Package org.biojava.bio.seq.io

Class SmartSequenceBuilder

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderBase

org.biojava.bio.seq.io.SmartSequenceBuilder

All Implemented Interfaces:

SeqIOListener, SequenceBuilder

public class SmartSequenceBuilder
extends SequenceBuilderBase

Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence. This may or may not bit-encode the symbols (using PackedSymbolList), and may or may not store the symbols in multiple fixed-length chunks (using ChunkedSymbolList).

More functionality is offered by SimpleRichSequenceBuilder, Use of this class is prefered.

Author:

David Huen, Matthew Pocock

Field Summary

Fields

Modifier and Type	Field	Description
static SequenceBuilderFactory	BIT_PACKED
static SequenceBuilderFactory	FACTORY

Fields inherited from class org.biojava.bio.seq.io.SequenceBuilderBase

annotation, ERROR_FEATURES_PROPERTY, name, seq, uri

Method Summary

Modifier and Type	Method	Description
void	addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)	Notify the listener of symbol data.
Sequence	makeSequence()	Return the Sequence object which has been constructed by this builder.

Methods inherited from class org.biojava.bio.seq.io.SequenceBuilderBase

addFeatureProperty, addProperty, addSequenceProperty, endFeature, endSequence, setName, setURI, startFeature, startSequence

Methods inherited from class java.lang.Object

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

Field Detail

FACTORY

public static final SequenceBuilderFactory FACTORY

BIT_PACKED

public static final SequenceBuilderFactory BIT_PACKED

Method Detail

addSymbols

public 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

Specified by:

addSymbols in class SequenceBuilderBase

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.

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

Overrides:

makeSequence in class SequenceBuilderBase

Throws:

BioException