## Uses of Class
org.biojava.bio.BioException

Packages that use BioException
org.biojava.bio.alignment: Implementation of the `Alignment` interface.
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.gff: GFF manipulation.
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.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.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 into alternate coordinate systems.
org.biojava.bio.seq.ragbag: The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.
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.math: Mathematical utility classes.

Uses of BioException in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment that throw BioException
`void` `ARAlignment.addSequence(AlignmentElement ae)`
`void` `FlexibleAlignment.addSequence(AlignmentElement ae)` add a new a alignment usings a location to the reference sequence.

Constructors in org.biojava.bio.alignment that throw BioException
`SimpleAlignmentElement(java.lang.Object label, SymbolList seq, Location loc)`
`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).

Uses of BioException in org.biojava.bio.chromatogram

Subclasses of BioException in org.biojava.bio.chromatogram
`class` `UnsupportedChromatogramFormatException` 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 BioException
`static boolean` `DistributionTools.areEmissionSpectraEqual(Distribution a, Distribution b)` Compares the emission spectra of two distributions
`static boolean` `DistributionTools.areEmissionSpectraEqual(Distribution[] a, Distribution[] b)` Compares the emission spectra of two distribution arrays

Uses of BioException in org.biojava.bio.dp

Subclasses of BioException in org.biojava.bio.dp
`class` `IllegalTransitionException` This exception indicates that there is no transition between two states.

Methods in org.biojava.bio.dp that throw BioException
`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.
`Sequence` `WeightMatrixAnnotator.annotate(Sequence seq)`
`void` `WMAsMM.registerWithTrainer(ModelTrainer modelTrainer)`
`DP` `DPFactory.createDP(MarkovModel model)`
`DP` `DPFactory.DefaultFactory.createDP(MarkovModel model)`
`static State[]` `DP.stateList(MarkovModel mm)`
`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.

Constructors in org.biojava.bio.dp that throw BioException
`DP(MarkovModel model)`

Uses of BioException in org.biojava.bio.dp.onehead

Constructors in org.biojava.bio.dp.onehead that throw BioException
`SingleDP(MarkovModel model)`

Uses of BioException in org.biojava.bio.dp.twohead

Methods in org.biojava.bio.dp.twohead that throw BioException
`CellCalculatorFactory` `CellCalculatorFactoryMaker.make(DP dp)`

Constructors in org.biojava.bio.dp.twohead that throw BioException
`PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)`

Uses of BioException in org.biojava.bio.gui

Methods in org.biojava.bio.gui that throw BioException
`void` `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 BioException
`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.

Uses of BioException in org.biojava.bio.program.das

Methods in org.biojava.bio.program.das that throw BioException
`Sequence` `DASSequenceDB.getSequence(java.lang.String id)`
`void` `DASSequence.addAnnotationSource(java.net.URL dataSourceURL)`
`void` `DASSequence.removeAnnotationSource(java.net.URL dataSourceURL)`
`protected SymbolList` `DASSequence.getSymbols()`
`Feature` `DASSequence.realizeFeature(FeatureHolder dest, Feature.Template temp)`
`SequenceDBLite` `DASSequenceDBProvider.getSequenceDB(java.util.Map config)`
`SequenceDB` `ReferenceServer.getDB()`
`DistDataSource` `ReferenceServer.getDistDataSource()`
`DistDataSource` `DataSource.getDistDataSource()`
`static java.util.Set` `DAS.getTypes(java.net.URL dasURL)`
`void` `DAS.addDasURL(java.net.URL dasURL)`

Constructors in org.biojava.bio.program.das that throw BioException
`DASSequenceDB(java.net.URL dataSourceURL)`

