
+            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 + "]" );
+                    }
+                }
+            }
+        }
+        else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
+                || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
+            parser = new NexusPhylogeniesParser();
+        }
+        else {
+            parser = new NHXParser();
+        }
+        return parser;
+    }
+
+    final public static PhylogenyParser createParserDependingOnFileType( final File file,
+                                                                         final boolean phyloxml_validate_against_xsd )
+            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 + "]" );
+                    }
+                }
+            }
+        }
+        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" ) ) {
+            parser = new NHXParser();
+        }
+        return parser;
+    }
+
+    final public static PhylogenyParser createParserDependingOnUrlContents( final URL url,
+                                                                            final boolean phyloxml_validate_against_xsd )
+            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();
+                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 {
+                        throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
+                                + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
+                    }
+                }
+            }
+            else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
+                    || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
+                parser = new NexusPhylogeniesParser();
+            }
+            else {
+                parser = new NHXParser();
+            }
+        }
+        return parser;
+    }
+
     public static BufferedReader createReader( final Object source ) throws IOException, FileNotFoundException {
         BufferedReader reader = null;
         if ( ( source instanceof File ) || ( source instanceof String ) ) {
@@ -70,4 +203,61 @@ public final class ParserUtils {
         }
         return reader;
     }
+
+    /**
+     * Extracts a code if and only if:
+     * one and only one _, 
+     * shorter than 25, 
+     * no |, 
+     * no ., 
+     * if / present it has to be after the _, 
+     * if PFAM_STYLE_ONLY: / must be present,
+     * tax code can only contain uppercase letters and numbers,
+     * and must contain at least one uppercase letter.
+     * Return null if no code extractable.
+     * 
+     * @param name
+     * @param limit_to_five
+     * @return
+     */
+    public static String extractTaxonomyCodeFromNodeName( final String name,
+                                                          final boolean limit_to_five,
+                                                          final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction ) {
+        if ( ( name.indexOf( "_" ) > 0 )
+                && ( name.length() < 31 )
+                //  && ( name.lastIndexOf( "_" ) == name.indexOf( "_" ) )
+                && ( name.indexOf( "|" ) < 0 )
+                && ( name.indexOf( "." ) < 0 )
+                && ( ( taxonomy_extraction != PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name
+                        .indexOf( "/" ) >= 0 ) )
+                && ( ( ( name.indexOf( "/" ) ) < 0 ) || ( name.indexOf( "/" ) > name.indexOf( "_" ) ) ) ) {
+            final String[] s = name.split( "[_/]" );
+            if ( s.length > 1 ) {
+                String str = s[ 1 ];
+                if ( ( str.length() < 6 ) || ( !limit_to_five && ( str.length() < 7 ) ) ) {
+                    if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
+                        str = str.substring( 0, 3 );
+                    }
+                    final Matcher uc_letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str );
+                    if ( !uc_letters_and_numbers.matches() ) {
+                        return null;
+                    }
+                    final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str );
+                    if ( numbers_only.matches() ) {
+                        return null;
+                    }
+                    return str;
+                }
+            }
+        }
+        return null;
+    }
+
+    public final static Phylogeny[] readPhylogenies( final File file ) throws FileNotFoundException, IOException {
+        return PhylogenyMethods.readPhylogenies( ParserUtils.createParserDependingOnFileType( file, true ), file );
+    }
+
+    public final static Phylogeny[] readPhylogenies( final String file_name ) throws FileNotFoundException, IOException {
+        return readPhylogenies( new File( file_name ) );
+    }
 }