+
+ /**
+ * 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;
+ }