org.biojava.bio.seq.io

Class SequenceBuilderBase

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderBase

All Implemented Interfaces:

SeqIOListener, SequenceBuilder

Direct Known Subclasses:

SequenceDBSequenceBuilder, SimpleAssemblyBuilder, SimpleSequenceBuilder, SmartSequenceBuilder

public abstract class SequenceBuilderBase
extends Object
implements SequenceBuilder

Basic SequenceBuilder implementation which accumulates all notified information. Subclass this to implement specific Sequence implementations. More functionality is offered by the SimpleRichSequenceBuilder.

Version:

1.2 [newio proposal]

Author:

Thomas Down, David Huen (modified SimpleSequence to make this)

Field Summary

Fields

Modifier and Type	Field and Description
protected Annotation	annotation
static Object	ERROR_FEATURES_PROPERTY
protected String	name
protected Sequence	seq
protected String	uri

Constructor Summary

Constructors

Constructor and Description
SequenceBuilderBase()

Method Summary

Modifier and Type	Method and Description
void	addFeatureProperty(Object key, Object value) Add an annotation-bundle entry to the feature.
protected void	addProperty(Annotation ann, Object key, Object value)
void	addSequenceProperty(Object key, Object value) Add an annotation-bundle entry to the sequence.
abstract void	addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) 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.
Sequence	makeSequence() Return the Sequence object which has been constructed by this builder.
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.

Methods inherited from class java.lang.Object

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

Field Detail

ERROR_FEATURES_PROPERTY

public static Object ERROR_FEATURES_PROPERTY

name

protected String name

uri

protected String uri

annotation

protected Annotation annotation

seq

protected Sequence seq

Constructor Detail

SequenceBuilderBase

public SequenceBuilderBase()

Method Detail

startSequence

public void startSequence()

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

endSequence

public void endSequence()

Description copied from interface: SeqIOListener

Notify the listener that processing of the sequence is complete.

Specified by:

endSequence in interface SeqIOListener

setName

public void setName(String name)

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

setURI

public void setURI(String uri)

Description copied from interface: SeqIOListener

Notify the listener of a URI identifying the current sequence.

Specified by:

setURI in interface SeqIOListener

addSymbols

public abstract void addSymbols(Alphabet alpha,
                                Symbol[] syms,
                                int pos,
                                int len)
                         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

pos - The start offset of valid data within the array

len - The number of valid symbols in the array

Throws:

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

addSequenceProperty

public void addSequenceProperty(Object key,
                                Object value)

Add an annotation-bundle entry to the sequence. If the annotation key isn't currently defined, the value is added directly. Otherwise:

• If the current value implements the Collection interface, the new value is added to that collection.
• Otherwise, the current value is replaced by a List object containing the old value then the new value in that order.

Specified by:

addSequenceProperty in interface SeqIOListener

startFeature

public void startFeature(Feature.Template templ)

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

addFeatureProperty

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

Add an annotation-bundle entry to the feature. If the annotation key isn't currently defined, the value is added directly. Otherwise:

• If the current value implements the Collection interface, the new value is added to that collection.
• Otherwise, the current value is replaced by a List object containing the old value then the new value in that order.

Specified by:

addFeatureProperty in interface SeqIOListener

Throws:

ParseException

endFeature

public void endFeature()

Description copied from interface: SeqIOListener

Mark the end of data associated with one specific feature.

Specified by:

endFeature in interface SeqIOListener

makeSequence

public Sequence makeSequence()
                      throws BioException

Description copied from interface: SequenceBuilder

Return the Sequence object which has been constructed by this builder. This method is only expected to succeed after the endSequence() notifier has been called.

Specified by:

makeSequence in interface SequenceBuilder

Throws:

BioException

addProperty

protected void addProperty(Annotation ann,
                           Object key,
                           Object value)