Uses of Class
org.biojava.bio.BioException
Packages that use BioException
Package
Description
Classes to generate and describe sequence alignments.
Databases of generic structured data (annotation) objects.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Experimental parsers using the tagvalue framework.
GFF manipulation.
Support for reading and writing GFF3.
Support classes for Homologene data.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Parser for Phred output
Parsers for the XML output from NCBI blast.
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Objects for representing Unigene clusters.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utilities to aid in performing various physical analysis of proteins.
Classes and interfaces to load Amino Acid Index database files.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
Taxonomy object for representing species information.
Open Bio Sequence Database Access (OBDA) registry support.
Mathematical utility classes.
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
Classes to represent biological entities and their relationships.
This package contains the interfaces that need to be implemented by discrete alignment services.
This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services
through the WWW.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of BioException in org.biojava.bio.alignment
Methods in org.biojava.bio.alignment that throw BioExceptionModifier and TypeMethodDescriptionvoid
ARAlignment.addSequence
(AlignmentElement ae) void
FlexibleAlignment.addSequence
(AlignmentElement ae) add a new a alignment usings a location to the reference sequence.AlignmentPair.formatOutput()
AlignmentPair.formatOutput
(int width) This method provides a BLAST-like formated alignment from the givenString
s, in which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to each line.static SubstitutionMatrix
SubstitutionMatrix.getSubstitutionMatrix
(BufferedReader reader) This constructor can be used to guess the alphabet of this substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getSubstitutionMatrix
(FiniteAlphabet alphabet, BufferedReader reader) Return a new substitution matrix with the specified alphabet.static SubstitutionMatrix
SubstitutionMatrix.getSubstitutionMatrix
(FiniteAlphabet alphabet, BufferedReader reader, String name) Return a new substitution matrix with the specified alphabet and name.short
SubstitutionMatrix.getValueAt
(Symbol row, Symbol col) There are some substitution matrices containing more columns than lines.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.NeedlemanWunsch.pairwiseAlignment
(SymbolList query, SymbolList subject) Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.Constructors in org.biojava.bio.alignment that throw BioExceptionModifierConstructorDescriptionAlignmentPair
(Sequence query, Sequence subject, int queryStart, int queryEnd, int subjectStart, int subjectEnd, SubstitutionMatrix subMatrix) AlignmentPair
(Sequence query, Sequence subject, SubstitutionMatrix subMatrix) FlexibleAlignment
(List<AlignmentElement> 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). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.SimpleAlignmentElement
(String label, SymbolList seq, Location loc) SubstitutionMatrix
(File file) This constructor can be used to guess the alphabet of this substitution matrix.SubstitutionMatrix
(FiniteAlphabet alpha, File matrixFile) This constructs aSubstitutionMatrix
object that contains twoMap
data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.SubstitutionMatrix
(FiniteAlphabet alpha, String matrixString, String name) With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file. -
Uses of BioException in org.biojava.bio.annodb
Constructors in org.biojava.bio.annodb that throw BioExceptionModifierConstructorDescriptionIndexedAnnotationDB
(String dbName, File storeLoc, Index2Model model, List toIndex, int maxKeyLen, AnnotationType schema, IndexedAnnotationDB.ParserListenerFactory plFactory) Create a new IndexedAnnotationDB. -
Uses of BioException in org.biojava.bio.chromatogram
Subclasses of BioException in org.biojava.bio.chromatogramModifier and TypeClassDescriptionclass
Exception indicating that some provided data does not represent a supported chromatogram format. -
Uses of BioException in org.biojava.bio.dist
Methods in org.biojava.bio.dist that throw BioExceptionModifier and TypeMethodDescriptionstatic final boolean
DistributionTools.areEmissionSpectraEqual
(Distribution[] a, Distribution[] b) Compares the emission spectra of two distribution arrays.static final boolean
DistributionTools.areEmissionSpectraEqual
(Distribution a, Distribution b) Compares the emission spectra of two distributions. -
Uses of BioException in org.biojava.bio.dp
Subclasses of BioException in org.biojava.bio.dpModifier and TypeClassDescriptionclass
This exception indicates that there is no transition between two states.Methods in org.biojava.bio.dp that throw BioExceptionModifier and TypeMethodDescriptionvoid
HMMTrainer.completeCycle()
indicate that a cycle of training is completed and the emission/transition matrices should be updated.void
SimpleHMMTrainer.completeCycle()
DPFactory.createDP
(MarkovModel model) DPFactory.DefaultFactory.createDP
(MarkovModel model) DP.forwardsBackwards
