Uses of Class
org.biojava.bio.BioException

Packages that use BioException

Package	Description
org.biojava.bio.annodb	Databases of generic structured data (annotation) objects.
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.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
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.ssaha	SSAHA sequence searching API.
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.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.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.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojavax.bio.alignment.blast	This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services through the WWW.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
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.

Uses of BioException in org.biojava.bio.annodb

Constructors in org.biojava.bio.annodb that throw BioException

Modifier	Constructor	Description
	IndexedAnnotationDB(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.dist

Methods in org.biojava.bio.dist that throw BioException

Modifier and Type	Method	Description
static 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.dp

Modifier and Type	Class	Description
class	IllegalTransitionException	This exception indicates that there is no transition between two states.

Methods in org.biojava.bio.dp that throw BioException

Modifier and Type	Method	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(Element root)
static MarkovModel	XmlMarkovModel.readModel(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	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

Modifier	Constructor	Description
	SingleDP(MarkovModel model)

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

Methods in org.biojava.bio.dp.twohead that throw BioException

Modifier and Type	Method	Description
CellCalculatorFactory	CellCalculatorFactoryMaker.make(DP dp)

Constructors in org.biojava.bio.dp.twohead that throw BioException

Modifier	Constructor	Description
	PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm)

Uses of BioException in org.biojava.bio.molbio

Methods in org.biojava.bio.molbio that throw BioException

Modifier and Type	Method	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.

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

Methods in org.biojava.bio.program.formats that throw BioException

Modifier and Type	Method	Description
static Format	FormatTools.getFormat(String formatName)	Attempt to find aformat for a format identifer string.

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

Methods in org.biojava.bio.program.gff that throw BioException

Modifier and Type	Method	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, 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 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(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	GFFTools.readGFF(File inFile)	Reads a GFFEntrySet 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	GFFTools.readGFF(String fileName)	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 BioException

Modifier and Type	Method	Description
protected 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

Modifier and Type	Class	Description
class	DuplicateTaxonException

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

Methods in org.biojava.bio.program.indexdb that throw BioException

Modifier and Type	Method	Description
BioStore	BioStoreFactory.createBioStore()	createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.
List	BioStore.get(String id, String namespace)
Record	IndexStore.get(String id)	get returns a record specified by a primary identifier.
List	IndexStore.get(String id, String namespace)	get returns a list of Records 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(String name, File location, 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(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

Modifier	Constructor	Description
	BioStore(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

Modifier and Type	Method	Description
static 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.ssaha

Methods in org.biojava.bio.program.ssaha that throw BioException

Modifier and Type	Method	Description
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold)
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	DataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)	Build a new DataStore.
DataStore	MappedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	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.unigene

Methods in org.biojava.bio.program.unigene that throw BioException

Modifier and Type	Method	Description
UnigeneCluster	UnigeneDB.addCluster(UnigeneCluster cluster)	Add a cluster to a database.
UnigeneDB	FlatFileUnigeneFactory.createUnigene(URL unigeneLoc)
UnigeneDB	SQLUnigeneFactory.createUnigene(URL dbURL)
UnigeneDB	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.
UnigeneCluster	UnigeneDB.getCluster(String clusterID)	Fetch a cluster by its cluster id.
UnigeneDB	FlatFileUnigeneFactory.loadUnigene(URL unigeneLoc)
UnigeneDB	SQLUnigeneFactory.loadUnigene(URL dbURL)
UnigeneDB	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 BioException

Modifier and Type	Method	Description
static void	XFFTools.annotateXFF(File xffFile, Sequence sequence)
static void	XFFTools.annotateXFF(File xffFile, Sequence sequence, Annotation ann)
static Sequence	XFFTools.readXFF(File xffFile, String seqID)
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 BioException

Modifier and Type	Method	Description
void	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 status

Constructors in org.biojava.bio.proteomics that throw BioException

Modifier	Constructor	Description
	Protease(String cleavageRes, boolean endoProtease)	Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
	Protease(String cleaveRes, boolean endoProtease, 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())

Uses of BioException in org.biojava.bio.proteomics.aaindex

Methods in org.biojava.bio.proteomics.aaindex that throw BioException

Modifier and Type	Method	Description
SymbolPropertyTable	AAindexStreamReader.nextTable()	Returns the next SymbolPropertyTable object.
SymbolPropertyTable	SymbolPropertyTableIterator.nextTable()	Returns the next SymbolPropertyTable object.

