org.biojavax.bio.seq.io

Class RichSeqIOAdapter

java.lang.Object

org.biojavax.bio.seq.io.RichSeqIOAdapter

All Implemented Interfaces:

SeqIOListener, RichSeqIOListener

Direct Known Subclasses:

SimpleRichSequenceBuilder

public class RichSeqIOAdapter
extends Object
implements RichSeqIOListener

This class implements all methods of RichSeqIOListener and takes no action. It should be overridden to implement custom listeners that only listen for a small subset of events.

Since:

1.5

Author:

Mark Schreiber

Field Summary

Fields

Modifier and Type	Field and Description
protected RichFeature	emptyFeature This is a dummy feature.

Constructor Summary

Constructors

Constructor and Description
RichSeqIOAdapter() Creates a new instance of RichSeqIOAdapter

Method Summary

Modifier and Type	Method and Description
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.
RichFeature	getCurrentFeature() Gets the feature currently being created.
void	setAccession(String accession) Call back method so the event emitter can tell the listener the accession of the record being read.
void	setCircular(boolean circular) Defined this sequence being parser as circular.
void	setComment(String comment) Call back method so the event emitter can tell the listener about a comment in the record being read.
void	setDescription(String description) Call back method so the event emitter can tell the listener the description of the record being read.
void	setDivision(String division) Call back method so the event emitter can tell the listener the division of the record being read.
void	setIdentifier(String identifier) Call back method so the event emitter can tell the listener the identifier of the record being read.
void	setName(String name) Notify the listener that the current sequence is generally known by a particular name.
void	setNamespace(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.
void	setRankedCrossRef(RankedCrossRef crossRef) Call back method so the event emitter can tell the listener about a cross reference.
void	setRankedDocRef(RankedDocRef ref) Call back method so the event emitter can tell the listener about a literature reference in the record being read.
void	setRelationship(BioEntryRelationship relationship) Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
void	setSeqVersion(String version) Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
void	setTaxon(NCBITaxon taxon) Call back method so the event emitter can tell the listener the Taxon of the record being read.
void	setURI(String uri) Notify the listener of a URI identifying the current sequence.
void	setVersion(int version) Call back method so the event emitter can tell the listener the version of the record being read.
void	startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.
void	startSequence() Start the processing of a sequence.

Methods inherited from class java.lang.Object

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

Field Detail

emptyFeature

protected RichFeature emptyFeature

This is a dummy feature. It is returned by the method getCurrentFeature(). Access is provided so you can override it.

Constructor Detail

RichSeqIOAdapter

public RichSeqIOAdapter()

Creates a new instance of RichSeqIOAdapter

Method Detail

setAccession

public void setAccession(String accession)
                  throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the accession of the record being read. It is possible that some records have more than one accession. As a guide the first one sent to the listener should be the primary one.

Specified by:

setAccession in interface RichSeqIOListener

Parameters:

accession - The accession of the record

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

See Also:

SeqIOListener.setName(String name), RichSeqIOListener.setURI(String uri), RichSeqIOListener.setIdentifier(String identifier)

setIdentifier

public void setIdentifier(String identifier)
                   throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the identifier of the record being read. There should be zero or one identifier per bioentry. If there is more than one the Listener should consider throwing an exception. For some formats like fasta the identifier may not exist. For others like GenBank the identifier best maps to the GI.

Specified by:

setIdentifier in interface RichSeqIOListener

Parameters:

identifier - The identifier of the Bioentry.

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

See Also:

SeqIOListener.setName(String name), RichSeqIOListener.setAccession(String accession), RichSeqIOListener.setURI(String uri)

setDivision

public void setDivision(String division)
                 throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the division of the record being read. If the source of the calls back is a GenBank parser the division will be a Genbank division. This method would typically be called 0 or 1 times. It should not be called more than once per entry and an exception could be thrown if it is.

Specified by:

setDivision in interface RichSeqIOListener

Parameters:

division - The division the entry belongs too.

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setDescription

public void setDescription(String description)
                    throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the description of the record being read. For example the description line of a FASTA format file would be the description. This method would typically be called 0 or 1 times and may cause an exception if it is called more than once per entry.

Specified by:

setDescription in interface RichSeqIOListener

Parameters:

description - The description of the record

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setVersion

public void setVersion(int version)
                throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the version of the record being read. This method would typically be called 0 or 1 times per entry. If it is not called the Listener should assume the version is 0. If it is called more than once per entry an exception should be thrown.

Specified by:

setVersion in interface RichSeqIOListener

Parameters:

version - the version of the record

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setSeqVersion

public void setSeqVersion(String version)
                   throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the version of the sequence of the record being read. This method would typically be called 0 or 1 times per entry. If it is not called the Listener should assume the version is 0. If it is called more than once per entry an exception should be thrown.