(SymbolList[] symList, ScoreType scoreType) DP.generate
(int length) Generates an alignment from a model.static WeightMatrix
XmlMarkovModel.readMatrix
(Element root) static MarkovModel
void
Trainable.registerWithTrainer
(ModelTrainer mt) Perform any registration that is necessary with mt.void
WMAsMM.registerWithTrainer
(ModelTrainer modelTrainer) State[]
DP.stateList
(MarkovModel mm) 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 BioException in org.biojava.bio.dp.onehead
Constructors in org.biojava.bio.dp.onehead that throw BioException -
Uses of BioException in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead that throw BioExceptionConstructors in org.biojava.bio.dp.twohead that throw BioException -
Uses of BioException in org.biojava.bio.gui
Methods in org.biojava.bio.gui that throw BioExceptionModifier and TypeMethodDescriptionvoid
FeatureTree.setSequenceDB
(SequenceDB db) Use this method to provide the sequences for the tree to work with. -
Uses of BioException in org.biojava.bio.molbio
Methods in org.biojava.bio.molbio that throw BioExceptionModifier and TypeMethodDescriptionint[]
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. -
Uses of BioException in org.biojava.bio.program.formats
Methods in org.biojava.bio.program.formats that throw BioException -
Uses of BioException in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff that throw BioExceptionModifier and TypeMethodDescriptionstatic 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, String id) Internal method to create a GFFRecord from an individual Feature.protected GFFRecord
GFFParser.createRecord
(GFFDocumentHandler handler, List aList, String rest, 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, String id) Emit any per-sequence header information.protected void
SequencesAsGFF.doProcessFeature
(Feature feature, GFFDocumentHandler handler, String id) Internal method to process an individual Feature.protected void
SequencesAsGFF.doProcessSequence
(Sequence seq, GFFDocumentHandler handler, 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
(String token, NumberFormatException nfe) void
GFFWriter.invalidFrame
(String token, NumberFormatException nfe) void
GFFWriter.invalidScore
(String token, NumberFormatException nfe) void
GFFWriter.invalidStart
(String token, NumberFormatException nfe) void
GFFWriter.invalidStrand
(String token) void
GFFParser.parse
(BufferedReader bReader, GFFDocumentHandler handler) Informs handler of each line of gff read from bReader.void
GFFParser.parse
(BufferedReader bReader, GFFDocumentHandler handler, String locator) Informs handler of each line of GFF read from bReadervoid
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
(BufferedReader gffIn) Read all GFF entries from a buffered reader.static GFFEntrySet
GFFTools.readGFF
(BufferedReader gffIn, GFFRecordFilter recFilt) Read all GFF entries matching a filter from a buffered reader.static GFFEntrySet
Reads aGFFEntrySet
from a file with no filtering.static GFFEntrySet
GFFTools.readGFF
(File inFile, GFFRecordFilter recFilt) Reads a GFFEntrySet from a file with the specified filter.static GFFEntrySet
Deprecated.use: readGff(File)static GFFEntrySet
GFFTools.readGFF
(String fileName, GFFRecordFilter recFilt) Deprecated.use: readGff(File,GFFRecordFilter) -
Uses of BioException in org.biojava.bio.program.gff3
Methods in org.biojava.bio.program.gff3 that throw BioExceptionModifier and TypeMethodDescriptionprotected GFF3Record
GFF3Parser.createRecord
(GFF3DocumentHandler handler, List aList, String rest, 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
(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology) Informs handler of each line of gff read from bReader.void
GFF3Parser.parse
(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator) Informs handler of each line of GFF read from bReader -
Uses of BioException in org.biojava.bio.program.homologene
Subclasses of BioException in org.biojava.bio.program.homologene -
Uses of BioException in org.biojava.bio.program.indexdb
Methods in org.biojava.bio.program.indexdb that throw BioExceptionModifier and TypeMethodDescriptionBioStoreFactory.createBioStore()
createBioStore
creates aBioStore
reflecting the current state of the factory and returns a reference to it.get
returns a record specified by a primary identifier.get
returns a list ofRecord
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
indexEmbl
indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.static void
IndexTools.indexFasta
(String name, File location, File[] seqFiles, int alphabetIdentifier) indexFasta
indexes DNA, RNA or protein Fasta format sequence files on primary identifier.static void
IndexTools.indexGenbank
(String name, File location, 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
(String name, File location, File[] seqFiles) indexSwissprot
indexes Swissprot format protein sequence files on ID as primary identifier.Constructors in org.biojava.bio.program.indexdb that throw BioException -
Uses of BioException in org.biojava.bio.program.phred
Methods in org.biojava.bio.program.phred that throw BioExceptionModifier and TypeMethodDescriptionstatic void
PhredTools.writePhredQuality
(OutputStream qual, OutputStream seq, SequenceDB db) Writes Phred quality data in a Fasta type format. -
Uses of BioException in org.biojava.bio.program.sax.blastxml
