Uses of Interface
org.biojava.bio.seq.db.SequenceDB

Packages that use SequenceDB

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.

Uses of SequenceDB in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment with parameters of type SequenceDB

Modifier and Type	Method and Description
List<AlignmentPair>	AlignmentAlgorithm.alignAll(SequenceIterator source, SequenceDB subjectDB)

Uses of SequenceDB in org.biojava.bio.dp

Methods in org.biojava.bio.dp with parameters of type SequenceDB

Modifier and Type	Method and Description
void	TrainingAlgorithm.train(SequenceDB db, double nullWeight, StoppingCriteria stopper) Trains the sequences in db untill stopper says to finnish.
void	AbstractTrainer.train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper) Trains the sequences in db until stopper says to finnish.

Uses of SequenceDB in org.biojava.bio.gui

Methods in org.biojava.bio.gui with parameters of type SequenceDB

Modifier and Type	Method and Description
void	FeatureTree.setSequenceDB(SequenceDB db) Use this method to provide the sequences for the tree to work with.

Uses of SequenceDB in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that return SequenceDB

Modifier and Type	Method and Description
static SequenceDB	GFFTools.annotateSequences(SequenceDB seqs, GFFEntrySet ents) Annotates all sequences in a sequence DB with features from a GFF entry set.

Methods in org.biojava.bio.program.gff with parameters of type SequenceDB

Modifier and Type	Method and Description
static SequenceDB	GFFTools.annotateSequences(SequenceDB seqs, GFFEntrySet ents) Annotates all sequences in a sequence DB with features from a GFF entry set.
static GFFEntrySet	GFFTools.gffFromSeqDB(SequenceDB seqDB) Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
void	SequencesAsGFF.processDB(SequenceDB seqDB, GFFDocumentHandler handler) Process all Sequences within a SequenceDB, informing handler of any suitable features.

Uses of SequenceDB in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred with parameters of type SequenceDB

Modifier and Type	Method and Description
static void	PhredTools.writePhredQuality(OutputStream qual, OutputStream seq, SequenceDB db) Writes Phred quality data in a Fasta type format.

Uses of SequenceDB in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha with parameters of type SequenceDB

Modifier and Type	Method and Description
DataStore	NIODataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	DataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.
DataStore	MappedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)

Constructors in org.biojava.bio.program.ssaha with parameters of type SequenceDB

Constructor and Description
SequenceDBStreamer(SequenceDB seqDB)

Uses of SequenceDB in org.biojava.bio.program.ssbind

Fields in org.biojava.bio.program.ssbind declared as SequenceDB

Modifier and Type	Field and Description
protected SequenceDB	ViewSequenceFactory.querySeqHolder

Methods in org.biojava.bio.program.ssbind that return SequenceDB

Modifier and Type	Method and Description
SequenceDB	ViewSequenceFactory.getQuerySeqHolder() getQuerySeqHolder returns the database of query sequences used to retrieve sequences for creation of the various result objects.

Methods in org.biojava.bio.program.ssbind with parameters of type SequenceDB

Modifier and Type	Method and Description
void	BlastLikeSearchBuilder.setQuerySeqHolder(SequenceDB querySeqHolder) setQuerySeqHolder sets the query sequence holder to a specific database.
void	ViewSequenceFactory.setQuerySeqHolder(SequenceDB querySeqHolder) setQuerySeqHolder sets the query sequence holder to a specific database.

Constructors in org.biojava.bio.program.ssbind with parameters of type SequenceDB

Constructor and Description
BlastLikeSearchBuilder(List target, SequenceDB querySeqHolder, SequenceDBInstallation subjectDBs) Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.

Uses of SequenceDB in org.biojava.bio.program.unigene

Methods in org.biojava.bio.program.unigene that return SequenceDB

Modifier and Type	Method and Description
SequenceDB	UnigeneCluster.getAll() All sequences that map to this cluster.

Uses of SequenceDB in org.biojava.bio.search

Methods in org.biojava.bio.search that return SequenceDB

Modifier and Type	Method and Description
SequenceDB	SequenceDBSearchResult.getSequenceDB() Deprecated.
SequenceDB	SimpleSeqSimilaritySearchResult.getSequenceDB()
SequenceDB	SeqSimilaritySearchResult.getSequenceDB() Returns the sequence database against which the search was performed.

Methods in org.biojava.bio.search with parameters of type SequenceDB

Modifier and Type	Method and Description
SeqSimilaritySearchResult	SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, Map searchParameters) Using this sequence similarity searcher, search with the given sequence against the given sequence database.

Constructors in org.biojava.bio.search with parameters of type SequenceDB

Constructor and Description
SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Deprecated. Creates a new SequenceDBSearchResult.
SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Creates a new SimpleSeqSimilaritySearchResult.