Specified by:

setSeqVersion in interface RichSeqIOListener

Parameters:

version - the version of the record

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setComment

public void setComment(String comment)
                throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener about a comment in the record being read. The comment is typically one or more comment lines relevant to the record as a whole and bundled in a Commment object. This method may be called zero or one times per entry. It can be called zero or more times.

Specified by:

setComment in interface RichSeqIOListener

Parameters:

comment - The comment

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setRankedDocRef

public void setRankedDocRef(RankedDocRef ref)
                     throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener about a literature reference in the record being read. This method may be called zero or more times.

Specified by:

setRankedDocRef in interface RichSeqIOListener

Parameters:

ref - A literature reference contained in the entry.

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setTaxon

public void setTaxon(NCBITaxon taxon)
              throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the Taxon of the record being read. This method may be called zero or one times. An exception may be thrown if it is called more than once. As a design decision NCBI's taxon model was chosen as it is commonly used and is supported by the BioSQL schema. The setting of an NCBI taxon should be considered entirely optional.

Specified by:

setTaxon in interface RichSeqIOListener

Parameters:

taxon - The taxon information relevant to this entry.

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setNamespace

public void setNamespace(Namespace namespace)
                  throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener the namespace of the record being read. The method can be called zero or one time. If it is called more than once an exception may be thrown.

The namespace is a concept from the BioSQL schema that enables Bioentries to be disambiguated. It is possible in BioSQL and should be possible in other collections of BioEntries to have records that have the same name, accession and version but different namespaces. This method would be expected to be called if you are reading a sequence from a biosql database or if you are implementing a listener that knows how to write to a biosql database. If you give a sequence a namespace and it is persited to biosql at somepoint in it's life you could expect it to be persisted to that namespace (if possible).

Specified by:

setNamespace in interface RichSeqIOListener

Parameters:

namespace - The namespace of the entry.

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setRelationship

public void setRelationship(BioEntryRelationship relationship)
                     throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry. This may be called zero or more times.

Specified by:

setRelationship in interface RichSeqIOListener

Parameters:

relationship - The relationship

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setRankedCrossRef

public void setRankedCrossRef(RankedCrossRef crossRef)
                       throws ParseException

Description copied from interface: RichSeqIOListener

Call back method so the event emitter can tell the listener about a cross reference. This could be called zero or more times per entry.

Specified by:

setRankedCrossRef in interface RichSeqIOListener

Parameters:

crossRef - the cross reference

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

setURI

public void setURI(String uri)
            throws ParseException

Description copied from interface: RichSeqIOListener

Notify the listener of a URI identifying the current sequence.

Specified by:

setURI in interface SeqIOListener

Specified by:

setURI in interface RichSeqIOListener

Throws:

ParseException

getCurrentFeature

public RichFeature getCurrentFeature()
                              throws ParseException

Description copied from interface: RichSeqIOListener

Gets the feature currently being created.

Specified by:

getCurrentFeature in interface RichSeqIOListener

Returns:

the feature under construction.

Throws:

ParseException - if a feature is not currently being created.

setCircular

public void setCircular(boolean circular)
                 throws ParseException

Description copied from interface: RichSeqIOListener

Defined this sequence being parser as circular. It is best to call this as early as possible during parsing. It should definitely be called before doing anything with locations or features.

Specified by:

setCircular in interface RichSeqIOListener

Parameters:

circular - set this to true if you want it to be circular.

Throws:

ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.

addFeatureProperty

public void addFeatureProperty(Object key,
                               Object value)
                        throws ParseException

Description copied from interface: SeqIOListener

Notify the listener of a feature property.

Specified by:

addFeatureProperty in interface SeqIOListener

Throws:

ParseException

endFeature

public void endFeature()
                throws ParseException

Description copied from interface: SeqIOListener

Mark the end of data associated with one specific feature.

Specified by:

endFeature in interface SeqIOListener

Throws:

ParseException

startFeature

public void startFeature(Feature.Template templ)
                  throws ParseException

Description copied from interface: SeqIOListener

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.

Specified by:

startFeature in interface SeqIOListener

Throws:

ParseException

addSequenceProperty

public void addSequenceProperty(Object key,
                                Object value)
                         throws ParseException

Description copied from interface: SeqIOListener

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

Specified by:

addSequenceProperty in interface SeqIOListener

Throws:

ParseException

addSymbols

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

Description copied from interface: SeqIOListener

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

Specified by:

addSymbols in interface SeqIOListener

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.

setName

public void setName(String name)
             throws ParseException

Description copied from interface: SeqIOListener

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

Specified by:

setName in interface SeqIOListener

Parameters:

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

Throws:

ParseException

endSequence

public void endSequence()
                 throws ParseException

Description copied from interface: SeqIOListener

Notify the listener that processing of the sequence is complete.

Specified by:

endSequence in interface SeqIOListener

Throws:

ParseException

startSequence

public void startSequence()
                   throws ParseException

Description copied from interface: SeqIOListener

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

Specified by:

startSequence in interface SeqIOListener

Throws:

ParseException