Constructors in org.biojava.bio.program.sax.blastxml that throw BioException -
Uses of BioException in org.biojava.bio.program.ssaha
Methods in org.biojava.bio.program.ssaha that throw BioExceptionModifier and TypeMethodDescriptionCompactedDataStoreFactory.buildDataStore
(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold) CompactedDataStoreFactory.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) void
SequenceStreamer.reset()
void
SequenceStreamer.FileStreamer.streamNext
(SeqIOListener listener) void
SequenceStreamer.SequenceDBStreamer.streamNext
(SeqIOListener listener) void
SequenceStreamer.streamNext
(SeqIOListener listener) -
Uses of BioException in org.biojava.bio.program.ssbind
Methods in org.biojava.bio.program.ssbind that throw BioExceptionModifier and TypeMethodDescriptionprotected Sequence
ViewSequenceFactory.makeQueryViewSequence
(String queryID) BlastLikeSearchBuilder.makeSearchResult()
protected Sequence
ViewSequenceFactory.makeSubjectViewSequence
(String subjectID) static FiniteAlphabet
AlphabetResolver.resolveAlphabet
(String identifier) resolveAlphabet
returns an appropriateAlphabet
for an arbitrary identifier. -
Uses of BioException in org.biojava.bio.program.unigene
Methods in org.biojava.bio.program.unigene that throw BioExceptionModifier and TypeMethodDescriptionUnigeneDB.addCluster
(UnigeneCluster cluster) Add a cluster to a database.FlatFileUnigeneFactory.createUnigene
(URL unigeneLoc) SQLUnigeneFactory.createUnigene
(URL dbURL) UnigeneFactory.createUnigene
(URL unigeneURL) static UnigeneDB
UnigeneTools.createUnigene
(URL dbURL) Create a new UnigeneDB instance referred to by a URL.static UnigeneFactory
UnigeneTools.findFactory
(URL dbURL) Find the UnigeneFactory that can accept a URL.UnigeneDB.getCluster
(String clusterID) Fetch a cluster by its cluster id.FlatFileUnigeneFactory.loadUnigene
(URL unigeneLoc) SQLUnigeneFactory.loadUnigene
(URL dbURL) UnigeneFactory.loadUnigene
(URL unigeneURL) static UnigeneDB
UnigeneTools.loadUnigene
(URL dbURL) Load a UnigeneDB instance referred to by a URL. -
Uses of BioException in org.biojava.bio.program.xff
Methods in org.biojava.bio.program.xff that throw BioExceptionModifier and TypeMethodDescriptionstatic void
XFFTools.annotateXFF
(File xffFile, Sequence sequence) static void
XFFTools.annotateXFF
(File xffFile, Sequence sequence, Annotation ann) static Sequence
static Sequence
XFFTools.readXFF
(File xffFile, String seqID, FiniteAlphabet alpha) -
Uses of BioException in org.biojava.bio.proteomics
Methods in org.biojava.bio.proteomics that throw BioExceptionModifier and TypeMethodDescriptionvoid
Digest.addDigestFeatures()
Adds peptides as features to the Sequence in this class.static Protease
ProteaseManager.createProtease
(String cleaveRes, boolean endoProtease, String name) static Protease
ProteaseManager.createProtease
(String cleaveRes, boolean endoProtease, String notCleaveRes, String name) static Protease
ProteaseManager.createProtease
(SymbolList cleaveRes, boolean endoProtease, String name) static Protease
ProteaseManager.createProtease
(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, 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 final Protease
Protease.getProteaseByName
(String proteaseName) Retrieves a reference to the named Protease.static Protease
ProteaseManager.getProteaseByName
(String proteaseName) Gets a Protease instance by name.static void
ProteaseManager.registerProtease
(Protease prot) Registers a protease and ensures its flyweight statusConstructors in org.biojava.bio.proteomics that throw BioExceptionModifierConstructorDescriptionDeprecated.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())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()) -
Uses of BioException in org.biojava.bio.proteomics.aaindex
Methods in org.biojava.bio.proteomics.aaindex that throw BioExceptionModifier and TypeMethodDescriptionAAindexStreamReader.nextTable()
Returns the nextSymbolPropertyTable
object.SymbolPropertyTableIterator.nextTable()
Returns the nextSymbolPropertyTable
object.Constructors in org.biojava.bio.proteomics.aaindex that throw BioExceptionModifierConstructorDescriptionSimpleSymbolPropertyTableDB
(SymbolPropertyTableIterator tableIterator) Initializes the database by copying all symbol property tables from a given iterator into the database. -
Uses of BioException in org.biojava.bio.search
Methods in org.biojava.bio.search that throw BioExceptionModifier and TypeMethodDescriptionSearchBuilder.makeSearchResult()
ThemakeSearchResult
method returns aSeqSimilaritySearchResult
instance created from accumulated data.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 that throw BioExceptionModifierConstructorDescriptionFilteringContentHandler
(BlastLikeSearchFilter filter, SearchContentHandler delegate) -
Uses of BioException in org.biojava.bio.seq
Methods in org.biojava.bio.seq that throw BioExceptionModifier and TypeMethodDescriptionstatic 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
(Class template, Class impl) Install a new mapping from a class of Feature.Template to a class of Feature implementations.Return an annotated version of a sequence.AbstractFeatureHolder.createFeature
(Feature.Template temp) 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).FeatureHolder.createFeature
