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 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
 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.