Uses of Class
org.biojava.bio.BioException

Packages that use BioException

org.biojava.bio.alignment	Implementation of the Alignment interface.
org.biojava.bio.annodb	Databases of generic structured data (annotation) objects.
org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.das	Development client for the Distributed Annotation System.
org.biojava.bio.program.das.dasalignment
org.biojava.bio.program.formats	Experimental parsers using the tagvalue framework.
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.program.homologene	Support classes for Homologene data.
org.biojava.bio.program.indexdb	A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.sax.blastxml	Parsers for the XML output from NCBI blast.
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.proteomics	Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.structure	Interfaces and classes for molecular structure.
org.biojava.bio.structure.io
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

Uses of BioException in org.biojava.bio.alignment

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

void	FlexibleAlignment.addSequence(AlignmentElement ae) add a new a alignment usings a location to the reference sequence.
void	ARAlignment.addSequence(AlignmentElement ae)

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

SimpleAlignmentElement(Object label, SymbolList seq, Location loc)

FlexibleAlignment(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.annodb

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

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.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

static WeightMatrix	XmlMarkovModel.readMatrix(Element root)
static MarkovModel	XmlMarkovModel.readModel(Element root)
void	WMAsMM.registerWithTrainer(ModelTrainer modelTrainer)
Sequence	WeightMatrixAnnotator.annotate(Sequence seq)
void	TrainingAlgorithm.train(SequenceDB db, double nullWeight, StoppingCriteria stopper) Trains the sequences in db untill stopper says to finnish.
void	Trainable.registerWithTrainer(ModelTrainer mt) Perform any registration that is necessary with mt.
void	SimpleHMMTrainer.completeCycle()
void	HMMTrainer.completeCycle() indicate that a cycle of training is completed and the emission/transition matrices should be updated.
DP	DPFactory.createDP(MarkovModel model)
DP	DPFactory.DefaultFactory.createDP(MarkovModel model)
State[]	DP.stateList(MarkovModel mm)
DPMatrix	DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)
StatePath	DP.generate(int length) Generates an alignment from a model.
void	AbstractTrainer.train(SequenceDB db, double nullModelWeight, StoppingCriteria stopper) Trains the sequences in db until stopper says to finnish.

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

SequenceDB	ReferenceServer.getDB()
DistDataSource	ReferenceServer.getDistDataSource()
DistDataSource	DataSource.getDistDataSource()
SequenceDBLite	DASSequenceDBProvider.getSequenceDB(Map config)
Sequence	DASSequenceDB.getSequence(String id)
void	DASSequence.addAnnotationSource(URL dataSourceURL)
void	DASSequence.removeAnnotationSource(URL dataSourceURL)
protected SymbolList	DASSequence.getSymbols()
Feature	DASSequence.realizeFeature(FeatureHolder dest, Feature.Template temp)
static Set	DAS.getTypes(URL dasURL)
void	DAS.addDasURL(URL dasURL)

Constructors in org.biojava.bio.program.das that throw BioException

DASSequenceDB(URL dataSourceURL)

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

Subclasses of BioException in org.biojava.bio.program.das.dasalignment

class

DASException An exception of one of the DAS classes.

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

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

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

protected void	SequencesAsGFF.doPreProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) Emit any per-sequence header information.
protected void	SequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) Internal method to process an individual Sequence.
protected void	SequencesAsGFF.doProcessFeature(Feature feature, GFFDocumentHandler handler, String id) Internal method to process an individual Feature.
protected SimpleGFFRecord	SequencesAsGFF.createGFFRecord(Feature feature, String id) Internal method to create a GFFRecord from an individual Feature.
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	GFFWriter.invalidStart(String token, NumberFormatException nfe)
void	GFFWriter.invalidEnd(String token, NumberFormatException nfe)
void	GFFWriter.invalidScore(String token, NumberFormatException nfe)
void	GFFWriter.invalidStrand(String token)
void	GFFWriter.invalidFrame(String token, NumberFormatException nfe)
static GFFEntrySet	GFFTools.readGFF(String fileName) Deprecated. use: readGff(File)
static GFFEntrySet	GFFTools.readGFF(String fileName, GFFRecordFilter recFilt) Deprecated. use: readGff(File,GFFRecordFilter)
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(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 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.
static GFFEntrySet	GFFTools.gffFromSeqDB(SequenceDB seqDB) Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
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
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.