(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.LazyFeatureHolder.createFeature
(Feature.Template template) NewSimpleAssembly.createFeature
(Feature.Template temp) SimpleAssembly.createFeature
(Feature.Template temp) RemoteFeature.getRemoteFeature()
Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.SequenceIterator.nextSequence()
Returns the next sequence in the iterator.FeatureRealizer.realizeFeature
(Sequence seq, FeatureHolder parent, Feature.Template template) Install a feature on the specified sequence.NewSimpleAssembly.realizeFeature
(FeatureHolder fh, Feature.Template temp) RealizingFeatureHolder.realizeFeature
(FeatureHolder parent, Feature.Template template) Realize a feature template.SimpleAssembly.realizeFeature
(FeatureHolder fh, Feature.Template temp) SimpleFeatureRealizer.realizeFeature
(Sequence seq, FeatureHolder parent, Feature.Template temp) void
AbstractFeatureHolder.removeFeature
(Feature f) void
FeatureHolder.removeFeature
(Feature f) Remove a feature from this FeatureHolder.void
LazyFeatureHolder.removeFeature
(Feature f) RemoteFeature.Resolver.resolve
(RemoteFeature rFeat) Resolve rFeat.static Object
FilterUtils.visitFilter
(FeatureFilter filter, Visitor visitor) Applies a visitor to a filter, and returns the visitor's result or null. -
Uses of BioException in org.biojava.bio.seq.db
Subclasses of BioException in org.biojava.bio.seq.dbMethods in org.biojava.bio.seq.db that throw BioExceptionModifier and TypeMethodDescriptionvoid
Add sequences from a file to the sequence database.void
AbstractSequenceDB.addSequence
(Sequence seq) void
DummySequenceDB.addSequence
(Sequence seq) void
SequenceDBLite.addSequence
(Sequence seq) Adds a sequence to the database.void
BioIndex.commit()
void
EmblCDROMIndexStore.commit()
commit
commits changes.void
IndexStore.commit()
Commit the stored indices to permanent storage.void
TabIndexStore.commit()
protected Sequence
AnnotatedSequenceDB.doAnnotation
(Sequence seq) Apply the annotation to a sequence.Fetch an Index based upon an ID.AnnotatedSequenceDB.getSequence
(String id) CachingSequenceDB.getSequence
(String id) DummySequenceDB.getSequence
(String id) GenpeptSequenceDB.getSequence
(String id) IndexedSequenceDB.getSequence
(String id) SequenceDBLite.getSequence
(String id) Retrieve a single sequence by its id.SubSequenceDB.getSequence
(String id) SwissprotSequenceDB.getSequence
(String id) ViewingSequenceDB.getSequence
(String id) WebSequenceDB.getSequence
(String id) Gets a sequence using its unique ID (eg for GenBank this would be the GI number)GenbankSequenceDB.getSequences
(Set list) Retrieve sequences from a GenbankGenbankSequenceDB.getSequences
(Set list, SequenceDB database) Retrieve sequences from a Genbankvoid
AbstractSequenceDB.removeSequence
(String id) void
DummySequenceDB.removeSequence
(String id) void
HashSequenceDB.removeSequence
(String id) void
SequenceDBLite.removeSequence
(String id) Remove the sequence associated with an ID from the database.void
NCBISequenceDB.setDatabase
(String dataBase) void
NCBISequenceDB.setSequenceFormat
(SequenceFormat format) void
store
adds anIndex
to the store.void
Add the Index to the store.void
Constructors in org.biojava.bio.seq.db that throw BioExceptionModifierConstructorDescriptionLoad an existing index file.SubSequenceDB
(SequenceDB parent, Set ids) TabIndexStore
(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser) Create a new TabIndexStore. -
Uses of BioException in org.biojava.bio.seq.db.biofetch
Methods in org.biojava.bio.seq.db.biofetch that throw BioExceptionModifier and TypeMethodDescriptionBioFetchSequenceDB.getSequence
(String id) BioFetchSequenceDBProvider.getSequenceDB
(Map config) -
Uses of BioException in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql that throw BioExceptionModifier and TypeMethodDescriptionstatic Taxon
TaxonSQL.addName
(Connection conn, Taxon taxon, String nameClass, String newName) Deprecated.Adds a new name of the givennameClass
to the taxon.void
BioSQLSequenceDB.addSequence
(Sequence seq) Deprecated.void
BioSQLSequenceDB.createDummySequence
(String id, Alphabet alphabet, int length) Deprecated.static Stack
TaxonSQL.getChildrenOf
(Connection conn, String scientificName) Deprecated.Returns all children of the specified taxon.static Stack
TaxonSQL.getChildrenOf
(Connection conn, Taxon t) Deprecated.Returns the children as aStack
of this given taxon.BioSQLSequenceDB.getSequence
(int bioentry_id) Deprecated.BioSQLSequenceDB.getSequence
(String id) Deprecated.BioSQLSequenceDBProvider.getSequenceDB
(Map config) Deprecated.static Taxon
TaxonSQL.removeName
(Connection conn, DBHelper helper, Taxon taxon, String nameClass, String oldName) Deprecated.Deletes the specified name from of the taxon from the database.void
BioSQLSequenceDB.removeSequence
(String id) Deprecated.static Taxon
TaxonSQL.removeTaxon
(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.removeTaxon
(Connection conn, DBHelper helper, 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.setCommonName
(Connection conn, Taxon taxon, String newName) Deprecated.With this method the common name of the given taxon can be changed or created, if there was none before.Constructors in org.biojava.bio.seq.db.biosql that throw BioExceptionModifierConstructorDescriptionBioSQLSequenceDB
