Package | Description |
---|---|
org.biojava.bio.alignment |
Classes to generate and describe sequence alignments.
|
org.biojava.bio.annodb |
Databases of generic structured data (annotation) objects.
|
org.biojava.bio.chromatogram |
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
|
org.biojava.bio.dist |
Probability distributions over Alphabets.
|
org.biojava.bio.dp |
HMM and Dynamic Programming Algorithms.
|
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.gui |
Graphical interfaces for biojava objects.
|
org.biojava.bio.molbio |
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
|
org.biojava.bio.program.das |
Development client for the Distributed Annotation System.
|
org.biojava.bio.program.das.dasalignment |
request alignments via DAS
|
org.biojava.bio.program.formats |
Experimental parsers using the tagvalue framework.
|
org.biojava.bio.program.gff |
GFF manipulation.
|
org.biojava.bio.program.gff3 |
Support for reading and writing GFF3.
|
org.biojava.bio.program.homologene |
Support classes for Homologene data.
|
org.biojava.bio.program.indexdb |
A flat-file ascii index of ascii flat files as per the OBDA specification.
|
org.biojava.bio.program.phred |
Parser for Phred output
|
org.biojava.bio.program.sax.blastxml |
Parsers for the XML output from NCBI blast.
|
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.program.xff |
Event-driven parsing system for the Extensible Feature Format (XFF).
|
org.biojava.bio.proteomics |
Utilities to aid in performing various physical analysis of proteins.
|
org.biojava.bio.proteomics.aaindex |
Classes and interfaces to load Amino Acid Index database files.
|
org.biojava.bio.search |
Interfaces and classes for representing sequence similarity search results.
|
org.biojava.bio.seq |
Classes and interfaces for defining biological sequences and informatics
objects.
|
org.biojava.bio.seq.db |
Collections of biological sequence data.
|
org.biojava.bio.seq.db.biofetch |
Client for the OBDA BioFetch protocol.
|
org.biojava.bio.seq.db.biosql |
General purpose Sequence storage in a relational database.
|
org.biojava.bio.seq.db.flat |
Support for OBDA flatfile databases.
|
org.biojava.bio.seq.distributed |
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
|
org.biojava.bio.seq.homol |
The classes and interfaces for defining sequence similarity and
honology.
|
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.biojava.bio.seq.projection |
Code for projecting Feature objects and systematically altering their
properties.
|
org.biojava.bio.structure |
Interfaces and classes for protein structure (PDB).
|
org.biojava.bio.structure.io |
Input and Output of Structures
|
org.biojava.bio.symbol |
Representation of the Symbols that make up a sequence, and locations within
them.
|
org.biojava.bio.taxa |
Taxonomy object for representing species information.
|
org.biojava.directory |
Open Bio Sequence Database Access (OBDA) registry support.
|
org.biojava.utils.automata | |
org.biojava.utils.math |
Mathematical utility classes.
|
org.biojava.utils.regex |
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
|
org.biojava.utils.walker | |
org.biojavax.bio |
Classes to represent biological entities and their relationships.
|
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.
|
org.biojavax.bio.seq |
Rich implementations of Sequences, Locations and Features.
|
org.biojavax.bio.seq.io |
Classes to support the I/O of RichSequence and
Bioentry objects.
|
Modifier and Type | Method and Description |
---|---|
void |
ARAlignment.addSequence(AlignmentElement ae) |
void |
FlexibleAlignment.addSequence(AlignmentElement ae)
add a new a alignment usings a location to the reference sequence.
|
java.util.List<Alignment> |
NeedlemanWunsch.alignAll(SequenceIterator source,
SequenceDB subjectDB) |
java.lang.String |
NeedlemanWunsch.getAlignmentString() |
static SubstitutionMatrix |
SubstitutionMatrix.getSubstitutionMatrix(java.io.BufferedReader reader)
This constructor can be used to guess the alphabet of this substitution
matrix.
|
short |
SubstitutionMatrix.getValueAt(Symbol row,
Symbol col)
There are some substitution matrices containing more columns than lines.
|
SubstitutionMatrix |
SubstitutionMatrix.normalizeMatrix()
With this method you can get a “normalized”
SubstitutionMatrix object; however, since this
implementation uses an short matrix, the normalized matrix will be scaled
by ten. |
Constructor and Description |
---|
FlexibleAlignment(java.util.List seqList)
construct this object with the reference sequence which can either be a gappedSymbolList or not
label in all cases refers to an object that holds the display name (generally just a String).
|
SimpleAlignmentElement(java.lang.Object label,
SymbolList seq,
Location loc) |
SubstitutionMatrix(java.io.File file)
This constructor can be used to guess the alphabet of this substitution
matrix.
|
SubstitutionMatrix(FiniteAlphabet alpha,
java.io.File matrixFile)
This constructs a
SubstitutionMatrix object that contains
two Map data structures having BioJava symbols as keys and
the value being the index of the matrix containing the substitution score. |
SubstitutionMatrix(FiniteAlphabet alpha,
java.lang.String matrixString,
java.lang.String name)
With this constructor it is possible to construct a SubstitutionMatrix
object from a substitution matrix file.
|
Constructor and Description |
---|
IndexedAnnotationDB(java.lang.String dbName,
java.io.File storeLoc,
Index2Model model,
java.util.List toIndex,
int maxKeyLen,
AnnotationType schema,
IndexedAnnotationDB.ParserListenerFactory plFactory)
Create a new IndexedAnnotationDB.
|
Modifier and Type | Class and Description |
---|---|
class |
UnsupportedChromatogramFormatException
Exception indicating that some provided data does not represent
a supported chromatogram format.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
DistributionTools.areEmissionSpectraEqual(Distribution[] a,
Distribution[] b)
Compares the emission spectra of two distribution arrays.
|
static boolean |
DistributionTools.areEmissionSpectraEqual(Distribution a,
Distribution b)
Compares the emission spectra of two distributions.
|
Modifier and Type | Class and Description |
---|---|
class |
IllegalTransitionException
This exception indicates that there is no transition between two states.
|
Modifier and Type | Method and Description |
---|---|
Sequence |
WeightMatrixAnnotator.annotate(Sequence seq) |
void |
HMMTrainer.completeCycle()
indicate that a cycle of training is completed and the
emission/transition matrices should be updated.
