package org.biojava.bio.program.formats; import org.biojava.bio.AnnotationType; import org.biojava.bio.program.tagvalue.ParserListener; import org.biojava.bio.program.tagvalue.TagValueListener; import org.biojava.utils.lsid.LifeScienceIdentifier; /** * A file format supported by the tag-value event-based parsing system. * *
Format should be implemented to provide pre-canned access to common * formats such as Embl, genbank, swissprot, enzyme etc. so that people do not * need to work out which events should be produced by a given file format. * It is expcected that implementations of Format will publish meta-data * about what tags are associated with which values. *
* * @author Matthew Pocock * @since 1.3 */ public interface Format { /** * Retrieve a ParserListener pair for the format that will pass all events * on to a listener. * * Call this method to get a working parser that can be fed into a tag-value * parsing pipeline. * * This method may well be called many times during the lifetime of an * applications.. You should make this threadsafe. To avoid buring too much * memory, and to facilitate the comparrison of object by the == operator, * it is usefull to shair as much data as possible between the parsers and * handlers returned by this method. * * @param listener a TagValueListener that all events should be passed onto * @return a ParserListener for the format */ ParserListener getParserListener(TagValueListener listener); /** * Get the AnnotationType that constrains the events that will be fired. * * If you feed the events from the ParserListener into somethign that builds * Annotation bundles, this is the AnnotationType that those bundles will * conform to. * * In the cases where the events have been sensibly crafted, it will be * possible to introspect a great deal about the parsing events from this * AnntoationType. Use it to dynamicaly bind events to object models, generate * gui componets, and to work out which formats contain cross-refferenceable * information. * * It is polite to return a full and constrained description of the types of * oevents that may be generated, how many of them could come (cardinality) * and what types of values will be associated with them. The use of * OmtologyTerm instances as property names is encouraged. * * @return an AnnotationType representingchema for the events */ AnnotationType getType(); /** * Retrieve the LSID associated with this format. * *The OBDA recomends taht file formats have identifiers assopciated with * them. This allows the format to be specified unambiguously across * different projects and groups. Idealy, a format LSID should conform to * the odda formats specification.
*/ LifeScienceIdentifier getLSID(); }