Constructors in org.biojava.bio.proteomics.aaindex that throw BioException

Modifier	Constructor	Description
	SimpleSymbolPropertyTableDB(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 BioException

Modifier and Type	Method	Description
SeqSimilaritySearchResult	SearchBuilder.makeSearchResult()	The makeSearchResult method returns a SeqSimilaritySearchResult instance created from accumulated data.
SeqSimilaritySearchResult	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 BioException

Modifier	Constructor	Description
	FilteringContentHandler(BlastLikeSearchFilter filter)
	FilteringContentHandler(BlastLikeSearchFilter filter, SearchContentHandler delegate)

Uses of BioException in org.biojava.bio.seq

Methods in org.biojava.bio.seq that throw BioException

Modifier and Type	Method	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(Class template, 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	AbstractFeatureHolder.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	FeatureHolder.createFeature(Feature.Template ft)	Create a new Feature, and add it to this FeatureHolder.
Feature	LazyFeatureHolder.createFeature(Feature.Template template)
Feature	NewSimpleAssembly.createFeature(Feature.Template temp)
Feature	SimpleAssembly.createFeature(Feature.Template temp)
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	FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)	Install a feature on the specified sequence.
Feature	NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)	Realize a feature template.
Feature	SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	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)
Feature	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.db

Modifier and Type	Class	Description
class	IllegalIDException

Methods in org.biojava.bio.seq.db that throw BioException

Modifier and Type	Method	Description
void	IndexedSequenceDB.addFile(File seqFile)	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.
Index	BioIndex.fetch(String id)
Index	EmblCDROMIndexStore.fetch(String id)
Index	IndexStore.fetch(String id)	Fetch an Index based upon an ID.
Index	TabIndexStore.fetch(String id)
Sequence	AnnotatedSequenceDB.getSequence(String id)
Sequence	CachingSequenceDB.getSequence(String id)
Sequence	DummySequenceDB.getSequence(String id)
Sequence	GenpeptSequenceDB.getSequence(String id)
Sequence	IndexedSequenceDB.getSequence(String id)
Sequence	SequenceDBLite.getSequence(String id)	Retrieve a single sequence by its id.
Sequence	SubSequenceDB.getSequence(String id)
Sequence	SwissprotSequenceDB.getSequence(String id)
Sequence	ViewingSequenceDB.getSequence(String id)
Sequence	WebSequenceDB.getSequence(String id)	Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
SequenceDB	GenbankSequenceDB.getSequences(Set list)	Retrieve sequences from a Genbank
SequenceDB	GenbankSequenceDB.getSequences(Set list, SequenceDB database)	Retrieve sequences from a Genbank
void	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	EmblCDROMIndexStore.store(Index index)	store adds an Index to the store.
void	IndexStore.store(Index indx)	Add the Index to the store.
void	TabIndexStore.store(Index indx)

Constructors in org.biojava.bio.seq.db that throw BioException

Modifier	Constructor	Description
	BioIndex(File indexDirectory)	Load an existing index file.
	BioIndex(File indexDirectory, String namespace, int idLength)
	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 BioException

Modifier and Type	Method	Description
Sequence	BioFetchSequenceDB.getSequence(String id)
SequenceDBLite	BioFetchSequenceDBProvider.getSequenceDB(Map config)

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

Methods in org.biojava.bio.seq.db.flat that throw BioException

Modifier and Type	Method	Description
Sequence	FlatSequenceDB.getSequence(String id)
SequenceDBLite	FlatSequenceDBProvider.getSequenceDB(Map config)

Constructors in org.biojava.bio.seq.db.flat that throw BioException

Modifier	Constructor	Description
	FlatSequenceDB(String location, String dbName)

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

Methods in org.biojava.bio.seq.distributed that throw BioException

Modifier and Type	Method	Description
FeatureHolder	DistDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)	Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
FeatureHolder	DistDataSource.getFeatures(FeatureFilter ff)	Get all features matching a FeatureFilter provided by this DistDataSource.
FeatureHolder	GFFDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
FeatureHolder	GFFDataSource.getFeatures(FeatureFilter ff)
FeatureHolder	SequenceDBDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
FeatureHolder	SequenceDBDataSource.getFeatures(FeatureFilter ff)
Sequence	DistDataSource.getSequence(String id)	Get a Sequence object for an ID.
Sequence	DistributedSequenceDB.getSequence(String id)
Sequence	GFFDataSource.getSequence(String id)
Sequence	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)
Set	DistDataSource.ids(boolean topLevel)	Get the complete set of sequence IDs provided by this DistDataSource.
Set	GFFDataSource.ids(boolean topLevel)
Set	SequenceDBDataSource.ids(boolean topLevel)