|
void |
SimpleHMMTrainer.completeCycle() |
DP |
DPFactory.createDP(MarkovModel model) |
DP |
DPFactory.DefaultFactory.createDP(MarkovModel model) |
DPMatrix |
DP.forwardsBackwards(SymbolList[] symList,
ScoreType scoreType) |
StatePath |
DP.generate(int length)
Generates an alignment from a model.
|
static WeightMatrix |
XmlMarkovModel.readMatrix(org.w3c.dom.Element root) |
static MarkovModel |
XmlMarkovModel.readModel(org.w3c.dom.Element root) |
void |
Trainable.registerWithTrainer(ModelTrainer mt)
Perform any registration that is necessary with mt.
|
void |
WMAsMM.registerWithTrainer(ModelTrainer modelTrainer) |
State[] |
DP.stateList(MarkovModel mm) |
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.
|
Constructor and Description |
---|
SingleDP(MarkovModel model) |
Modifier and Type | Method and Description |
---|---|
CellCalculatorFactory |
CellCalculatorFactoryMaker.make(DP dp) |
Constructor and Description |
---|
PairwiseDP(MarkovModel mm,
CellCalculatorFactoryMaker ccfm) |
Modifier and Type | Method and Description |
---|---|
void |
FeatureTree.setSequenceDB(SequenceDB db)
Use this method to provide the sequences for the tree to work with.
|
Modifier and Type | Method and Description |
---|---|
int[] |
RestrictionEnzyme.getUpstreamCut()
getUpstreamCut returns the cut site upstream of
the recognition site. |
int |
RestrictionEnzyme.getUpstreamEndType()
getUpstreamEndType returns the double-stranded end
type produced by the secondary (upstream) cut. |
Modifier and Type | Method and Description |
---|---|
void |
DASSequence.addAnnotationSource(java.net.URL dataSourceURL) |
void |
DAS.addDasURL(java.net.URL dasURL) |
SequenceDB |
ReferenceServer.getDB() |
DistDataSource |
ReferenceServer.getDistDataSource() |
DistDataSource |
DataSource.getDistDataSource() |
Sequence |
DASSequenceDB.getSequence(java.lang.String id) |
SequenceDBLite |
DASSequenceDBProvider.getSequenceDB(java.util.Map config) |
protected SymbolList |
DASSequence.getSymbols() |
static java.util.Set |
DAS.getTypes(java.net.URL dasURL) |
Feature |
DASSequence.realizeFeature(FeatureHolder dest,
Feature.Template temp) |
void |
DASSequence.removeAnnotationSource(java.net.URL dataSourceURL) |
Constructor and Description |
---|
DASSequenceDB(java.net.URL dataSourceURL) |
Modifier and Type | Class and Description |
---|---|
class |
DASException
An exception of one of the DAS classes.
|
Modifier and Type | Method and Description |
---|---|
static Format |
FormatTools.getFormat(java.lang.String formatName)
Attempt to find aformat for a format identifer string.
|
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.
|
protected SimpleGFFRecord |
SequencesAsGFF.createGFFRecord(Feature feature,
java.lang.String id)
Internal method to create a GFFRecord
from an individual Feature.
|
protected GFFRecord |
GFFParser.createRecord(GFFDocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment)
Actually turns a list of tokens, some value string and a comment into a
GFFRecord and informs
handler.
|
protected void |
SequencesAsGFF.doPreProcessSequence(Sequence seq,
GFFDocumentHandler handler,
java.lang.String id)
Emit any per-sequence header information.
|
protected void |
SequencesAsGFF.doProcessFeature(Feature feature,
GFFDocumentHandler handler,
java.lang.String id)
Internal method to process an individual Feature.
|
protected void |
SequencesAsGFF.doProcessSequence(Sequence seq,
GFFDocumentHandler handler,
java.lang.String id)
Internal method to process an individual Sequence.
|
static GFFEntrySet |
GFFTools.gffFromSeqDB(SequenceDB seqDB)
Creates a GFFEntrySet containing one entry for each feature on each
sequence of a SequenceDB.
|
static GFFEntrySet |
GFFTools.gffFromSequence(Sequence seq)
Creates a GFFEntrySet containing one entry for each feature on a sequence.
|
void |
GFFWriter.invalidEnd(java.lang.String token,
java.lang.NumberFormatException nfe) |
void |
GFFWriter.invalidFrame(java.lang.String token,
java.lang.NumberFormatException nfe) |
void |
GFFWriter.invalidScore(java.lang.String token,
java.lang.NumberFormatException nfe) |
void |
GFFWriter.invalidStart(java.lang.String token,
java.lang.NumberFormatException nfe) |
void |
GFFWriter.invalidStrand(java.lang.String token) |
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler)
Informs handler of each line of
gff read from bReader.
|
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler,
java.lang.String locator)
Informs handler of each line of
GFF read from bReader
|
void |
SequencesAsGFF.processDB(SequenceDB seqDB,
GFFDocumentHandler handler)
Process all Sequences within a
SequenceDB, informing
handler of any suitable features.
|
void |
SequencesAsGFF.processSequence(Sequence seq,
GFFDocumentHandler handler)
Process an individual Sequence, informing
handler of any suitable features.
|
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn)
Read all GFF entries from a buffered reader.
|
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn,
GFFRecordFilter recFilt)
Read all GFF entries matching a filter from a buffered reader.
|
static GFFEntrySet |
GFFTools.readGFF(java.io.File inFile)
Reads a
GFFEntrySet from a file with no filtering. |
static GFFEntrySet |
GFFTools.readGFF(java.io.File inFile,
GFFRecordFilter recFilt)
Reads a GFFEntrySet from a file with the specified filter.
|
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName)
Deprecated.
use: readGff(File)
|
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName,
GFFRecordFilter recFilt)
Deprecated.
use: readGff(File,GFFRecordFilter)
|
Modifier and Type | Method and Description |
---|---|
protected GFF3Record |
GFF3Parser.createRecord(GFF3DocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment,
Ontology ontology,
Ontology fallBack)
Actually turns a list of tokens, some value string and a comment into a
GFF3Record and informs
handler.
|
void |
GFF3Parser.parse(java.io.BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology)
Informs handler of each line of
gff read from bReader.
