// 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
// 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
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 ) ) {
}
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 ) );
+ }
}
git://source.jalview.org / jalview.git / blobdiff