Uses of Interface org.biojava.bio.seq.db.SequenceDB (BioJava-1.5-beta API)

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

Packages that use SequenceDB
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.das | Development client for the Distributed Annotation System.
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 |
org.biojavax.bio.db.ncbi |

Uses of SequenceDB in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment with parameters of type SequenceDB
`List` | `NeedlemanWunsch.alignAll(SequenceIterator source, SequenceDB subjectDB)`
`abstract List` | `SequenceAlignment.alignAll(SequenceIterator source, SequenceDB subjectDB)`

Uses of SequenceDB in org.biojava.bio.dp

Methods in org.biojava.bio.dp with parameters of type SequenceDB
`void` | `AbstractTrainer.train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper)` Trains the sequences in db until stopper says to finnish.
`void` | `TrainingAlgorithm.train(SequenceDB db, double nullWeight, StoppingCriteria stopper)` Trains the sequences in db untill stopper says to finnish.

Uses of SequenceDB in org.biojava.bio.gui

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

Classes in org.biojava.bio.program.das that implement SequenceDB
`class` | `DASSequenceDB` Collection of sequences retrieved from the DAS network.

Methods in org.biojava.bio.program.das that return SequenceDB
`SequenceDB` | `ReferenceServer.getDB()`

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

Methods in org.biojava.bio.program.gff that return SequenceDB
`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
`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
`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
`DataStore` | `CompactedDataStoreFactory.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` | `NIODataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)`
`DataStore` | `MappedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)`

Constructors in org.biojava.bio.program.ssaha with parameters of type SequenceDB
`SequenceStreamer.SequenceDBStreamer(SequenceDB seqDB)`

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

Fields in org.biojava.bio.program.ssbind declared as SequenceDB
`protected SequenceDB` | `ViewSequenceFactory.querySeqHolder`

Methods in org.biojava.bio.program.ssbind that return SequenceDB
`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
`void` | `ViewSequenceFactory.setQuerySeqHolder(SequenceDB querySeqHolder)` `setQuerySeqHolder` sets the query sequence holder to a specific database.
`void` | `BlastLikeSearchBuilder.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
`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
`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
`SequenceDB` | `SeqSimilaritySearchResult.getSequenceDB()` Returns the sequence database against which the search was performed.
`SequenceDB` | `SequenceDBSearchResult.getSequenceDB()` Deprecated.
`SequenceDB` | `SimpleSeqSimilaritySearchResult.getSequenceDB()`

Methods in org.biojava.bio.search with parameters of type SequenceDB
`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
`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
`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
`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
`SequenceDB` | `GenbankSequenceDB.getSequences(Set list, SequenceDB database)` Retrieve sequences from a Genbank

Constructors in org.biojava.bio.seq.db with parameters of type SequenceDB
`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
`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
`class` | `DistributedSequenceDB` Sequence database from the meta-DAS system.

Constructors in org.biojava.bio.seq.distributed with parameters of type SequenceDB
`SequenceDBDataSource(SequenceDB seqDB)`

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

Methods in org.biojava.bio.seq.impl that return SequenceDB
`SequenceDB` | `SimpleRemoteFeature.DBResolver.getSeqDB()`

Constructors in org.biojava.bio.seq.impl with parameters of type SequenceDB
`SimpleRemoteFeature.DBResolver(SequenceDB seqDB)`

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

Methods in org.biojava.bio.seq.io that return SequenceDB
`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
`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
`SequenceDBSequenceBuilder(SequenceDB db, int mode)` constructor

Uses of SequenceDB in org.biojavax.bio.db

Subinterfaces of SequenceDB in org.biojavax.bio.db
`interface` | `RichSequenceDB` A database of RichSequences with accessible keys and iterators over all sequences.

Classes in org.biojavax.bio.db that implement SequenceDB
`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
`class` | `BioSQLRichSequenceDB`

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

Classes in org.biojavax.bio.db.ncbi that implement SequenceDB
`class` | `GenbankRichSequenceDB` This class contains functions accessing DNA sequences in Genbank format.

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