|
void |
GFF3Parser.parse(java.io.BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology,
java.lang.String locator)
Informs handler of each line of
GFF read from bReader
|
Modifier and Type | Class and Description |
---|---|
class |
DuplicateTaxonException |
Modifier and Type | Method and Description |
---|---|
BioStore |
BioStoreFactory.createBioStore()
createBioStore creates a BioStore
reflecting the current state of the factory and returns a
reference to it. |
Record |
IndexStore.get(java.lang.String id)
get returns a record specified by a primary
identifier. |
java.util.List |
BioStore.get(java.lang.String id,
java.lang.String namespace) |
java.util.List |
IndexStore.get(java.lang.String id,
java.lang.String namespace)
get returns a list of Record s by
searching against the primary identifiers if the namespace
argument is equal to the primary namespace or otherwise by
searching the secondary namespaces. |
static void |
IndexTools.indexEmbl(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexEmbl indexes DNA, RNA or protein EMBL format
sequence files on ID as primary identifier and AC as secondary. |
static void |
IndexTools.indexFasta(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexFasta indexes DNA, RNA or protein Fasta
format sequence files on primary identifier. |
static void |
IndexTools.indexGenbank(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexGenbank indexes DNA, RNA or protein Genbank
format sequence files on LOCUS as primary identifier and
ACCESSION as secondary. |
static void |
IndexTools.indexSwissprot(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles)
indexSwissprot indexes Swissprot format protein
sequence files on ID as primary identifier. |
Constructor and Description |
---|
BioStore(java.io.File location,
boolean cache)
Creates a new
BioStore flatfile index at the
specified location with the specified caching behaviour. |
Modifier and Type | Method and Description |
---|---|
static void |
PhredTools.writePhredQuality(java.io.OutputStream qual,
java.io.OutputStream seq,
SequenceDB db)
Writes Phred quality data in a Fasta type format.
|
Constructor and Description |
---|
BlastXMLParserFacade() |
Modifier and Type | Method and Description |
---|---|
DataStore |
DataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
Build a new DataStore.
|
DataStore |
CompactedDataStoreFactory.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) |
DataStore |
NIODataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold) |
DataStore |
CompactedDataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceStreamer streamer,
Packing packing,
int wordLength,
int stepSize,
int threshold) |
void |
SequenceStreamer.reset() |
void |
SequenceStreamer.streamNext(SeqIOListener listener) |
void |
SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener) |
void |
SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener) |
Modifier and Type | Method and Description |
---|---|
protected Sequence |
ViewSequenceFactory.makeQueryViewSequence(java.lang.String queryID) |
SeqSimilaritySearchResult |
BlastLikeSearchBuilder.makeSearchResult() |
protected Sequence |
ViewSequenceFactory.makeSubjectViewSequence(java.lang.String subjectID) |
static FiniteAlphabet |
AlphabetResolver.resolveAlphabet(java.lang.String identifier)
resolveAlphabet returns an appropriate
Alphabet for an arbitrary identifier. |
Modifier and Type | Method and Description |
---|---|
UnigeneCluster |
UnigeneDB.addCluster(UnigeneCluster cluster)
Add a cluster to a database.
|
UnigeneDB |
FlatFileUnigeneFactory.createUnigene(java.net.URL unigeneLoc) |
UnigeneDB |
SQLUnigeneFactory.createUnigene(java.net.URL dbURL) |
static UnigeneDB |
UnigeneTools.createUnigene(java.net.URL dbURL)
Create a new UnigeneDB instance referred to by a URL.
|
UnigeneDB |
UnigeneFactory.createUnigene(java.net.URL unigeneURL) |
static UnigeneFactory |
UnigeneTools.findFactory(java.net.URL dbURL)
Find the UnigeneFactory that can accept a URL.
|
UnigeneCluster |
UnigeneDB.getCluster(java.lang.String clusterID)
Fetch a cluster by its cluster id.
|
UnigeneDB |
FlatFileUnigeneFactory.loadUnigene(java.net.URL unigeneLoc) |
UnigeneDB |
SQLUnigeneFactory.loadUnigene(java.net.URL dbURL) |
static UnigeneDB |
UnigeneTools.loadUnigene(java.net.URL dbURL)
Load a UnigeneDB instance referred to by a URL.
|
UnigeneDB |
UnigeneFactory.loadUnigene(java.net.URL unigeneURL) |
Modifier and Type | Method and Description |
---|---|
static void |
XFFTools.annotateXFF(java.io.File xffFile,
Sequence sequence) |
static void |
XFFTools.annotateXFF(java.io.File xffFile,
Sequence sequence,
Annotation ann) |
static Sequence |
XFFTools.readXFF(java.io.File xffFile,
java.lang.String seqID) |
static Sequence |
XFFTools.readXFF(java.io.File xffFile,
java.lang.String seqID,
FiniteAlphabet alpha) |
Modifier and Type | Method and Description |
---|---|
void |
Digest.addDigestFeatures()
Adds peptides as features to the Sequence in this class.
|
static Protease |
ProteaseManager.createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String name) |
static Protease |
ProteaseManager.createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String notCleaveRes,
java.lang.String name) |
static Protease |
ProteaseManager.createProtease(SymbolList cleaveRes,
boolean endoProtease,
java.lang.String name) |
static Protease |
ProteaseManager.createProtease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes,
java.lang.String name)
Creates and registers a new Protease.
|
static double |
IsoelectricPointCalc.getIsoelectricPoint(SymbolList peptide)
Static public method to compute the pI for a polypeptide in
denaturating and reduced conditions with both free ends.
|
double |
IsoelectricPointCalc.getPI(SymbolList peptide,
boolean hasFreeNTerm,
boolean hasFreeCTerm)
Computes isoelectric point of specified peptide.
|
static Protease |
Protease.getProteaseByName(java.lang.String proteaseName)
Retrieves a reference to the named Protease.
|
static Protease |
ProteaseManager.getProteaseByName(java.lang.String proteaseName)
Gets a Protease instance by name.
|
static void |
ProteaseManager.registerProtease(Protease prot)
Registers a protease and ensures its flyweight status
|
Constructor and Description |
---|
Protease(java.lang.String cleavageRes,
boolean endoProtease)
Deprecated.
Creating a Protease with this constructor will not register it
with the ProteaseManager (use ProteaseManager.createProtease())
|
Protease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String notCleaveRes)
Deprecated.
Creating a Protease with this constructor will not register it
with the ProteaseManager (use ProteaseManager.createProtease())
|
Protease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes)
Deprecated.
