org.biojava.bio.seq.io
Interface SeqIOListener

All Known Subinterfaces:

RichSeqIOListener, RichSequenceBuilder, SeqFileFormer, SequenceBuilder

All Known Implementing Classes:

DebuggingRichSeqIOListener, EmblFileFormer, EmblProcessor, FastaDescriptionLineParser, GenbankFileFormer, GenbankProcessor, OrganismParser, ProteinRefSeqFileFormer, ProteinRefSeqProcessor, RichSeqIOAdapter, SeqIOAdapter, SeqIOFilter, SequenceBuilderBase, SequenceBuilderFilter, SequenceDBSequenceBuilder, SimpleAssemblyBuilder, SimpleRichSequenceBuilder, SimpleSequenceBuilder, SmartSequenceBuilder, SwissprotFileFormer, SwissprotProcessor

public interface SeqIOListener

Notification interface for objects which listen to a sequence stream parser. More functionality is offered by the RichSeqIOListener.

Since:

1.1

Author:

Thomas Down, Matthew Pocock

See Also:

RichSeqIOListener

Method Summary

void	addFeatureProperty(Object key, Object value) Notify the listener of a feature property.
void	addSequenceProperty(Object key, Object value) Notify the listener of a sequence-wide property.
void	addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Notify the listener of symbol data.
void	endFeature() Mark the end of data associated with one specific feature.
void	endSequence() Notify the listener that processing of the sequence is complete.
void	setName(String name) Notify the listener that the current sequence is generally known by a particular name.
void	setURI(String uri) Notify the listener of a URI identifying the current sequence.
void	startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.
void	startSequence() Start the processing of a sequence.

Method Detail

startSequence

void startSequence()
                   throws ParseException

Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.

Throws:

ParseException

endSequence

void endSequence()
                 throws ParseException

Notify the listener that processing of the sequence is complete.

Throws:

ParseException

setName

void setName(String name)
             throws ParseException

Notify the listener that the current sequence is generally known by a particular name.

Parameters:

name - the String that should be returned by getName for the sequence being parsed

Throws:

ParseException

setURI

void setURI(String uri)
            throws ParseException

Notify the listener of a URI identifying the current sequence.

Throws:

ParseException

addSymbols

void addSymbols(Alphabet alpha,
                Symbol[] syms,
                int start,
                int length)
                throws IllegalAlphabetException

Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception

Parameters:

alpha - The alphabet of the symbol data

syms - An array containing symbols

start - The start offset of valid data within the array

length - The number of valid symbols in the array

Throws:

IllegalAlphabetException - if we can't cope with this alphabet.

addSequenceProperty

void addSequenceProperty(Object key,
                         Object value)
                         throws ParseException

Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.

Throws:

ParseException

startFeature

void startFeature(Feature.Template templ)
                  throws ParseException

Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.

Throws:

ParseException

endFeature

void endFeature()
                throws ParseException

Mark the end of data associated with one specific feature.

Throws:

ParseException

addFeatureProperty

void addFeatureProperty(Object key,
                        Object value)
                        throws ParseException

Notify the listener of a feature property.

Throws:

ParseException