(String dbURL, String dbUser, String dbPass, String biodatabase, boolean create) Deprecated.Connect to a BioSQL database.BioSQLSequenceDB
(String dbDriver, String dbURL, String dbUser, String dbPass, String biodatabase, boolean create) Deprecated.Connect to a BioSQL database.BioSQLSequenceDB
(DataSource ds, String biodatabase, boolean create) Deprecated. -
Uses of BioException in org.biojava.bio.seq.db.flat
Methods in org.biojava.bio.seq.db.flat that throw BioExceptionModifier and TypeMethodDescriptionFlatSequenceDB.getSequence
(String id) FlatSequenceDBProvider.getSequenceDB
(Map config) Constructors in org.biojava.bio.seq.db.flat that throw BioException -
Uses of BioException in org.biojava.bio.seq.distributed
Methods in org.biojava.bio.seq.distributed that throw BioExceptionModifier and TypeMethodDescriptionDistDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.DistDataSource.getFeatures
(FeatureFilter ff) Get all features matching a FeatureFilter provided by this DistDataSource.GFFDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) GFFDataSource.getFeatures
(FeatureFilter ff) SequenceDBDataSource.getFeatures
(String id, FeatureFilter ff, boolean recurse) SequenceDBDataSource.getFeatures
(FeatureFilter ff) DistDataSource.getSequence
(String id) Get a Sequence object for an ID.DistributedSequenceDB.getSequence
(String id) GFFDataSource.getSequence
(String id) SequenceDBDataSource.getSequence
(String id) boolean
DistDataSource.hasFeatures
(String id) Find out if this DistDataSource can provide features on a sequence with a particular ID.boolean
GFFDataSource.hasFeatures
(String id) boolean
SequenceDBDataSource.hasFeatures
(String id) boolean
DistDataSource.hasSequence
(String id) Find out if this DistDataSource provides the sequence information for a sequence ID.boolean
GFFDataSource.hasSequence
(String id) boolean
SequenceDBDataSource.hasSequence
(String id) DistDataSource.ids
(boolean topLevel) Get the complete set of sequence IDs provided by this DistDataSource.GFFDataSource.ids
(boolean topLevel) SequenceDBDataSource.ids
(boolean topLevel) -
Uses of BioException in org.biojava.bio.seq.homol
Methods in org.biojava.bio.seq.homol that throw BioExceptionModifier and TypeMethodDescriptionvoid
SimpleHomology.setAlignment
(Alignment alignment) setAlignment
sets the alignment which describes the homology. -
Uses of BioException in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that throw BioExceptionModifier and TypeMethodDescriptionDummySequence.createFeature
(Feature.Template template) LazyFilterFeatureHolder.createFeature
(Feature.Template temp) RevCompSequence.createFeature
(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.SimpleFeature.createFeature
(Feature.Template temp) SimpleGappedSequence.createFeature
(Feature.Template templ) SimpleSequence.createFeature
(Feature.Template template) SimpleSequence.createFeature
(FeatureHolder fh, Feature.Template template) Deprecated.Please use new 1-arg createFeature instead.SubSequence.createFeature
(Feature.Template templ) ViewSequence.createFeature
(Feature.Template template) 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.SimpleFeature.realizeFeature
(FeatureHolder fh, Feature.Template templ) SimpleSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) ViewSequence.realizeFeature
(FeatureHolder parent, Feature.Template template) void
DummySequence.removeFeature
(Feature feature) void
LazyFilterFeatureHolder.removeFeature
(Feature f) void
RevCompSequence.removeFeature
(Feature f) void
SimpleGappedSequence.removeFeature
(Feature f) void
SimpleSequence.removeFeature
(Feature f) Remove a feature attached to this sequence.void
SubSequence.removeFeature
(Feature f) SimpleRemoteFeature.DBResolver.resolve
(RemoteFeature rFeat) -
Uses of BioException in org.biojava.bio.seq.io
Subclasses of BioException in org.biojava.bio.seq.ioModifier and TypeClassDescriptionclass
ParseException should be thrown to indicate that there was a problem with parsing sequence information.Methods in org.biojava.bio.seq.io that throw BioExceptionModifier and TypeMethodDescriptionSimpleAssemblyBuilder.addComponentSequence
(ComponentFeature.Template cft) static void
SeqIOTools.biojavaToFile
(int fileType, OutputStream os, Object biojava) Deprecated.Converts a Biojava object to the given filetype.static void
SeqIOTools.biojavaToFile
(String formatName, String alphabetName, OutputStream os, Object biojava) Deprecated.Writes a BiojavaSequenceIterator
,SequenceDB
,Sequence
orAligment
to anOutputStream
void
FeatureTableParser.endFeature()
Deprecated.void
FeatureTableParser.featureData
(String line) Deprecated.static Object
SeqIOTools.fileToBiojava
(int fileType, BufferedReader br) Deprecated.Reads a file and returns the corresponding Biojava object.static Object
SeqIOTools.fileToBiojava
(String formatName, String alphabetName, BufferedReader br) Deprecated.Reads a file with the specified format and alphabetstatic SequenceBuilderFactory
SeqIOTools.formatToFactory
(SequenceFormat format, Alphabet alpha) Deprecated.as this essentially duplicates the operation available in the methodidentifyBuilderFactory
.static FiniteAlphabet
SeqIOTools.getAlphabet
(int identifier) Deprecated.getAlphabet
accepts a value which represents a sequence format and returns the relevantFiniteAlphabet
object.static SequenceBuilderFactory