Creating a Protease with this constructor will not register it
with the ProteaseManager (use ProteaseManager.createProtease())
|
Modifier and Type | Method and Description |
---|---|
SymbolPropertyTable |
AAindexStreamReader.nextTable()
Returns the next
SymbolPropertyTable
object. |
SymbolPropertyTable |
SymbolPropertyTableIterator.nextTable()
Returns the next
SymbolPropertyTable
object. |
Constructor and Description |
---|
SimpleSymbolPropertyTableDB(SymbolPropertyTableIterator tableIterator)
Initializes the database by copying all symbol property tables from
a given iterator into the database.
|
Modifier and Type | Method and Description |
---|---|
SeqSimilaritySearchResult |
SearchBuilder.makeSearchResult()
The
makeSearchResult method returns a
SeqSimilaritySearchResult instance created from
accumulated data. |
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.
|
Constructor and Description |
---|
FilteringContentHandler(BlastLikeSearchFilter filter) |
FilteringContentHandler(BlastLikeSearchFilter filter,
SearchContentHandler delegate) |
Modifier and Type | Method and Description |
---|---|
static void |
SequenceTools.addAllFeatures(Sequence seq,
FeatureHolder fh)
Add features to a sequence that contain the same information as all
those in a feature holder.
|
void |
SimpleFeatureRealizer.addImplementation(java.lang.Class template,
java.lang.Class impl)
Install a new mapping from a class of Feature.Template to
a class of Feature implementations.
|
Sequence |
SequenceAnnotator.annotate(Sequence seq)
Return an annotated version of a sequence.
|
Feature |
SimpleAssembly.createFeature(Feature.Template temp) |
Feature |
AbstractFeatureHolder.createFeature(Feature.Template temp) |
Feature |
FeatureHolder.createFeature(Feature.Template ft)
Create a new Feature, and add it to this FeatureHolder.
|
Feature |
NewSimpleAssembly.createFeature(Feature.Template temp) |
Feature |
CircularView.createFeature(Feature.Template template)
Over rides ViewSequence to allow the use of locations that have
coordinates outside of the sequence length (which are needed to
describe locations that overlap the origin of a circular sequence).
|
Feature |
LazyFeatureHolder.createFeature(Feature.Template template) |
Feature |
RemoteFeature.getRemoteFeature()
Retrieve the Feature on some assembly Sequence that can represent this
RemoteFeature properly.
|
Sequence |
SequenceIterator.nextSequence()
Returns the next sequence in the iterator.
|
Feature |
SimpleAssembly.realizeFeature(FeatureHolder fh,
Feature.Template temp) |
Feature |
NewSimpleAssembly.realizeFeature(FeatureHolder fh,
Feature.Template temp) |
Feature |
RealizingFeatureHolder.realizeFeature(FeatureHolder parent,
Feature.Template template)
Realize a feature template.
|
Feature |
SimpleFeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template temp) |
Feature |
FeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template template)
Install a feature on the specified sequence.
|
void |
AbstractFeatureHolder.removeFeature(Feature f) |
void |
FeatureHolder.removeFeature(Feature f)
Remove a feature from this FeatureHolder.
|
void |
LazyFeatureHolder.removeFeature(Feature f) |
Feature |
RemoteFeature.Resolver.resolve(RemoteFeature rFeat)
Resolve rFeat.
|
static java.lang.Object |
FilterUtils.visitFilter(FeatureFilter filter,
Visitor visitor)
Applies a visitor to a filter, and returns the visitor's result or null.
|
Modifier and Type | Class and Description |
---|---|
class |
IllegalIDException |
Modifier and Type | Method and Description |
---|---|
void |
IndexedSequenceDB.addFile(java.io.File seqFile)
Add sequences from a file to the sequence database.
|
void |
DummySequenceDB.addSequence(Sequence seq) |
void |
SequenceDBLite.addSequence(Sequence seq)
Adds a sequence to the database.
|
void |
AbstractSequenceDB.addSequence(Sequence seq) |
void |
EmblCDROMIndexStore.commit()
commit commits changes. |
void |
TabIndexStore.commit() |
void |
BioIndex.commit() |
void |
IndexStore.commit()
Commit the stored indices to permanent storage.
|
protected Sequence |
AnnotatedSequenceDB.doAnnotation(Sequence seq)
Apply the annotation to a sequence.
|
Index |
EmblCDROMIndexStore.fetch(java.lang.String id) |
Index |
TabIndexStore.fetch(java.lang.String id) |
Index |
BioIndex.fetch(java.lang.String id) |
Index |
IndexStore.fetch(java.lang.String id)
Fetch an Index based upon an ID.
|
Sequence |
IndexedSequenceDB.getSequence(java.lang.String id) |
Sequence |
DummySequenceDB.getSequence(java.lang.String id) |
Sequence |
SequenceDBLite.getSequence(java.lang.String id)
Retrieve a single sequence by its id.
|
Sequence |
CachingSequenceDB.getSequence(java.lang.String id) |
Sequence |
GenpeptSequenceDB.getSequence(java.lang.String id) |
Sequence |
AnnotatedSequenceDB.getSequence(java.lang.String id) |
Sequence |
ViewingSequenceDB.getSequence(java.lang.String id) |
Sequence |
SubSequenceDB.getSequence(java.lang.String id) |
Sequence |
SwissprotSequenceDB.getSequence(java.lang.String id) |
Sequence |
WebSequenceDB.getSequence(java.lang.String id)
Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
|
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
|
void |
DummySequenceDB.removeSequence(java.lang.String id) |
void |
SequenceDBLite.removeSequence(java.lang.String id)
Remove the sequence associated with an ID from the database.
|
void |
HashSequenceDB.removeSequence(java.lang.String id) |
void |
AbstractSequenceDB.removeSequence(java.lang.String id) |
void |
NCBISequenceDB.setDatabase(java.lang.String dataBase) |
void |
NCBISequenceDB.setSequenceFormat(SequenceFormat format) |
void |
EmblCDROMIndexStore.store(Index index)
store adds an Index to the store. |
void |
TabIndexStore.store(Index indx) |
void |
IndexStore.store(Index indx)
Add the Index to the store.
|
Constructor and Description |
---|
BioIndex(java.io.File indexDirectory)
Load an existing index file.
|
BioIndex(java.io.File indexDirectory,
java.lang.String namespace,
int idLength) |
SubSequenceDB(SequenceDB parent,
java.util.Set ids) |
TabIndexStore(java.io.File storeFile,
java.io.File indexFile,
java.lang.String name,
SequenceFormat format,
SequenceBuilderFactory sbFactory,
SymbolTokenization symbolParser)
Create a new TabIndexStore.
|
Modifier and Type | Method and Description |
---|---|
Sequence |
BioFetchSequenceDB.getSequence(java.lang.String id) |
SequenceDBLite |
BioFetchSequenceDBProvider.getSequenceDB(java.util.Map config) |
Modifier and Type | Method and Description |
---|---|
static Taxon |
TaxonSQL.addName(java.sql.Connection conn,
Taxon taxon,
java.lang.String nameClass,
java.lang.String newName)
Deprecated.