Uses of SequenceDB in org.biojava.bio.seq.db

Classes in org.biojava.bio.seq.db that implement SequenceDB

Modifier and Type	Class and Description
class	AbstractSequenceDB An abstract implementation of SequenceDB that provides the sequenceIterator method.
class	AnnotatedSequenceDB SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
class	CachingSequenceDB SequenceDB implementation that caches the results of another SequenceDB.
class	DummySequenceDB DummySequenceDB is an implementation which contains only a DummySequence.
class	HashSequenceDB An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
class	IndexedSequenceDB This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
class	SequenceDBWrapper An abstract implementation of SequenceDB that wraps up another database.
class	SubSequenceDB
class	ViewingSequenceDB SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.

Methods in org.biojava.bio.seq.db that return SequenceDB

Modifier and Type	Method and Description
SequenceDB	SequenceDBWrapper.getParent() Return the parent SequenceDB.
SequenceDB	AnnotatedSequenceDB.getParent() Get the original sequenceDB from this annotated sequenceDB.
SequenceDB	GenbankSequenceDB.getSequences(Set list) Retrieve sequences from a Genbank
SequenceDB	GenbankSequenceDB.getSequences(Set list, SequenceDB database) Retrieve sequences from a Genbank

Methods in org.biojava.bio.seq.db with parameters of type SequenceDB

Modifier and Type	Method and Description
SequenceDB	GenbankSequenceDB.getSequences(Set list, SequenceDB database) Retrieve sequences from a Genbank

Constructors in org.biojava.bio.seq.db with parameters of type SequenceDB

Constructor and Description
AnnotatedSequenceDB(SequenceDB parent, SequenceAnnotator a)
CachingSequenceDB(SequenceDB parent) Create a new CachingSequenceDB that caches the sequences in parent.
SequenceDBWrapper(SequenceDB parent)
SubSequenceDB(SequenceDB parent, Set ids)
ViewingSequenceDB(SequenceDB parent) Create a new ViewingSequenceDB that views the sequences in parent.

Uses of SequenceDB in org.biojava.bio.seq.db.biosql

Classes in org.biojava.bio.seq.db.biosql that implement SequenceDB

Modifier and Type	Class and Description
class	BioSQLSequenceDB Deprecated. Use hibernate and org.biojavax.bio.db.*

Uses of SequenceDB in org.biojava.bio.seq.distributed

Classes in org.biojava.bio.seq.distributed that implement SequenceDB

Modifier and Type	Class and Description
class	DistributedSequenceDB Sequence database from the meta-DAS system.

Constructors in org.biojava.bio.seq.distributed with parameters of type SequenceDB

Constructor and Description
SequenceDBDataSource(SequenceDB seqDB)

Uses of SequenceDB in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return SequenceDB

Modifier and Type	Method and Description
SequenceDB	SimpleRemoteFeature.DBResolver.getSeqDB()

Constructors in org.biojava.bio.seq.impl with parameters of type SequenceDB

Constructor and Description
DBResolver(SequenceDB seqDB)

Uses of SequenceDB in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that return SequenceDB

Modifier and Type	Method and Description
static SequenceDB	SeqIOTools.readFasta(InputStream seqFile, Alphabet alpha) Deprecated. Create a sequence database from a fasta file provided as an input stream.

Methods in org.biojava.bio.seq.io with parameters of type SequenceDB

Modifier and Type	Method and Description
static void	SeqIOTools.writeFasta(OutputStream os, SequenceDB db) Deprecated. Write a sequenceDB to an output stream in fasta format.

Constructors in org.biojava.bio.seq.io with parameters of type SequenceDB

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

Uses of SequenceDB in org.biojavax.bio.db

Subinterfaces of SequenceDB in org.biojavax.bio.db

Modifier and Type	Interface and Description
interface	RichSequenceDB A database of RichSequences with accessible keys and iterators over all sequences.

Classes in org.biojavax.bio.db that implement SequenceDB

Modifier and Type	Class and Description
class	AbstractRichSequenceDB An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
class	HashRichSequenceDB An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.

Uses of SequenceDB in org.biojavax.bio.db.biosql

Classes in org.biojavax.bio.db.biosql that implement SequenceDB

Modifier and Type	Class and Description
class	BioSQLRichSequenceDB

Uses of SequenceDB in org.biojavax.bio.db.ncbi

Classes in org.biojavax.bio.db.ncbi that implement SequenceDB

Modifier and Type	Class and Description
class	GenbankRichSequenceDB This class contains functions accessing DNA sequences in Genbank format.
class	GenpeptRichSequenceDB This class contains functions accessing Peptide sequences in Genpept format.