SeqIOTools.getBuilderFactory
(int identifier) Deprecated.getBuilderFactory
accepts a value which represents a sequence format and returns the relevantSequenceBuilderFactory
object.static SequenceFormat
SeqIOTools.getSequenceFormat
(int identifier) Deprecated.getSequenceFormat
accepts a value which represents a sequence format and returns the relevantSequenceFormat
object.ChunkedSymbolListFactory.make
(SymbolReader sr) Method to create a Sequence with a SymbolReader.SequenceBuilder.makeSequence()
Return the Sequence object which has been constructed by this builder.SequenceBuilderBase.makeSequence()
SequenceBuilderFilter.makeSequence()
SequenceDBSequenceBuilder.makeSequence()
create the sequenceSimpleAssemblyBuilder.makeSequence()
SimpleSequenceBuilder.makeSequence()
SmartSequenceBuilder.makeSequence()
StreamReader.nextSequence()
Pull the next sequence out of the stream.EmblLikeLocationParser.parseLocation
(String location, Feature.Template theTemplate) Deprecated.parseLocation
creates aLocation
from the String and returns a stranded location.static SequenceDB
SeqIOTools.readFasta
(InputStream seqFile, Alphabet alpha) Deprecated.Create a sequence database from a fasta file provided as an input stream.boolean
SequenceFormat.readSequence
(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.void
FeatureTableParser.startFeature
(String type) Deprecated.void
FastaAlignmentFormat.write
(OutputStream os, Alignment align, int fileType) Writes out the alignment to an FASTA file.void
MSFAlignmentFormat.write
(OutputStream os, Alignment align, int fileType) void
FastaAlignmentFormat.writeDna
(OutputStream os, Alignment align) void
MSFAlignmentFormat.writeDna
(OutputStream os, Alignment align) static void
SeqIOTools.writeGenpept
(OutputStream os, Sequence seq) Deprecated.Writes a single Sequence to an OutputStream in Genpept format.static void
SeqIOTools.writeGenpept
(OutputStream os, SequenceIterator in) Deprecated.Writes a stream of Sequences to an OutputStream in Genpept format.void
FastaAlignmentFormat.writeProtein
(OutputStream os, Alignment align) void
MSFAlignmentFormat.writeProtein
(OutputStream os, Alignment align) static void
SeqIOTools.writeSwissprot
(OutputStream os, Sequence seq) Deprecated.Writes a single Sequence to an OutputStream in SwissProt format.static void
SeqIOTools.writeSwissprot
(OutputStream os, SequenceIterator in) Deprecated.Writes a stream of Sequences to an OutputStream in SwissProt format.Constructors in org.biojava.bio.seq.io that throw BioException -
Uses of BioException in org.biojava.bio.seq.projection
Methods in org.biojava.bio.seq.projection that throw BioExceptionModifier and TypeMethodDescriptionProjectedFeature.createFeature
(Feature.Template temp) ProjectedFeatureHolder.createFeature
(Feature.Template templ) ProjectionContext.createFeature
(Feature.Template projTempl) Create a projected feature with properties matching the template.ProjectionContext.createFeature
(Feature projParent, Feature.Template projTempl) Create a new projected feature.final Feature
ReparentContext.createFeature
(Feature.Template projTempl) final Feature
ReparentContext.createFeature
(Feature f, Feature.Template projTempl) void
ProjectedFeature.removeFeature
(Feature f) void
ProjectedFeatureHolder.removeFeature
(Feature dyingChild) void
ProjectionContext.removeFeature
(Feature dyingChild) Remove the dying child.void
ProjectionContext.removeFeature
(Feature projParent, Feature dyingChild) Remove the dying child.final void
ReparentContext.removeFeature
(Feature dyingChild) final void
ReparentContext.removeFeature
(Feature f, Feature f2) -
Uses of BioException in org.biojava.bio.symbol
Subclasses of BioException in org.biojava.bio.symbolModifier and TypeClassDescriptionclass
The exception to indicate that an invalid alphabet has been used.class
The exception to indicate that a symbol is not valid within a context.Methods in org.biojava.bio.symbol that throw BioExceptionModifier and TypeMethodDescriptionstatic AlphabetIndex
AlphabetManager.getAlphabetIndex
(Symbol[] syms) Get an indexer for an array of symbols.AbstractAlphabet.getTokenization
(String name) Alphabet.getTokenization
(String name) Get a SymbolTokenization by name.DoubleAlphabet.SubDoubleAlphabet.getTokenization
(String name) SoftMaskedAlphabet.getTokenization
(String type) static void
AlphabetManager.loadAlphabets
(InputSource is) Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.static MergeLocation
MergeLocation.mergeLocations
(List componentLocations) Static Factory method for getting an instance of aMergeLocation
static MergeLocation
MergeLocation.mergeLocations
(Location locA, Location locB) void
void
void
handles storage of a CodonPref objectstatic CodonPref[]
CodonPrefTools.readFromXML
(InputStream prefStream) static CodonPref
CodonPrefTools.readFromXML
(InputStream prefStream, String name) reads a specified CodonPref from an file.static void
CodonPrefTools.readFromXML
(InputStream prefStream, CodonPrefFilter filter) read an CodonPref XML stream and handle it with a CodonPrefFilter object.static void
CodonPrefTools.writeToXML
(CodonPref codonPref, PrintWriter writer) write out a specified CodonPref object in XML format. -
Uses of BioException in org.biojava.bio.taxa
Subclasses of BioException in org.biojava.bio.taxa -
Uses of BioException in org.biojava.directory