Adds a new name of the given
nameClass to the taxon. |
void |
BioSQLSequenceDB.addSequence(Sequence seq)
Deprecated.
|
void |
BioSQLSequenceDB.createDummySequence(java.lang.String id,
Alphabet alphabet,
int length)
Deprecated.
|
static java.util.Stack |
TaxonSQL.getChildrenOf(java.sql.Connection conn,
java.lang.String scientificName)
Deprecated.
Returns all children of the specified taxon.
|
static java.util.Stack |
TaxonSQL.getChildrenOf(java.sql.Connection conn,
Taxon t)
Deprecated.
Returns the children as a
Stack of this given taxon. |
Sequence |
BioSQLSequenceDB.getSequence(int bioentry_id)
Deprecated.
|
Sequence |
BioSQLSequenceDB.getSequence(java.lang.String id)
Deprecated.
|
SequenceDBLite |
BioSQLSequenceDBProvider.getSequenceDB(java.util.Map config)
Deprecated.
|
static Taxon |
TaxonSQL.removeName(java.sql.Connection conn,
DBHelper helper,
Taxon taxon,
java.lang.String nameClass,
java.lang.String oldName)
Deprecated.
Deletes the specified name from of the taxon from the database.
|
void |
BioSQLSequenceDB.removeSequence(java.lang.String id)
Deprecated.
|
static Taxon |
TaxonSQL.removeTaxon(java.sql.Connection conn,
DBHelper helper,
java.lang.String name)
Deprecated.
Deletes a taxon specified by one of it's names with all it's different
names, annotations and sequences from the database.
|
static Taxon |
TaxonSQL.removeTaxon(java.sql.Connection conn,
int ncbi_id,
DBHelper helper)
Deprecated.
Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the
removed taxon.
|
static Taxon |
TaxonSQL.setCommonName(java.sql.Connection conn,
Taxon taxon,
java.lang.String newName)
Deprecated.
With this method the common name of the given taxon can be changed or created,
if there was none before.
|
Constructor and Description |
---|
BioSQLSequenceDB(javax.sql.DataSource ds,
java.lang.String biodatabase,
boolean create)
Deprecated.
|
BioSQLSequenceDB(java.lang.String dbURL,
java.lang.String dbUser,
java.lang.String dbPass,
java.lang.String biodatabase,
boolean create)
Deprecated.
Connect to a BioSQL database.
|
BioSQLSequenceDB(java.lang.String dbDriver,
java.lang.String dbURL,
java.lang.String dbUser,
java.lang.String dbPass,
java.lang.String biodatabase,
boolean create)
Deprecated.
Connect to a BioSQL database.
|
Modifier and Type | Method and Description |
---|---|
Sequence |
FlatSequenceDB.getSequence(java.lang.String id) |
SequenceDBLite |
FlatSequenceDBProvider.getSequenceDB(java.util.Map config) |
Constructor and Description |
---|
FlatSequenceDB(java.lang.String location,
java.lang.String dbName) |
Modifier and Type | Method and Description |
---|---|
FeatureHolder |
SequenceDBDataSource.getFeatures(FeatureFilter ff) |
FeatureHolder |
DistDataSource.getFeatures(FeatureFilter ff)
Get all features matching a FeatureFilter provided by this DistDataSource.
|
FeatureHolder |
GFFDataSource.getFeatures(FeatureFilter ff) |
FeatureHolder |
SequenceDBDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse) |
FeatureHolder |
DistDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse)
Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
|
FeatureHolder |
GFFDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse) |
Sequence |
SequenceDBDataSource.getSequence(java.lang.String id) |
Sequence |
DistributedSequenceDB.getSequence(java.lang.String id) |
Sequence |
DistDataSource.getSequence(java.lang.String id)
Get a Sequence object for an ID.
|
Sequence |
GFFDataSource.getSequence(java.lang.String id) |
boolean |
SequenceDBDataSource.hasFeatures(java.lang.String id) |
boolean |
DistDataSource.hasFeatures(java.lang.String id)
Find out if this DistDataSource can provide features on a sequence with a particular ID.
|
boolean |
GFFDataSource.hasFeatures(java.lang.String id) |
boolean |
SequenceDBDataSource.hasSequence(java.lang.String id) |
boolean |
DistDataSource.hasSequence(java.lang.String id)
Find out if this DistDataSource provides the sequence information for a sequence ID.
|
boolean |
GFFDataSource.hasSequence(java.lang.String id) |
java.util.Set |
SequenceDBDataSource.ids(boolean topLevel) |
java.util.Set |
DistDataSource.ids(boolean topLevel)
Get the complete set of sequence IDs provided by this DistDataSource.
|
java.util.Set |
GFFDataSource.ids(boolean topLevel) |
Modifier and Type | Method and Description |
---|---|
void |
SimpleHomology.setAlignment(Alignment alignment)
setAlignment sets the alignment which describes
the homology. |
Modifier and Type | Method and Description |
---|---|
Feature |
DummySequence.createFeature(Feature.Template template) |
Feature |
RevCompSequence.createFeature(Feature.Template ft)
createFeature() will call createFeature() on the underlying Sequence.
|
Feature |
ViewSequence.createFeature(Feature.Template template) |
Feature |
SimpleGappedSequence.createFeature(Feature.Template templ) |
Feature |
LazyFilterFeatureHolder.createFeature(Feature.Template temp) |
Feature |
SimpleFeature.createFeature(Feature.Template temp) |
Feature |
SimpleSequence.createFeature(Feature.Template template) |
Feature |
SubSequence.createFeature(Feature.Template templ) |
Feature |
SimpleSequence.createFeature(FeatureHolder fh,
Feature.Template template)
Deprecated.