Uses of BioException in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that throw BioException
`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
`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.
`static GFFEntrySet` `GFFTools.readGFF(java.lang.String fileName)` Reads a `GFFEntrySet` from a file with no filtering
`static GFFEntrySet` `GFFTools.readGFF(java.lang.String fileName, GFFRecordFilter recFilt)` Reads a GFFEntrySet from a file with the specified filter
`static GFFEntrySet` `GFFTools.readGFF(java.io.BufferedReader gffIn)`
`static GFFEntrySet` `GFFTools.readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt)`
`static SequenceDB` `GFFTools.annotateSequences(SequenceDB seqs, GFFEntrySet ents)` Annotates all sequences in a sequence DB with features from a GFF entry set.
`static GFFEntrySet` `GFFTools.gffFromSequence(Sequence seq)` Creates a GFFEntrySet containing one entry for each feature on a sequence.
`void` `GFFWriter.invalidStart(java.lang.String token, java.lang.NumberFormatException nfe)`
`void` `GFFWriter.invalidEnd(java.lang.String token, java.lang.NumberFormatException nfe)`
`void` `GFFWriter.invalidScore(java.lang.String token, java.lang.NumberFormatException nfe)`
`void` `GFFWriter.invalidStrand(java.lang.String token)`
`void` `GFFWriter.invalidFrame(java.lang.String token, java.lang.NumberFormatException nfe)`
`protected void` `SequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id)` Internal method to process an individual Sequence.
`protected void` `SequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id)` Internal method to process an individual Sequence.
`void` `SequencesAsGFF.processSequence(Sequence seq, GFFDocumentHandler handler)` Process an individual Sequence, informing handler of any suitable features.
`void` `SequencesAsGFF.processSequence(Sequence seq, GFFDocumentHandler handler)` Process an individual Sequence, informing handler of any suitable features.
`void` `SequencesAsGFF.processDB(SequenceDB seqDB, GFFDocumentHandler handler)` Process all Sequences within a SequenceDB, informing handler of any suitable features.
`void` `SequencesAsGFF.processDB(SequenceDB seqDB, GFFDocumentHandler handler)` Process all Sequences within a SequenceDB, informing handler of any suitable features.

Uses of BioException in org.biojava.bio.program.indexdb

Methods in org.biojava.bio.program.indexdb that throw BioException
`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.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.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.
`java.util.List` `BioStore.get(java.lang.String id, java.lang.String namespace)`
`Record` `IndexStore.get(java.lang.String id)` `get` returns a record specified by a primary identifier.
`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.
`BioStore` `BioStoreFactory.createBioStore()` `createBioStore` creates a `BioStore` reflecting the current state of the factory and returns a reference to it.

Constructors in org.biojava.bio.program.indexdb that throw BioException
`BioStore(java.io.File location, boolean cache)` Creates a new `BioStore` flatfile index at the specified location with the specified caching behaviour.

Uses of BioException in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred that throw BioException
`static void` `PhredTools.writePhredQuality(java.io.OutputStream qual, java.io.OutputStream seq, SequenceDB db)` Writes Phred quality data in a Fasta type format.

Uses of BioException in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha that throw BioException
`DataStore` `CompactedDataStoreFactory.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.streamNext(SeqIOListener listener)`
`void` `SequenceStreamer.reset()`
`void` `SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener)`
`void` `SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener)`
`DataStore` `DataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)` Build a new DataStore.
`DataStore` `NIODataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)`
`DataStore` `MappedDataStoreFactory.buildDataStore(java.io.File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)`

Uses of BioException in org.biojava.bio.program.ssbind

Methods in org.biojava.bio.program.ssbind that throw BioException
`protected Sequence` `ViewSequenceFactory.makeQueryViewSequence(java.lang.String queryID)`
`protected Sequence` `ViewSequenceFactory.makeSubjectViewSequence(java.lang.String subjectID)`
`SeqSimilaritySearchResult` `BlastLikeSearchBuilder.makeSearchResult()`
`static FiniteAlphabet` `AlphabetResolver.resolveAlphabet(java.lang.String identifier)` `resolveAlphabet` returns an appropriate `Alphabet` for an arbitrary identifier.

Uses of BioException in org.biojava.bio.program.unigene

Methods in org.biojava.bio.program.unigene that throw BioException
`static UnigeneDB` `UnigeneTools.loadUnigene(java.net.URL dbURL)` Load a UnigeneDB instance referred to by a URL.
`static UnigeneDB` `UnigeneTools.createUnigene(java.net.URL dbURL)` Create a new UnigeneDB instance referred to by a URL.
`static UnigeneFactory` `UnigeneTools.findFactory(java.net.URL dbURL)` Find the UnigeneFactory that can accept a URL.
`UnigeneDB` `FlatFileUnigeneFactory.loadUnigene(java.net.URL unigeneLoc)`
`UnigeneDB` `FlatFileUnigeneFactory.createUnigene(java.net.URL unigeneLoc)`
`UnigeneDB` `SQLUnigeneFactory.loadUnigene(java.net.URL dbURL)`
`UnigeneDB` `SQLUnigeneFactory.createUnigene(java.net.URL dbURL)`
`UnigeneCluster` `UnigeneDB.getCluster(java.lang.String clusterID)` Fetch a cluster by its cluster id.
`UnigeneCluster` `UnigeneDB.addCluster(UnigeneCluster cluster)` Add a cluster to a database.
`UnigeneDB` `UnigeneFactory.loadUnigene(java.net.URL unigeneURL)`
`UnigeneDB` `UnigeneFactory.createUnigene(java.net.URL unigeneURL)`