Methods in org.biojava.directory that throw BioExceptionModifier and TypeMethodDescriptionRegistry.getDatabase
(String dbName) getDatabase
retrieves a database instance known by a nameString
.SequenceDBProvider.getSequenceDB
(Map config) Get a sequence database. -
Uses of BioException in org.biojava.utils.automata
Subclasses of BioException in org.biojava.utils.automataModifier and TypeClassDescriptionclass
An exception thrown by classes of this package. -
Uses of BioException in org.biojava.utils.math
Methods in org.biojava.utils.math that throw BioExceptionModifier and TypeMethodDescriptionstatic double
BinarySearch.solve
(double min, double max, double tolerance, ComputeObject obj) method that will attempt solving the equation. -
Uses of BioException in org.biojava.utils.regex
Subclasses of BioException in org.biojava.utils.regexModifier and TypeClassDescriptionclass
An exception thrown by classes of this package. -
Uses of BioException in org.biojava.utils.walker
Methods in org.biojava.utils.walker that throw BioException -
Uses of BioException in org.biojavax.bio
Methods in org.biojavax.bio that throw BioException -
Uses of BioException in org.biojavax.bio.alignment
Methods in org.biojavax.bio.alignment that throw BioExceptionModifier and TypeMethodDescriptionRemotePairwiseAlignmentProperties.getAlignmentOption
(String key) Method that returns the value associated with the key given in parameter.RemotePairwiseAlignmentService.getAlignmentResults
(String rid, RemotePairwiseAlignmentOutputProperties out) Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.RemotePairwiseAlignmentOutputProperties.getOutputOption
(String key) Method that returns the value associated with the key given in parameter.boolean
Simple method to check if the specified request has been completed by the service used.RemotePairwiseAlignmentService.sendAlignmentRequest
(String str, RemotePairwiseAlignmentProperties rpa) Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence objectRemotePairwiseAlignmentService.sendAlignmentRequest
(RichSequence rs, RemotePairwiseAlignmentProperties rpa) Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object -
Uses of BioException in org.biojavax.bio.alignment.blast
Methods in org.biojavax.bio.alignment.blast that throw BioExceptionModifier and TypeMethodDescriptionRemoteQBlastAlignmentProperties.getAlignmentOption
(String key) RemoteQBlastService.getAlignmentResults
(String id, RemotePairwiseAlignmentOutputProperties rb) This method extracts the actual Blast report for this request ID.RemoteQBlastOutputProperties.getOutputOption
(String o) Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.boolean
This method is used only for the executeBlastSearch method to check for completion of request using the NCBI specified RTOE variablevoid
RemoteQBlastService.printRemoteBlastInfo()
A simple method to check the availability of the QBlast serviceRemoteQBlastService.sendAlignmentRequest
(int gid, RemotePairwiseAlignmentProperties rpa) This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a GenBank GID.RemoteQBlastService.sendAlignmentRequest
(String str, RemotePairwiseAlignmentProperties rpa) This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence.RemoteQBlastService.sendAlignmentRequest
(RichSequence rs, RemotePairwiseAlignmentProperties rpa) This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence.void
RemoteQBlastOutputProperties.setAlignmentOutputFormat
(RemoteQBlastOutputFormat rf) This method is use to set the alignment output format to get from the QBlast servicevoid
RemoteQBlastAlignmentProperties.setBlastProgram
(String program) This method set the program to be use with blastall.void
RemoteQBlastOutputProperties.setOutputFormat
(RemoteQBlastOutputFormat rf) This method is use to set the stream output format to get from the QBlast serviceConstructors in org.biojavax.bio.alignment.blast that throw BioExceptionModifierConstructorDescriptionThe constructor for a QBlast service request. -
Uses of BioException in org.biojavax.bio.db
Methods in org.biojavax.bio.db that throw BioExceptionModifier and TypeMethodDescriptionvoid
AbstractBioEntryDB.addBioEntry
(BioEntry seq) void
AbstractRichSequenceDB.addBioEntry
(BioEntry seq) void
BioEntryDBLite.addBioEntry
(BioEntry seq) Adds a sequence to the database.protected void
HashBioEntryDB.addBioEntry
(String id, BioEntry seq) void
HashBioEntryDB.addBioEntry
(BioEntry seq) Add a BioEntry, the name of the BioEntry will be used as the IDvoid
AbstractRichSequenceDB.addRichSequence
(RichSequence seq) protected void
HashRichSequenceDB.addRichSequence
(String id, RichSequence seq) void
HashRichSequenceDB.addRichSequence
(RichSequence seq) Add a sequence.void
RichSequenceDBLite.addRichSequence
(RichSequence seq) Adds a sequence to the database.void
AbstractRichSequenceDB.addSequence
(Sequence seq) AbstractRichSequenceDB.getBioEntry
(String id) BioEntryDBLite.getBioEntry
(String id) Retrieve a single BioEntry by its id.HashBioEntryDB.getBioEntry
(String id) AbstractRichSequenceDB.getBioEntrys
(Set ids) AbstractRichSequenceDB.getBioEntrys
(Set ids, BioEntryDB db) BioEntryDBLite.getBioEntrys
(Set ids) Retrieve multiple BioEntry by their ids.BioEntryDBLite.getBioEntrys
(Set ids, BioEntryDB db) Retrieve multiple BioEntry into a specific sequence database.HashBioEntryDB.getBioEntrys