Please use new 1-arg createFeature instead.
|
Feature |
SimpleRemoteFeature.getRemoteFeature() |
static Feature.Template |
TemplateUtils.instantiateTemplate(Feature feat)
This attempts to divine the 'best' template class for a feature and return
a new instance readly for pupulating.
|
static Feature.Template |
TemplateUtils.makeTemplate(Feature feat) |
static void |
TemplateUtils.populate(Feature.Template templ,
Feature feat)
This attempts to populate the fields of a template using
the publically accessible information in a feature.
|
Feature |
ViewSequence.realizeFeature(FeatureHolder parent,
Feature.Template template) |
Feature |
SimpleFeature.realizeFeature(FeatureHolder fh,
Feature.Template templ) |
Feature |
SimpleSequence.realizeFeature(FeatureHolder parent,
Feature.Template template) |
void |
DummySequence.removeFeature(Feature feature) |
void |
RevCompSequence.removeFeature(Feature f) |
void |
SimpleGappedSequence.removeFeature(Feature f) |
void |
LazyFilterFeatureHolder.removeFeature(Feature f) |
void |
SimpleSequence.removeFeature(Feature f)
Remove a feature attached to this sequence.
|
void |
SubSequence.removeFeature(Feature f) |
Feature |
SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat) |
Modifier and Type | Class and Description |
---|---|
class |
ParseException
ParseException should be thrown to indicate that there was a problem with
parsing sequence information.
|
Modifier and Type | Method and Description |
---|---|
ComponentFeature |
SimpleAssemblyBuilder.addComponentSequence(ComponentFeature.Template cft) |
static void |
SeqIOTools.biojavaToFile(int fileType,
java.io.OutputStream os,
java.lang.Object biojava)
Deprecated.
Converts a Biojava object to the given filetype.
|
static void |
SeqIOTools.biojavaToFile(java.lang.String formatName,
java.lang.String alphabetName,
java.io.OutputStream os,
java.lang.Object biojava)
Deprecated.
Writes a Biojava
SequenceIterator ,
SequenceDB , Sequence or Aligment
to an OutputStream |
void |
FeatureTableParser.endFeature()
Deprecated.
|
void |
FeatureTableParser.featureData(java.lang.String line)
Deprecated.
|
static java.lang.Object |
SeqIOTools.fileToBiojava(int fileType,
java.io.BufferedReader br)
Deprecated.
Reads a file and returns the corresponding Biojava object.
|
static java.lang.Object |
SeqIOTools.fileToBiojava(java.lang.String formatName,
java.lang.String alphabetName,
java.io.BufferedReader br)
Deprecated.
Reads a file with the specified format and alphabet
|
static SequenceBuilderFactory |
SeqIOTools.formatToFactory(SequenceFormat format,
Alphabet alpha)
Deprecated.
as this essentially duplicates the operation
available in the method
identifyBuilderFactory . |
static FiniteAlphabet |
SeqIOTools.getAlphabet(int identifier)
Deprecated.
getAlphabet accepts a value which represents a
sequence format and returns the relevant
FiniteAlphabet object. |
static SequenceBuilderFactory |
SeqIOTools.getBuilderFactory(int identifier)
Deprecated.
getBuilderFactory accepts a value which represents
a sequence format and returns the relevant
SequenceBuilderFactory object. |
static SequenceFormat |
SeqIOTools.getSequenceFormat(int identifier)
Deprecated.
getSequenceFormat accepts a value which represents
a sequence format and returns the relevant
SequenceFormat object. |
SymbolList |
ChunkedSymbolListFactory.make(SymbolReader sr)
Method to create a Sequence with a SymbolReader.
|
Sequence |
SimpleAssemblyBuilder.makeSequence() |
Sequence |
SequenceDBSequenceBuilder.makeSequence()
create the sequence
|
Sequence |
SequenceBuilderBase.makeSequence() |
Sequence |
SequenceBuilder.makeSequence()
Return the Sequence object which has been constructed
by this builder.
|
Sequence |
SimpleSequenceBuilder.makeSequence() |
Sequence |
SequenceBuilderFilter.makeSequence() |
Sequence |
SmartSequenceBuilder.makeSequence() |
Sequence |
StreamReader.nextSequence()
Pull the next sequence out of the stream.
|
Feature.Template |
EmblLikeLocationParser.parseLocation(java.lang.String location,
Feature.Template theTemplate)
Deprecated.
parseLocation creates a Location from
the String and returns a stranded location. |
static SequenceDB |
SeqIOTools.readFasta(java.io.InputStream seqFile,
Alphabet alpha)
Deprecated.
Create a sequence database from a fasta file provided as an
input stream.
|
boolean |
SequenceFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
void |
FeatureTableParser.startFeature(java.lang.String type)
Deprecated.
|
void |
MSFAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType) |
void |
FastaAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType)
Writes out the alignment to an FASTA file.
|
void |
MSFAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align) |
void |
FastaAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align) |
static void |
SeqIOTools.writeGenpept(java.io.OutputStream os,
Sequence seq)
Deprecated.
Writes a single Sequence to an OutputStream in Genpept format.
|
static void |
SeqIOTools.writeGenpept(java.io.OutputStream os,
SequenceIterator in)
Deprecated.
Writes a stream of Sequences to an OutputStream in Genpept
format.
|
void |
MSFAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align) |
void |
FastaAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align) |
static void |
SeqIOTools.writeSwissprot(java.io.OutputStream os,
Sequence seq)
Deprecated.
Writes a single Sequence to an OutputStream in SwissProt format.
|
static void |
SeqIOTools.writeSwissprot(java.io.OutputStream os,
SequenceIterator in)
Deprecated.
Writes a stream of Sequences to an OutputStream in SwissProt
format.
|
Constructor and Description |
---|
CrossProductTokenization(Alphabet alpha) |
Modifier and Type | Method and Description |
---|---|
Feature |
ProjectedFeature.createFeature(Feature.Template temp) |
Feature |
ReparentContext.createFeature(Feature.Template projTempl) |
Feature |
ProjectionContext.createFeature(Feature.Template projTempl)
Create a projected feature with properties matching the template.
|
Feature |
ProjectedFeatureHolder.createFeature(Feature.Template templ) |
Feature |
ReparentContext.createFeature(Feature f,
Feature.Template projTempl) |
Feature |
ProjectionContext.createFeature(Feature projParent,
Feature.Template projTempl)
Create a new projected feature.
|
void |
ProjectedFeature.removeFeature(Feature f) |
void |
ReparentContext.removeFeature(Feature dyingChild) |
void |
ProjectionContext.removeFeature(Feature dyingChild)
Remove the dying child.
