- 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 = 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 = 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;
- }
-
- final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDate() ) {
- node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
- }
- }
-
- final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDistribution() ) {
- node.getNodeData().setDistribution( new Distribution( "" ) );
- }
- }
-
- public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasSequence() ) {
- node.getNodeData().setSequence( new Sequence() );
- }
- }
-
- public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- }
-
- /**
- * 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 ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction ) {
- if ( ( name.indexOf( "_" ) > 0 )
- && ( name.length() < 25 )
- && ( name.lastIndexOf( "_" ) == name.indexOf( "_" ) )
- && ( name.indexOf( "|" ) < 0 )
- && ( name.indexOf( "." ) < 0 )
- && ( ( taxonomy_extraction != ForesterUtil.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 ( limit_to_five ) {
- if ( str.length() > 5 ) {
- str = str.substring( 0, 5 );
- }
- else if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
- str = str.substring( 0, 3 );
- }
- }
- final Matcher letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str );
- if ( !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;
- }
-