(Set ids) HashBioEntryDB.getBioEntrys
(Set ids, BioEntryDB db) HashRichSequenceDB.getRichSequence
(String id) RichSequenceDBLite.getRichSequence
(String id) Retrieve a single RichSequence by its id.HashRichSequenceDB.getRichSequences
(Set ids) HashRichSequenceDB.getRichSequences
(Set ids, RichSequenceDB db) RichSequenceDBLite.getRichSequences
(Set ids) Retrieve multiple RichSequence by its id.RichSequenceDBLite.getRichSequences
(Set ids, RichSequenceDB db) Retrieve multiple RichSequence into a specific sequence database.AbstractRichSequenceDB.getSequence
(String id) void
AbstractBioEntryDB.removeBioEntry
(String id) void
AbstractRichSequenceDB.removeBioEntry
(String id) void
BioEntryDBLite.removeBioEntry
(String id) Remove the BioEntry associated with an ID from the database.void
HashBioEntryDB.removeBioEntry
(String id) void
AbstractRichSequenceDB.removeRichSequence
(String id) void
RichSequenceDBLite.removeRichSequence
(String id) Remove the RichSequence associated with an ID from the database.void
AbstractRichSequenceDB.removeSequence
(String id) void
HashRichSequenceDB.removeSequence
(String id) -
Uses of BioException in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql that throw BioExceptionModifier and TypeMethodDescriptionvoid
BioSQLBioEntryDB._addBioEntry
(BioEntry seq) void
BioSQLBioEntryDB.addBioEntry
(BioEntry seq) void
BioSQLRichSequenceDB.addRichSequence
(RichSequence seq) BioSQLRichSequenceDB.fullyLoadRichSequence
(RichSequence id) BioSQLBioEntryDB.getBioEntry
(String id) BioSQLBioEntryDB.getBioEntrys
(Set ids) BioSQLBioEntryDB.getBioEntrys
(Set ids, BioEntryDB db) BioSQLRichSequenceDB.getRichSequence
(String id) BioSQLRichSequenceDB.getRichSequences
(Set ids) BioSQLRichSequenceDB.getRichSequences
(Set ids, RichSequenceDB db) void
BioSQLBioEntryDB.removeBioEntry
(String id) void
BioSQLRichSequenceDB.removeRichSequence
(String id) -
Uses of BioException in org.biojavax.bio.db.ncbi
Methods in org.biojavax.bio.db.ncbi that throw BioExceptionModifier and TypeMethodDescriptionGenbankRichSequenceDB.getRichSequence
(String id) Given the appropriate Genbank ID, return the matching RichSequence object.GenbankRichSequenceDB.getRichSequence
(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.GenpeptRichSequenceDB.getRichSequence
(String id) Given the appropriate Genbank ID, return the matching RichSequence object.GenpeptRichSequenceDB.getRichSequence
(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.GenbankRichSequenceDB.getRichSequences
(Set list) Retrieve rich sequences from a GenbankGenbankRichSequenceDB.getRichSequences
(Set list, RichSequenceDB database) Retrieve rich sequences from a GenbankGenpeptRichSequenceDB.getRichSequences
(Set list) Retrieve rich sequences from a GenbankGenpeptRichSequenceDB.getRichSequences
(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank -
Uses of BioException in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that throw BioExceptionModifier and TypeMethodDescriptionSimpleRichFeature.createFeature
(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.ThinRichSequence.createFeature
(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.static RichSequence
RichSequence.Tools.createRichSequence
(String namespace, String name, String seqString, Alphabet alpha) Create a new RichSequence in the specified namespace.static RichSequence
RichSequence.Tools.createRichSequence
(String name, String seqString, Alphabet alpha) Create a new RichSequence in the default namespace.static RichSequence
RichSequence.Tools.createRichSequence
(Namespace ns, String name, String seqString, Alphabet alpha) Create a new RichSequence in the specified namespace.RichSequenceIterator.nextRichSequence()
static RichSequenceIterator
RichSequence.IOTools.readHashedFastaDNA
(BufferedInputStream is, Namespace ns) Iterate over the sequences in an FASTA-format stream of DNA sequences.void
SimpleRichFeature.removeFeature
(Feature f) Remove a feature from this FeatureHolder.void
ThinRichSequence.removeFeature
(Feature f) Remove a feature from this FeatureHolder.protected void
SimpleRichSequence.setAlphabetName
(String alphaname) protected void
ThinRichSequence.setAlphabetName
(String alphaname) protected void
SimpleRichSequence.setStringSequence
(String seq) -
Uses of BioException in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that throw BioExceptionModifier and TypeMethodDescriptionRichSequenceBuilder.makeRichSequence()
Build a RichSequence.SimpleRichSequenceBuilder.makeRichSequence()
Build a RichSequence.RichSequenceBuilder.makeSequence()
Return the Sequence object which has been constructed by this builder.SimpleRichSequenceBuilder.makeSequence()
Return the Sequence object which has been constructed by this builder.HashedFastaIterator.nextBioEntry()
RichStreamReader.nextBioEntry()
HashedFastaIterator.nextRichSequence()
RichStreamReader.nextRichSequence()
HashedFastaIterator.nextSequence()
RichStreamReader.nextSequence()
Returns the next sequence in the iterator.boolean
RichSequenceFormat.readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener listener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.Constructors in org.biojavax.bio.seq.io that throw BioExceptionModifierConstructorDescriptionHashedFastaIterator
(BufferedInputStream is, Alphabet alpha, Namespace ns)