org.biojava.bio.seq.io

Class SequenceDBSequenceBuilder

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderBase

org.biojava.bio.seq.io.SequenceDBSequenceBuilder

All Implemented Interfaces:

SeqIOListener, SequenceBuilder

public class SequenceDBSequenceBuilder
extends SequenceBuilderBase

This SequenceBuilder has a variety of modes of operation. It can take a sequence from an existing SequenceDB and apply annotations to it.

If the SequenceDB has persistence, then it can also create a sequence in the sequenceDB and apply the annotation to that. However, performance under those circumstances can vary depending on how well the persistent SequenceDB handles this.

Following the introduction of biojavax persistence is handled by Hibernate refer to BioSQLRichObjectBuilder

Author:

David Huen

Field Summary

Fields

Modifier and Type	Field and Description
static int	ANNOTATE_EXISTING
static int	CREATE_DUMMYSEQ
static int	CREATE_REALSEQ

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

annotation, ERROR_FEATURES_PROPERTY, name, seq, uri

Constructor Summary

Constructors

Constructor and Description
SequenceDBSequenceBuilder(SequenceDB db, int mode) constructor

Method Summary

Methods

Modifier and Type	Method and Description
void	addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) does nothing for now.
Sequence	makeSequence() create the sequence

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

ANNOTATE_EXISTING

public static final int ANNOTATE_EXISTING

See Also:

Constant Field Values

CREATE_DUMMYSEQ

public static final int CREATE_DUMMYSEQ

See Also:

Constant Field Values

CREATE_REALSEQ

public static final int CREATE_REALSEQ

See Also:

Constant Field Values

Constructor Detail

SequenceDBSequenceBuilder

public SequenceDBSequenceBuilder(SequenceDB db,
                         int mode)

constructor

Method Detail

addSymbols

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

does nothing for now.

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

makeSequence

public Sequence makeSequence()
                      throws BioException

create the sequence

Specified by:

makeSequence in interface SequenceBuilder

Overrides:

makeSequence in class SequenceBuilderBase

Throws:

BioException