Uses of BioException in org.biojava.bio.program.xff

Methods in org.biojava.bio.program.xff that throw BioException
`static void` `XFFTools.annotateXFF(java.io.File xffFile, Sequence sequence)`
`static Sequence` `XFFTools.readXFF(java.io.File xffFile, java.lang.String seqID, FiniteAlphabet alpha)`

Uses of BioException in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that throw BioException
`double` `IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)` Computes isoelectric point of specified peptide.
`void` `Digest.addDigestFeatures()` Adds peptides as features to the Sequence in this class.
`static Protease` `Protease.getProteaseByName(java.lang.String proteaseName)` Retrieves a reference to the named Protease.
`static Protease` `ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, java.lang.String name)` Creates and registers a new Protease.
`static Protease` `ProteaseManager.createProtease(SymbolList 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(java.lang.String cleaveRes, boolean endoProtease, java.lang.String name)`
`static void` `ProteaseManager.registerProtease(Protease prot)` Registers a protease and ensures its flyweight status
`static Protease` `ProteaseManager.getProteaseByName(java.lang.String proteaseName)` Gets a Protease instance by name.

Constructors in org.biojava.bio.proteomics that throw BioException
`Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes)` 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(java.lang.String cleavageRes, boolean endoProtease)` Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())

Uses of BioException in org.biojava.bio.search

Methods in org.biojava.bio.search that throw BioException
`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.

Uses of BioException in org.biojava.bio.seq

Methods in org.biojava.bio.seq that throw BioException
`Feature` `FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)` Install a feature on the specified sequence.
`void` `Feature.Template.populate(Feature feat)` This attempts to populate the fields of this template using the publically accessible information in a feature.
`Sequence` `SequenceIterator.nextSequence()` Returns the next sequence in the iterator.
`Sequence` `SequenceAnnotator.annotate(Sequence seq)` Return an annotated version of a sequence.
`Feature` `ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`
`Feature` `ViewSequence.createFeature(Feature.Template template)`
`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` `SimpleAssembly.createFeature(Feature.Template temp)`
`Feature` `SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)`
`Feature` `FeatureHolder.createFeature(Feature.Template ft)` Create a new Feature, and add it to this FeatureHolder.
`Feature` `SimpleGappedSequence.createFeature(Feature.Template templ)`
`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.
`Feature` `SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)`
`Feature` `ProjectedFeatureHolder.createFeature(Feature.Template templ)`
`Feature` `ProjectedFeatureHolder.createFeature(Feature f, Feature.Template templ)`
`Feature` `RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)` Realize a feature template.
`Feature` `RemoteFeature.getRemoteFeature()` Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
`Feature` `RemoteFeature.Resolver.resolve(RemoteFeature rFeat)` Resolve rFeat.
`Feature` `AbstractFeatureHolder.createFeature(Feature.Template temp)`
`Feature` `SubSequence.createFeature(Feature.Template templ)`
`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.
`Feature` `DummySequence.createFeature(Feature.Template template)`
`Feature` `LazyFeatureHolder.createFeature(Feature.Template template)`

Uses of BioException in org.biojava.bio.seq.db

Subclasses of BioException in org.biojava.bio.seq.db
`class` `IllegalIDException`

