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Packages that use SequenceDB | |
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. |
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. |
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(java.io.OutputStream qual,
java.io.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(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
|
DataStore |
DataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
Build a new DataStore. |
DataStore |
NIODataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
|
DataStore |
MappedDataStoreFactory.buildDataStore(java.io.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(java.util.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 |
SimpleSeqSimilaritySearchResult.getSequenceDB()
|
SequenceDB |
SequenceDBSearchResult.getSequenceDB()
Deprecated. |
Methods in org.biojava.bio.search with parameters of type SequenceDB | |
SeqSimilaritySearchResult |
SeqSimilaritySearcher.search(SymbolList querySeq,
SequenceDB db,
java.util.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 | |
SimpleSeqSimilaritySearchResult(Sequence querySequence,
SequenceDB sequenceDB,
java.util.Map searchParameters,
java.util.List hits,
Annotation annotation)
Creates a new SimpleSeqSimilaritySearchResult . |
|
SequenceDBSearchResult(Sequence querySequence,
SequenceDB sequenceDB,
java.util.Map searchParameters,
java.util.List hits,
Annotation annotation)
Deprecated. Creates a new SequenceDBSearchResult . |
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 |
AnnotatedSequenceDB.getParent()
Get the original sequenceDB from this annotated sequenceDB. |
SequenceDB |
SequenceDBWrapper.getParent()
Return the parent SequenceDB. |
SequenceDB |
GenbankSequenceDB.getSequences(java.util.Set list)
Retrieve sequences from a Genbank |
SequenceDB |
GenbankSequenceDB.getSequences(java.util.Set list,
SequenceDB database)
Retrieve sequences from a Genbank |
Methods in org.biojava.bio.seq.db with parameters of type SequenceDB | |
SequenceDB |
GenbankSequenceDB.getSequences(java.util.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)
|
|
SequenceDBWrapper(SequenceDB parent)
|
|
CachingSequenceDB(SequenceDB parent)
Create a new CachingSequenceDB that caches the sequences in parent. |
|
ViewingSequenceDB(SequenceDB parent)
Create a new ViewingSequenceDB that views the sequences in parent. |
|
SubSequenceDB(SequenceDB parent,
java.util.Set ids)
|
Uses of SequenceDB in org.biojava.bio.seq.db.biosql |
Classes in org.biojava.bio.seq.db.biosql that implement SequenceDB | |
class |
BioSQLSequenceDB
SequenceDB keyed off a BioSQL database. |
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(java.io.InputStream seqFile,
Alphabet alpha)
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(java.io.OutputStream os,
SequenceDB db)
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 |
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