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

Methods in org.biojava.bio.seq.homol that throw BioException

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
Feature	DummySequence.createFeature(Feature.Template template)
Feature	LazyFilterFeatureHolder.createFeature(Feature.Template temp)
Feature	RevCompSequence.createFeature(Feature.Template ft)	createFeature() will call createFeature() on the underlying Sequence.
Feature	SimpleFeature.createFeature(Feature.Template temp)
Feature	SimpleGappedSequence.createFeature(Feature.Template templ)
Feature	SimpleSequence.createFeature(Feature.Template template)
Feature	SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)	Deprecated. Please use new 1-arg createFeature instead.
Feature	SubSequence.createFeature(Feature.Template templ)
Feature	ViewSequence.createFeature(Feature.Template template)
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	SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)
Feature	SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
Feature	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)
Feature	SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat)

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

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

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
ComponentFeature	SimpleAssemblyBuilder.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 Biojava SequenceIterator, SequenceDB, Sequence or Aligment to an OutputStream
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 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	SequenceBuilder.makeSequence()	Return the Sequence object which has been constructed by this builder.
Sequence	SequenceBuilderBase.makeSequence()
Sequence	SequenceBuilderFilter.makeSequence()
Sequence	SimpleAssemblyBuilder.makeSequence()
Sequence	SimpleSequenceBuilder.makeSequence()
Sequence	SmartSequenceBuilder.makeSequence()
Sequence	StreamReader.nextSequence()	Pull the next sequence out of the stream.
Feature.Template	EmblLikeLocationParser.parseLocation(String location, Feature.Template theTemplate)	Deprecated. parseLocation creates a Location 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

Modifier	Constructor	Description
	CrossProductTokenization(Alphabet alpha)

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

Methods in org.biojava.bio.seq.projection that throw BioException

Modifier and Type	Method	Description
Feature	ProjectedFeature.createFeature(Feature.Template temp)
Feature	ProjectedFeatureHolder.createFeature(Feature.Template templ)
Feature	ProjectionContext.createFeature(Feature.Template projTempl)	Create a projected feature with properties matching the template.
Feature	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.symbol

Modifier and Type	Class	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.

Methods in org.biojava.bio.symbol that throw BioException

Modifier and Type	Method	Description
static AlphabetIndex	AlphabetManager.getAlphabetIndex(Symbol[] syms)	Get an indexer for an array of symbols.
SymbolTokenization	AbstractAlphabet.getTokenization(String name)
SymbolTokenization	Alphabet.getTokenization(String name)	Get a SymbolTokenization by name.
SymbolTokenization	DoubleAlphabet.SubDoubleAlphabet.getTokenization(String name)
SymbolTokenization	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 a MergeLocation
static MergeLocation	MergeLocation.mergeLocations(Location locA, Location locB)
void	CodonPrefFilter.ByName.put(CodonPref codonPref)
void	CodonPrefFilter.EverythingToXML.put(CodonPref codonPref)
void	CodonPrefFilter.put(CodonPref codonPref)	handles storage of a CodonPref object
static 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

Modifier and Type	Class	Description
class	CircularReferenceException	Deprecated. replaced by classes in org.biojavax.bio.taxa

Uses of BioException in org.biojava.directory

Methods in org.biojava.directory that throw BioException

Modifier and Type	Method	Description
SequenceDBLite	Registry.getDatabase(String dbName)	getDatabase retrieves a database instance known by a name String.
SequenceDBLite	SequenceDBProvider.getSequenceDB(Map config)	Get a sequence database.

Uses of BioException in org.biojava.utils.automata

Subclasses of BioException in org.biojava.utils.automata

Modifier and Type	Class	Description
class	AutomatonException	An exception thrown by classes of this package.

Uses of BioException in org.biojava.utils.math

Methods in org.biojava.utils.math that throw BioException

Modifier and Type	Method	Description
static 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.regex

Modifier and Type	Class	Description
class	RegexException	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

Modifier and Type	Method	Description
Walker	WalkerFactory.getWalker(Visitor visitor)	Get a Walker that is customosed to a particular visitor.

Uses of BioException in org.biojavax.bio

Methods in org.biojavax.bio that throw BioException

Modifier and Type	Method	Description
BioEntry	BioEntryIterator.nextBioEntry()

Uses of BioException in org.biojavax.bio.alignment

Methods in org.biojavax.bio.alignment that throw BioException

Modifier and Type	Method	Description
String	RemotePairwiseAlignmentProperties.getAlignmentOption(String key)	Method that returns the value associated with the key given in parameter.
InputStream	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.
String	RemotePairwiseAlignmentOutputProperties.getOutputOption(String key)	Method that returns the value associated with the key given in parameter.
boolean	RemotePairwiseAlignmentService.isReady(String id, long present)	Simple method to check if the specified request has been completed by the service used.
String	RemotePairwiseAlignmentService.sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa)	Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
String	RemotePairwiseAlignmentService.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 BioException

