Uses of Interface
org.biojava.bio.seq.db.SequenceDB
Packages that use SequenceDB
Package
Description
Classes to generate and describe sequence alignments.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
GFF manipulation.
Parser for Phred output
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Objects for representing Unigene clusters.
Interfaces and classes for representing sequence similarity search results.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
-
Uses of SequenceDB in org.biojava.bio.alignment
Methods in org.biojava.bio.alignment with parameters of type SequenceDBModifier and TypeMethodDescriptionAlignmentAlgorithm.alignAll
(SequenceIterator source, SequenceDB subjectDB) -
Uses of SequenceDB in org.biojava.bio.dp
Methods in org.biojava.bio.dp with parameters of type SequenceDBModifier and TypeMethodDescriptionvoid
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 SequenceDBModifier and TypeMethodDescriptionvoid
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 SequenceDBModifier and TypeMethodDescriptionstatic 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 SequenceDBModifier and TypeMethodDescriptionstatic 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 SequenceDBModifier and TypeMethodDescriptionstatic 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 SequenceDBModifier and TypeMethodDescriptionCompactedDataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) DataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Build a new DataStore.MappedDataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) NIODataStoreFactory.buildDataStore
(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold) Constructors in org.biojava.bio.program.ssaha with parameters of type SequenceDB -
Uses of SequenceDB in org.biojava.bio.program.ssbind
Fields in org.biojava.bio.program.ssbind declared as SequenceDBMethods in org.biojava.bio.program.ssbind that return SequenceDBModifier and TypeMethodDescriptionViewSequenceFactory.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 SequenceDBModifier and TypeMethodDescriptionvoid
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 SequenceDBModifierConstructorDescriptionBlastLikeSearchBuilder
(List target, SequenceDB querySeqHolder, SequenceDBInstallation subjectDBs) Creates a newBlastLikeSearchBuilder
which will instantiate results into theList
target. -
Uses of SequenceDB in org.biojava.bio.program.unigene
Methods in org.biojava.bio.program.unigene that return SequenceDBModifier and TypeMethodDescriptionUnigeneCluster.getAll()
All sequences that map to this cluster. -
Uses of SequenceDB in org.biojava.bio.search
Methods in org.biojava.bio.search that return SequenceDBModifier and TypeMethodDescriptionSeqSimilaritySearchResult.getSequenceDB()
Returns the sequence database against which the search was performed.SequenceDBSearchResult.getSequenceDB()
Deprecated.SimpleSeqSimilaritySearchResult.getSequenceDB()
Methods in org.biojava.bio.search with parameters of type SequenceDBModifier and TypeMethodDescriptionSeqSimilaritySearcher.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 SequenceDBModifierConstructorDescriptionSequenceDBSearchResult
(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Deprecated.Creates a newSequenceDBSearchResult
.SimpleSeqSimilaritySearchResult
(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Creates a newSimpleSeqSimilaritySearchResult
. -
Uses of SequenceDB in org.biojava.bio.seq.db
Classes in org.biojava.bio.seq.db that implement SequenceDBModifier and TypeClassDescriptionclass
An abstract implementation of SequenceDB that provides the sequenceIterator method.class
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.class
SequenceDB implementation that caches the results of another SequenceDB.class
DummySequenceDB
is an implementation which contains only aDummySequence
.class
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.final class
This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.class
An abstract implementation of SequenceDB that wraps up another database.class
class
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.Methods in org.biojava.bio.seq.db that return SequenceDBModifier and TypeMethodDescriptionAnnotatedSequenceDB.getParent()
Get the original sequenceDB from this annotated sequenceDB.SequenceDBWrapper.getParent()
Return the parent SequenceDB.GenbankSequenceDB.getSequences
(Set list) Retrieve sequences from a GenbankGenbankSequenceDB.getSequences
(Set list, SequenceDB database) Retrieve sequences from a GenbankMethods in org.biojava.bio.seq.db with parameters of type SequenceDBModifier and TypeMethodDescriptionGenbankSequenceDB.getSequences
(Set list, SequenceDB database) Retrieve sequences from a GenbankConstructors in org.biojava.bio.seq.db with parameters of type SequenceDBModifierConstructorDescriptionAnnotatedSequenceDB
(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 SequenceDBModifier and TypeClassDescriptionclass
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 SequenceDBModifier and TypeClassDescriptionclass
Sequence database from the meta-DAS system.Constructors in org.biojava.bio.seq.distributed with parameters of type SequenceDB -
Uses of SequenceDB in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that return SequenceDBConstructors in org.biojava.bio.seq.impl with parameters of type SequenceDB -
Uses of SequenceDB in org.biojava.bio.seq.io
Methods in org.biojava.bio.seq.io that return SequenceDBModifier and TypeMethodDescriptionstatic 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 SequenceDBModifier and TypeMethodDescriptionstatic 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 -
Uses of SequenceDB in org.biojavax.bio.db
Subinterfaces of SequenceDB in org.biojavax.bio.dbModifier and TypeInterfaceDescriptioninterface
A database of RichSequences with accessible keys and iterators over all sequences.Classes in org.biojavax.bio.db that implement SequenceDBModifier and TypeClassDescriptionclass
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.class
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 -
Uses of SequenceDB in org.biojavax.bio.db.ncbi
Classes in org.biojavax.bio.db.ncbi that implement SequenceDBModifier and TypeClassDescriptionclass
This class contains functions accessing DNA sequences in Genbank format.class
This class contains functions accessing Peptide sequences in Genpept format.