Methods in org.biojava.bio.seq.db that throw BioException
`void` `EmblCDROMIndexStore.store(Index index)` `store` adds an `Index` to the store.
`void` `EmblCDROMIndexStore.commit()` `commit` commits changes.
`Index` `EmblCDROMIndexStore.fetch(java.lang.String id)`
`Sequence` `AnnotatedSequenceDB.getSequence(java.lang.String id)`
`protected Sequence` `AnnotatedSequenceDB.doAnnotation(Sequence seq)` Apply the annotation to a sequence.
`Sequence` `DummySequenceDB.getSequence(java.lang.String id)`
`void` `DummySequenceDB.addSequence(Sequence seq)`
`void` `DummySequenceDB.removeSequence(java.lang.String id)`
`void` `TabIndexStore.store(Index indx)`
`Index` `TabIndexStore.fetch(java.lang.String id)`
`void` `TabIndexStore.commit()`
`void` `IndexedSequenceDB.addFile(java.io.File seqFile)` Add sequences from a file to the sequence database.
`Sequence` `IndexedSequenceDB.getSequence(java.lang.String id)`
`Sequence` `GenpeptSequenceDB.getSequence(java.lang.String id)`
`void` `AbstractSequenceDB.addSequence(Sequence seq)`
`void` `AbstractSequenceDB.removeSequence(java.lang.String id)`
`Sequence` `SequenceDBLite.getSequence(java.lang.String id)` Retrieve a single sequence by its id.
`void` `SequenceDBLite.addSequence(Sequence seq)` Adds a sequence to the database.
`void` `SequenceDBLite.removeSequence(java.lang.String id)` Remove the sequence associated with an ID from the database.
`void` `IndexStore.store(Index indx)` Add the Index to the store.
`void` `IndexStore.commit()` Commit the stored indices to permanent storage.
`Index` `IndexStore.fetch(java.lang.String id)` Fetch an Index based upon an ID.
`void` `NCBISequenceDB.setDatabase(java.lang.String dataBase)`
`void` `NCBISequenceDB.setSequenceFormat(SequenceFormat format)`
`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)
`Index` `BioIndex.fetch(java.lang.String id)`
`void` `BioIndex.commit()`
`void` `HashSequenceDB.removeSequence(java.lang.String id)`
`Sequence` `CachingSequenceDB.getSequence(java.lang.String id)`
`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
`Sequence` `ViewingSequenceDB.getSequence(java.lang.String id)`
`Sequence` `SubSequenceDB.getSequence(java.lang.String id)`

Constructors in org.biojava.bio.seq.db that throw BioException
`TabIndexStore(java.io.File storeFile, java.io.File indexFile, java.lang.String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)`
`BioIndex(java.io.File indexDirectory, java.lang.String namespace, int idLength)`
`BioIndex(java.io.File indexDirectory)` Load an existing index file.
`SubSequenceDB(SequenceDB parent, java.util.Set ids)`

Uses of BioException in org.biojava.bio.seq.db.biofetch

Methods in org.biojava.bio.seq.db.biofetch that throw BioException
`Sequence` `BioFetchSequenceDB.getSequence(java.lang.String id)`
`SequenceDBLite` `BioFetchSequenceDBProvider.getSequenceDB(java.util.Map config)`

Uses of BioException in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that throw BioException
`void` `BioSQLSequenceDB.createDummySequence(java.lang.String id, Alphabet alphabet, int length)`
`void` `BioSQLSequenceDB.addSequence(Sequence seq)`
`Sequence` `BioSQLSequenceDB.getSequence(java.lang.String id)`
`void` `BioSQLSequenceDB.removeSequence(java.lang.String id)`
`SequenceDBLite` `BioSQLSequenceDBProvider.getSequenceDB(java.util.Map config)`

Constructors in org.biojava.bio.seq.db.biosql that throw BioException
`BioSQLSequenceDB(java.lang.String dbURL, java.lang.String dbUser, java.lang.String dbPass, java.lang.String biodatabase, boolean create)` Connect to a BioSQL database.

Uses of BioException in org.biojava.bio.seq.db.flat

Methods in org.biojava.bio.seq.db.flat that throw BioException
`Sequence` `FlatSequenceDB.getSequence(java.lang.String id)`
`SequenceDBLite` `FlatSequenceDBProvider.getSequenceDB(java.util.Map config)`

Constructors in org.biojava.bio.seq.db.flat that throw BioException
`FlatSequenceDB(java.lang.String location, java.lang.String dbName)`