Modifier and Type	Method	Description
String	RemoteQBlastAlignmentProperties.getAlignmentOption(String key)
InputStream	RemoteQBlastService.getAlignmentResults(String id, RemotePairwiseAlignmentOutputProperties rb)	This method extracts the actual Blast report for this request ID.
String	RemoteQBlastOutputProperties.getOutputOption(String o)	Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.
boolean	RemoteQBlastService.isReady(String id, long present)	This method is used only for the executeBlastSearch method to check for completion of request using the NCBI specified RTOE variable
void	RemoteQBlastService.printRemoteBlastInfo()	A simple method to check the availability of the QBlast service
String	RemoteQBlastService.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.
String	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.
String	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 service
void	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 service

Constructors in org.biojavax.bio.alignment.blast that throw BioException

Modifier	Constructor	Description
	RemoteQBlastService()	The constructor for a QBlast service request.

Uses of BioException in org.biojavax.bio.db

Methods in org.biojavax.bio.db that throw BioException

Modifier and Type	Method	Description
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(String id, BioEntry seq)
void	HashBioEntryDB.addBioEntry(BioEntry seq)	Add a BioEntry, the name of the BioEntry will be used as the ID
void	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)
BioEntry	AbstractRichSequenceDB.getBioEntry(String id)
BioEntry	BioEntryDBLite.getBioEntry(String id)	Retrieve a single BioEntry by its id.
BioEntry	HashBioEntryDB.getBioEntry(String id)
BioEntryDB	AbstractRichSequenceDB.getBioEntrys(Set ids)
BioEntryDB	AbstractRichSequenceDB.getBioEntrys(Set ids, BioEntryDB db)
BioEntryDB	BioEntryDBLite.getBioEntrys(Set ids)	Retrieve multiple BioEntry by their ids.
BioEntryDB	BioEntryDBLite.getBioEntrys(Set ids, BioEntryDB db)	Retrieve multiple BioEntry into a specific sequence database.
BioEntryDB	HashBioEntryDB.getBioEntrys(Set ids)
BioEntryDB	HashBioEntryDB.getBioEntrys(Set ids, BioEntryDB db)
RichSequence	HashRichSequenceDB.getRichSequence(String id)
RichSequence	RichSequenceDBLite.getRichSequence(String id)	Retrieve a single RichSequence by its id.
RichSequenceDB	HashRichSequenceDB.getRichSequences(Set ids)
RichSequenceDB	HashRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)
RichSequenceDB	RichSequenceDBLite.getRichSequences(Set ids)	Retrieve multiple RichSequence by its id.
RichSequenceDB	RichSequenceDBLite.getRichSequences(Set ids, RichSequenceDB db)	Retrieve multiple RichSequence into a specific sequence database.
Sequence	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.ncbi

Methods in org.biojavax.bio.db.ncbi that throw BioException

Modifier and Type	Method	Description
RichSequence	GenbankRichSequenceDB.getRichSequence(String id)	Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenbankRichSequenceDB.getRichSequence(String id, Namespace nsp)	Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenpeptRichSequenceDB.getRichSequence(String id)	Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenpeptRichSequenceDB.getRichSequence(String id, Namespace nsp)	Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequenceDB	GenbankRichSequenceDB.getRichSequences(Set list)	Retrieve rich sequences from a Genbank
RichSequenceDB	GenbankRichSequenceDB.getRichSequences(Set list, RichSequenceDB database)	Retrieve rich sequences from a Genbank
RichSequenceDB	GenpeptRichSequenceDB.getRichSequences(Set list)	Retrieve rich sequences from a Genbank
RichSequenceDB	GenpeptRichSequenceDB.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 BioException

Modifier and Type	Method	Description
Feature	SimpleRichFeature.createFeature(Feature.Template ft)	Create a new Feature, and add it to this FeatureHolder.
Feature	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.
RichSequence	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 BioException

Modifier and Type	Method	Description
RichSequence	RichSequenceBuilder.makeRichSequence()	Build a RichSequence.
RichSequence	SimpleRichSequenceBuilder.makeRichSequence()	Build a RichSequence.
Sequence	RichSequenceBuilder.makeSequence()	Return the Sequence object which has been constructed by this builder.
Sequence	SimpleRichSequenceBuilder.makeSequence()	Return the Sequence object which has been constructed by this builder.
BioEntry	HashedFastaIterator.nextBioEntry()
BioEntry	RichStreamReader.nextBioEntry()
RichSequence	HashedFastaIterator.nextRichSequence()
RichSequence	RichStreamReader.nextRichSequence()
Sequence	HashedFastaIterator.nextSequence()
Sequence	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 BioException

Modifier	Constructor	Description
	HashedFastaIterator(BufferedInputStream is, Alphabet alpha, Namespace ns)