From: cmzmasek@gmail.com Date: Wed, 12 Feb 2014 23:41:55 +0000 (+0000) Subject: cleanup X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=473f1d74784af1ff6e87f45ab7219a642b948785;p=jalview.git cleanup --- 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 2ce0667..a465d4a 100644 --- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java +++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java @@ -56,19 +56,19 @@ import org.forester.util.ForesterUtil; public final class ParserUtils { final public static String TAX_CODE = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA"; + final public static Pattern TAXOMONY_CODE_PATTERN_A = Pattern.compile( "(?:\\b|_)(" + TAX_CODE + ")\\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 = Pattern .compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_([A-Z][a-z]+_[a-z]{2,}(?:_[a-z][a-z0-9_]+)?)\\b" ); final private static Pattern TAXOMONY_CODE_PATTERN_PFS = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_(" + TAX_CODE + ")/\\d+-\\d+\\b" ); - final public static Pattern TAXOMONY_CODE_PATTERN_PFR = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_(" - + TAX_CODE + ")\\b" ); - final public static Pattern TAXOMONY_CODE_PATTERN_A = Pattern.compile( "(?:\\b|_)(" + TAX_CODE + ")\\b" ); - final public static Pattern TAXOMONY_CODE_PATTERN_BRACKETED = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" ); final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_A = Pattern.compile( "(?:\\b|_)(\\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 private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR = Pattern .compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_(\\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 ) @@ -120,45 +120,6 @@ public final class ParserUtils { return parser; } - /** - * 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; - } - final public static PhylogenyParser createParserDependingOnUrlContents( final URL url, final boolean phyloxml_validate_against_xsd ) throws FileNotFoundException, IOException { @@ -329,4 +290,43 @@ 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; + } }