Uses of BioException in org.biojava.bio.seq.distributed

Methods in org.biojava.bio.seq.distributed that throw BioException
`boolean` `GFFDataSource.hasSequence(java.lang.String id)`
`boolean` `GFFDataSource.hasFeatures(java.lang.String id)`
`FeatureHolder` `GFFDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` `GFFDataSource.getFeatures(java.lang.String id, FeatureFilter ff, boolean recurse)`
`Sequence` `GFFDataSource.getSequence(java.lang.String id)`
`java.util.Set` `GFFDataSource.ids(boolean topLevel)`
`boolean` `SequenceDBDataSource.hasSequence(java.lang.String id)`
`boolean` `SequenceDBDataSource.hasFeatures(java.lang.String id)`
`FeatureHolder` `SequenceDBDataSource.getFeatures(FeatureFilter ff)`
`FeatureHolder` `SequenceDBDataSource.getFeatures(java.lang.String id, FeatureFilter ff, boolean recurse)`
`Sequence` `SequenceDBDataSource.getSequence(java.lang.String id)`
`java.util.Set` `SequenceDBDataSource.ids(boolean topLevel)`
`boolean` `DistDataSource.hasSequence(java.lang.String id)` Find out if this DistDataSource provides the sequence information for a sequence ID.
`boolean` `DistDataSource.hasFeatures(java.lang.String id)` Find out if this DistDataSource can provide features on a sequence with a particular ID.
`FeatureHolder` `DistDataSource.getFeatures(FeatureFilter ff)` Get all features matching a FeatureFilter provided by this DistDataSource.
`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.
`Sequence` `DistDataSource.getSequence(java.lang.String id)` Get a Sequence object for an ID.
`java.util.Set` `DistDataSource.ids(boolean topLevel)` Get the complete set of sequence IDs provided by this DistDataSource.
`Sequence` `DistributedSequenceDB.getSequence(java.lang.String id)`

Uses of BioException in org.biojava.bio.seq.homol

Methods in org.biojava.bio.seq.homol that throw BioException
`void` `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 BioException
`Feature` `SimpleRemoteFeature.getRemoteFeature()`
`Feature` `SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat)`
`Feature` `SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)`
`Feature` `SimpleSequence.createFeature(Feature.Template template)`
`Feature` `SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)` Deprecated. Please use new 1-arg createFeature instead.
`Feature` `SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)`
`Feature` `SimpleFeature.createFeature(Feature.Template temp)`
`Feature` `RevCompSequence.createFeature(Feature.Template ft)` createFeature() will call createFeature() on the underlying Sequence.

Uses of BioException in org.biojava.bio.seq.io

Subclasses of BioException in org.biojava.bio.seq.io
`class` `ParseException` ParseException should be thrown to indicate that there was a problem with parsing sequence information.

Methods in org.biojava.bio.seq.io that throw BioException
`Sequence` `SequenceBuilder.makeSequence()` Return the Sequence object which has been constructed by this builder.
`Sequence` `StreamReader.nextSequence()` Pull the next sequence out of the stream.
`Sequence` `SequenceBuilderFilter.makeSequence()`
`void` `FastaAlignmentFormat.write(java.io.OutputStream os, Alignment align, int fileType)` Writes out the alignment to an FASTA file.
`void` `FastaAlignmentFormat.writeDna(java.io.OutputStream os, Alignment align)`
`void` `FastaAlignmentFormat.writeProtein(java.io.OutputStream os, Alignment align)`
`void` `FeatureTableParser.startFeature(java.lang.String type)`
`void` `FeatureTableParser.featureData(java.lang.String line)`
`void` `FeatureTableParser.endFeature()`
`SymbolList` `ChunkedSymbolListFactory.make(SymbolReader sr)` Method to create a Sequence with a SymbolReader.
`boolean` `SequenceFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Read a sequence and pass data on to a SeqIOListener.
`void` `MSFAlignmentFormat.write(java.io.OutputStream os, Alignment align, int fileType)`
`void` `MSFAlignmentFormat.writeDna(java.io.OutputStream os, Alignment align)`
`void` `MSFAlignmentFormat.writeProtein(java.io.OutputStream os, Alignment align)`
`ComponentFeature` `SimpleAssemblyBuilder.addComponentSequence(ComponentFeature.Template cft)`
`Feature.Template` `EmblLikeLocationParser.parseLocation(java.lang.String location, Feature.Template theTemplate)` `parseLocation` creates a `Location` from the String and returns a stranded location.
`static SequenceDB` `SeqIOTools.readFasta(java.io.InputStream seqFile, Alphabet alpha)` Create a sequence database from a fasta file provided as an input stream.
`static void` `SeqIOTools.writeSwissprot(java.io.OutputStream os, SequenceIterator in)` Writes a stream of Sequences to an OutputStream in SwissProt format.
`static void` `SeqIOTools.writeSwissprot(java.io.OutputStream os, Sequence seq)` Writes a single Sequence to an OutputStream in SwissProt format.
`static void` `SeqIOTools.writeGenpept(java.io.OutputStream os, SequenceIterator in)` Writes a stream of Sequences to an OutputStream in Genpept format.
`static void` `SeqIOTools.writeGenpept(java.io.OutputStream os, Sequence seq)` Writes a single Sequence to an OutputStream in Genpept format.
`static SequenceFormat` `SeqIOTools.getSequenceFormat(int identifier)` `getSequenceFormat` accepts a value which represents a sequence format and returns the relevant `SequenceFormat` object.
`static SequenceBuilderFactory` `SeqIOTools.getBuilderFactory(int identifier)` `getBuilderFactory` accepts a value which represents a sequence format and returns the relevant `SequenceBuilderFactory` object.
`static FiniteAlphabet` `SeqIOTools.getAlphabet(int identifier)` `getAlphabet` accepts a value which represents a sequence format and returns the relevant `FiniteAlphabet` object.
`static SequenceBuilderFactory` `SeqIOTools.formatToFactory(SequenceFormat format, Alphabet alpha)` Deprecated. as this essentially duplicates the operation available in the method `identifyBuilderFactory`.
`static java.lang.Object` `SeqIOTools.fileToBiojava(java.lang.String formatName, java.lang.String alphabetName, java.io.BufferedReader br)` Reads a file with the specified format and alphabet
`static java.lang.Object` `SeqIOTools.fileToBiojava(int fileType, java.io.BufferedReader br)` Reads a file and returns the corresponding Biojava object.
`static void` `SeqIOTools.biojavaToFile(java.lang.String formatName, java.lang.String alphabetName, java.io.OutputStream os, java.lang.Object biojava)` Writes a Biojava `SequenceIterator`, `SequenceDB`, `Sequence` or `Aligment` to an `OutputStream`
`static void` `SeqIOTools.biojavaToFile(int fileType, java.io.OutputStream os, java.lang.Object biojava)` Converts a Biojava object to the given filetype.

