Package org.biojava.bio.program.formats

Class Ligand.Reaction

java.lang.Object

org.biojava.bio.program.formats.Ligand.Reaction

All Implemented Interfaces:

Format

Enclosing class:

Ligand

public static class Ligand.Reaction
extends Object
implements Format

Constructor Summary

Constructors

Constructor	Description
Reaction()

Method Summary

Modifier and Type	Method	Description
LifeScienceIdentifier	getLSID()	Retrieve the LSID associated with this format.
ParserListener	getParserListener(TagValueListener listener)	Retrieve a ParserListener pair for the format that will pass all events on to a listener.
AnnotationType	getType()	Get the AnnotationType that constrains the events that will be fired.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Reaction

public Reaction()

Method Detail

getParserListener

public ParserListener getParserListener(TagValueListener listener)

Description copied from 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.

Specified by:

getParserListener in interface Format

Parameters:

listener - a TagValueListener that all events should be passed onto

Returns:

a ParserListener for the format

getType

public AnnotationType getType()

Description copied from interface: Format

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.

Specified by:

getType in interface Format

Returns:

an AnnotationType representingchema for the events

getLSID

public LifeScienceIdentifier getLSID()

Description copied from interface: Format

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.

Specified by:

getLSID in interface Format