|
void |
ProjectedFeatureHolder.removeFeature(Feature dyingChild) |
void |
ReparentContext.removeFeature(Feature f,
Feature f2) |
void |
ProjectionContext.removeFeature(Feature projParent,
Feature dyingChild)
Remove the dying child.
|
Modifier and Type | Class and Description |
---|---|
class |
StructureException
An exception during the parsing of a PDB file.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBParseException
An exception during the parsing of a PDB file.
|
Modifier and Type | Method and Description |
---|---|
static SubstitutionMatrix |
SeqRes2AtomAligner.getSubstitutionMatrix(FiniteAlphabet alphabet) |
Modifier and Type | Class and Description |
---|---|
class |
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.
|
class |
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.
|
Modifier and Type | Method and Description |
---|---|
static AlphabetIndex |
AlphabetManager.getAlphabetIndex(Symbol[] syms)
Get an indexer for an array of symbols.
|
SymbolTokenization |
Alphabet.getTokenization(java.lang.String name)
Get a SymbolTokenization by name.
|
SymbolTokenization |
DoubleAlphabet.SubDoubleAlphabet.getTokenization(java.lang.String name) |
SymbolTokenization |
AbstractAlphabet.getTokenization(java.lang.String name) |
SymbolTokenization |
SoftMaskedAlphabet.getTokenization(java.lang.String type) |
static void |
AlphabetManager.loadAlphabets(org.xml.sax.InputSource is)
Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.
|
static MergeLocation |
MergeLocation.mergeLocations(java.util.List componentLocations)
Static Factory method for getting an instance of a
MergeLocation |
static MergeLocation |
MergeLocation.mergeLocations(Location locA,
Location locB) |
void |
CodonPrefFilter.put(CodonPref codonPref)
handles storage of a CodonPref object
|
void |
CodonPrefFilter.ByName.put(CodonPref codonPref) |
void |
CodonPrefFilter.EverythingToXML.put(CodonPref codonPref) |
static CodonPref[] |
CodonPrefTools.readFromXML(java.io.InputStream prefStream) |
static void |
CodonPrefTools.readFromXML(java.io.InputStream prefStream,
CodonPrefFilter filter)
read an CodonPref XML stream and handle it with a CodonPrefFilter object.
|
static CodonPref |
CodonPrefTools.readFromXML(java.io.InputStream prefStream,
java.lang.String name)
reads a specified CodonPref from an file.
|
static void |
CodonPrefTools.writeToXML(CodonPref codonPref,
java.io.PrintWriter writer)
write out a specified CodonPref object in XML format.
|
Modifier and Type | Class and Description |
---|---|
class |
CircularReferenceException
Deprecated.
replaced by classes in
org.biojavax.bio.taxa |
Modifier and Type | Method and Description |
---|---|
SequenceDBLite |
Registry.getDatabase(java.lang.String dbName)
getDatabase retrieves a database instance known by
a name String . |
SequenceDBLite |
SequenceDBProvider.getSequenceDB(java.util.Map config)
Get a sequence database.
|
Modifier and Type | Class and Description |
---|---|
class |
AutomatonException
An exception thrown by classes of this package.
|
Modifier and Type | Method and Description |
---|---|
static double |
BinarySearch.solve(double min,
double max,
double tolerance,
ComputeObject obj)
method that will attempt solving the equation.
|
Modifier and Type | Class and Description |
---|---|
class |
RegexException
An exception thrown by classes of this package.
|
Modifier and Type | Method and Description |
---|---|
Walker |
WalkerFactory.getWalker(Visitor visitor)
Get a Walker that is customosed to a particular visitor.
|
Modifier and Type | Method and Description |
---|---|
BioEntry |
BioEntryIterator.nextBioEntry() |
Modifier and Type | Method and Description |
---|---|
void |
HashBioEntryDB.addBioEntry(BioEntry seq)
Add a BioEntry, the name of the BioEntry will be used as the ID
|
void |
AbstractBioEntryDB.addBioEntry(BioEntry seq) |
void |
AbstractRichSequenceDB.addBioEntry(BioEntry seq) |
void |
BioEntryDBLite.addBioEntry(BioEntry seq)
Adds a sequence to the database.
|
protected void |
HashBioEntryDB.addBioEntry(java.lang.String id,
BioEntry seq) |
void |
HashRichSequenceDB.addRichSequence(RichSequence seq)
Add a sequence.
|
void |
RichSequenceDBLite.addRichSequence(RichSequence seq)
Adds a sequence to the database.
|
void |
AbstractRichSequenceDB.addRichSequence(RichSequence seq) |
protected void |
HashRichSequenceDB.addRichSequence(java.lang.String id,
RichSequence seq) |
void |
AbstractRichSequenceDB.addSequence(Sequence seq) |
BioEntry |
HashBioEntryDB.getBioEntry(java.lang.String id) |
BioEntry |
AbstractRichSequenceDB.getBioEntry(java.lang.String id) |
BioEntry |
BioEntryDBLite.getBioEntry(java.lang.String id)
Retrieve a single BioEntry by its id.
|
BioEntryDB |
HashBioEntryDB.getBioEntrys(java.util.Set ids) |
BioEntryDB |
AbstractRichSequenceDB.getBioEntrys(java.util.Set ids) |
BioEntryDB |
BioEntryDBLite.getBioEntrys(java.util.Set ids)
Retrieve multiple BioEntry by their ids.
|
BioEntryDB |
HashBioEntryDB.getBioEntrys(java.util.Set ids,
BioEntryDB db) |
BioEntryDB |
AbstractRichSequenceDB.getBioEntrys(java.util.Set ids,
BioEntryDB db) |
BioEntryDB |
BioEntryDBLite.getBioEntrys(java.util.Set ids,
BioEntryDB db)
Retrieve multiple BioEntry into a specific sequence database.
|
RichSequence |
HashRichSequenceDB.getRichSequence(java.lang.String id) |
RichSequence |
RichSequenceDBLite.getRichSequence(java.lang.String id)
Retrieve a single RichSequence by its id.
|
RichSequenceDB |
HashRichSequenceDB.getRichSequences(java.util.Set ids) |
RichSequenceDB |
RichSequenceDBLite.getRichSequences(java.util.Set ids)
Retrieve multiple RichSequence by its id.