Constructors in org.biojava.bio.seq.io that throw BioException
`CrossProductTokenization(Alphabet alpha)`

Uses of BioException in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that throw BioException
`Feature` `ProjectedFeature.createFeature(Feature.Template temp)`
`Feature` `ProjectionContext.createFeature(Feature f, Feature.Template templ)` Delegate for createFeature

Uses of BioException in org.biojava.bio.seq.ragbag

Methods in org.biojava.bio.seq.ragbag that throw BioException
`org.biojava.bio.seq.ragbag.RagbagFileParser` `RagbagFileParserFactory.getParser(java.io.File inputFile)` Return a RagbagFileParser for given file

Constructors in org.biojava.bio.seq.ragbag that throw BioException
`RagbagAssembly(java.lang.String name, java.lang.String urn, java.io.File thisDir, RagbagSequenceFactory seqFactory, RagbagComponentDirectory compDir)`

Uses of BioException in org.biojava.bio.symbol

Subclasses of BioException in org.biojava.bio.symbol
`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.

Methods in org.biojava.bio.symbol that throw BioException
`SymbolTokenization` `AbstractAlphabet.getTokenization(java.lang.String name)`
`static void` `AlphabetManager.loadAlphabets(org.xml.sax.InputSource is)` Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.
`static AlphabetIndex` `AlphabetManager.getAlphabetIndex(Symbol[] syms)` Get an indexer for an array of symbols.
`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)`
`SymbolTokenization` `Alphabet.getTokenization(java.lang.String name)` Get a SymbolTokenization by name.
`SymbolTokenization` `DoubleAlphabet.SubDoubleAlphabet.getTokenization(java.lang.String name)`

Constructors in org.biojava.bio.symbol that throw BioException
`PackedDnaSymbolList(SymbolList symList)` constructor taking another symbol list.
`PackedDnaSymbolList(int length, byte[] byteArray)` constructor taking a byte array previously created by another PackedDnaSymbolList object.

Uses of BioException in org.biojava.bio.taxa

Subclasses of BioException in org.biojava.bio.taxa
`class` `CircularReferenceException`

Uses of BioException in org.biojava.directory

Methods in org.biojava.directory that throw BioException
`SequenceDBLite` `SequenceDBProvider.getSequenceDB(java.util.Map config)` Get a sequence database.
`SequenceDBLite` `Registry.getDatabase(java.lang.String dbName)` `getDatabase` retrieves a database instance known by a name `String`.

Uses of BioException in org.biojava.utils.math

Methods in org.biojava.utils.math that throw BioException
`static double` `BinarySearch.solve(double min, double max, double tolerance, ComputeObject obj)` method that will attempt solving the equation.