|
RichSequenceDB |
HashRichSequenceDB.getRichSequences(java.util.Set ids,
RichSequenceDB db) |
RichSequenceDB |
RichSequenceDBLite.getRichSequences(java.util.Set ids,
RichSequenceDB db)
Retrieve multiple RichSequence into a specific sequence database.
|
Sequence |
AbstractRichSequenceDB.getSequence(java.lang.String id) |
void |
HashBioEntryDB.removeBioEntry(java.lang.String id) |
void |
AbstractBioEntryDB.removeBioEntry(java.lang.String id) |
void |
AbstractRichSequenceDB.removeBioEntry(java.lang.String id) |
void |
BioEntryDBLite.removeBioEntry(java.lang.String id)
Remove the BioEntry associated with an ID from the database.
|
void |
RichSequenceDBLite.removeRichSequence(java.lang.String id)
Remove the RichSequence associated with an ID from the database.
|
void |
AbstractRichSequenceDB.removeRichSequence(java.lang.String id) |
void |
HashRichSequenceDB.removeSequence(java.lang.String id) |
void |
AbstractRichSequenceDB.removeSequence(java.lang.String id) |
Modifier and Type | Method and Description |
---|---|
void |
BioSQLBioEntryDB._addBioEntry(BioEntry seq) |
void |
BioSQLBioEntryDB.addBioEntry(BioEntry seq) |
void |
BioSQLRichSequenceDB.addRichSequence(RichSequence seq) |
RichSequence |
BioSQLRichSequenceDB.fullyLoadRichSequence(RichSequence id) |
BioEntry |
BioSQLBioEntryDB.getBioEntry(java.lang.String id) |
BioEntryDB |
BioSQLBioEntryDB.getBioEntrys(java.util.Set ids) |
BioEntryDB |
BioSQLBioEntryDB.getBioEntrys(java.util.Set ids,
BioEntryDB db) |
RichSequence |
BioSQLRichSequenceDB.getRichSequence(java.lang.String id) |
RichSequenceDB |
BioSQLRichSequenceDB.getRichSequences(java.util.Set ids) |
RichSequenceDB |
BioSQLRichSequenceDB.getRichSequences(java.util.Set ids,
RichSequenceDB db) |
void |
BioSQLBioEntryDB.removeBioEntry(java.lang.String id) |
void |
BioSQLRichSequenceDB.removeRichSequence(java.lang.String id) |
Modifier and Type | Method and Description |
---|---|
RichSequence |
GenpeptRichSequenceDB.getRichSequence(java.lang.String id)
Given the appropriate Genbank ID, return the matching RichSequence object.
|
RichSequence |
GenbankRichSequenceDB.getRichSequence(java.lang.String id)
Given the appropriate Genbank ID, return the matching RichSequence object.
|
RichSequence |
GenpeptRichSequenceDB.getRichSequence(java.lang.String id,
Namespace nsp)
Given the appropriate Genbank ID, return the matching RichSequence object.
|
RichSequence |
GenbankRichSequenceDB.getRichSequence(java.lang.String id,
Namespace nsp)
Given the appropriate Genbank ID, return the matching RichSequence object.
|
RichSequenceDB |
GenpeptRichSequenceDB.getRichSequences(java.util.Set list)
Retrieve rich sequences from a Genbank
|
RichSequenceDB |
GenbankRichSequenceDB.getRichSequences(java.util.Set list)
Retrieve rich sequences from a Genbank
|
RichSequenceDB |
GenpeptRichSequenceDB.getRichSequences(java.util.Set list,
RichSequenceDB database)
Retrieve rich sequences from a Genbank
|
RichSequenceDB |
GenbankRichSequenceDB.getRichSequences(java.util.Set list,
RichSequenceDB database)
Retrieve rich sequences from a Genbank
|
Modifier and Type | Method and Description |
---|---|
Feature |
ThinRichSequence.createFeature(Feature.Template ft)
Create a new Feature, and add it to this FeatureHolder.
|
Feature |
SimpleRichFeature.createFeature(Feature.Template ft)
Create a new Feature, and add it to this FeatureHolder.
|
static RichSequence |
RichSequence.Tools.createRichSequence(Namespace ns,
java.lang.String name,
java.lang.String seqString,
Alphabet alpha)
Create a new RichSequence in the specified namespace.
|
static RichSequence |
RichSequence.Tools.createRichSequence(java.lang.String name,
java.lang.String seqString,
Alphabet alpha)
Create a new RichSequence in the default namespace.
|
static RichSequence |
RichSequence.Tools.createRichSequence(java.lang.String namespace,
java.lang.String name,
java.lang.String seqString,
Alphabet alpha)
Create a new RichSequence in the specified namespace.
|
RichSequence |
RichSequenceIterator.nextRichSequence() |
static RichSequenceIterator |
RichSequence.IOTools.readHashedFastaDNA(java.io.BufferedInputStream is,
Namespace ns)
Iterate over the sequences in an FASTA-format stream of DNA
sequences.
|
void |
ThinRichSequence.removeFeature(Feature f)
Remove a feature from this FeatureHolder.
|
void |
SimpleRichFeature.removeFeature(Feature f)
Remove a feature from this FeatureHolder.
|
protected void |
ThinRichSequence.setAlphabetName(java.lang.String alphaname) |
protected void |
SimpleRichSequence.setAlphabetName(java.lang.String alphaname) |
protected void |
SimpleRichSequence.setStringSequence(java.lang.String seq) |
Modifier and Type | Method and Description |
---|---|
RichSequence |
SimpleRichSequenceBuilder.makeRichSequence()
Build a RichSequence.
|
RichSequence |
RichSequenceBuilder.makeRichSequence()
Build a RichSequence.
|
Sequence |
SimpleRichSequenceBuilder.makeSequence()
Return the Sequence object which has been constructed
by this builder.
|
Sequence |
RichSequenceBuilder.makeSequence()
Return the Sequence object which has been constructed
by this builder.
|
BioEntry |
RichStreamReader.nextBioEntry() |
BioEntry |
HashedFastaIterator.nextBioEntry() |
RichSequence |
RichStreamReader.nextRichSequence() |
RichSequence |
HashedFastaIterator.nextRichSequence() |
Sequence |
RichStreamReader.nextSequence()
Returns the next sequence in the iterator.
|
Sequence |
HashedFastaIterator.nextSequence() |
boolean |
RichSequenceFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener listener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
Constructor and Description |
---|
HashedFastaIterator(java.io.BufferedInputStream is,
Alphabet alpha,
Namespace ns) |