Uses of BioException in org.biojava.bio.program.gff3

Methods in org.biojava.bio.program.gff3 that throw BioException

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
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.

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

Subclasses of BioException in org.biojava.bio.program.homologene

class

DuplicateTaxonException

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

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

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.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.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.
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.
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)

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

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

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.sax.blastxml

Constructors in org.biojava.bio.program.sax.blastxml that throw BioException

BlastXMLParserFacade()

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

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

void	SequenceStreamer.streamNext(SeqIOListener listener)
void	SequenceStreamer.reset()
void	SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener)
void	SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener)
DataStore	NIODataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	MappedDataStoreFactory.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	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceDB seqDB, Packing packing, int wordLength, int threshold)
DataStore	CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, 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(String queryID)
protected Sequence	ViewSequenceFactory.makeSubjectViewSequence(String subjectID)
SeqSimilaritySearchResult	BlastLikeSearchBuilder.makeSearchResult()
static FiniteAlphabet	AlphabetResolver.resolveAlphabet(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(URL dbURL) Load a UnigeneDB instance referred to by a URL.
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	UnigeneFactory.loadUnigene(URL unigeneURL)
UnigeneDB	UnigeneFactory.createUnigene(URL unigeneURL)
UnigeneCluster	UnigeneDB.getCluster(String clusterID) Fetch a cluster by its cluster id.
UnigeneCluster	UnigeneDB.addCluster(UnigeneCluster cluster) Add a cluster to a database.
UnigeneDB	SQLUnigeneFactory.loadUnigene(URL dbURL)
UnigeneDB	SQLUnigeneFactory.createUnigene(URL dbURL)
UnigeneDB	FlatFileUnigeneFactory.loadUnigene(URL unigeneLoc)
UnigeneDB	FlatFileUnigeneFactory.createUnigene(URL unigeneLoc)

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

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

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, FiniteAlphabet alpha)
static Sequence	XFFTools.readXFF(File xffFile, String seqID)

Uses of BioException in org.biojava.bio.proteomics

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

static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.
static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, String name)
static Protease	ProteaseManager.createProtease(String cleaveRes, boolean endoProtease, String notCleaveRes, String name)
static Protease	ProteaseManager.createProtease(String cleaveRes, boolean endoProtease, String name)
static void	ProteaseManager.registerProtease(Protease prot) Registers a protease and ensures its flyweight status
static Protease	ProteaseManager.getProteaseByName(String proteaseName) Gets a Protease instance by name.
static Protease	Protease.getProteaseByName(String proteaseName) Retrieves a reference to the named Protease.
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.

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

Protease(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	SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, Map searchParameters) Using this sequence similarity searcher, search with the given sequence against the given sequence database.
SeqSimilaritySearchResult	SearchBuilder.makeSearchResult() The makeSearchResult method returns a SeqSimilaritySearchResult instance created from accumulated data.

Uses of BioException in org.biojava.bio.seq

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

void	SimpleFeatureRealizer.addImplementation(Class template, 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	SimpleAssembly.createFeature(Feature.Template temp)
Feature	SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
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.
Sequence	SequenceIterator.nextSequence() Returns the next sequence in the iterator.
Sequence	SequenceAnnotator.annotate(Sequence seq) Return an annotated version of a sequence.
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	RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template) Realize a feature template.
Feature	NewSimpleAssembly.createFeature(Feature.Template temp)
Feature	NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
Feature	LazyFeatureHolder.createFeature(Feature.Template template)
void	LazyFeatureHolder.removeFeature(Feature f)
static Object	FilterUtils.visitFilter(FeatureFilter filter, Visitor visitor) Applies a visitor to a filter, and returns the visitor's result or null.
Feature	FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template) Install a feature on the specified sequence.
Feature	FeatureHolder.createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
void	FeatureHolder.removeFeature(Feature f) Remove a feature from this FeatureHolder.
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	AbstractFeatureHolder.createFeature(Feature.Template temp)
void	AbstractFeatureHolder.removeFeature(Feature f)

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

Sequence	WebSequenceDB.getSequence(String id) Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
Sequence	ViewingSequenceDB.getSequence(String id)
void	TabIndexStore.store(Index indx)
Index	TabIndexStore.fetch(String id)
void	TabIndexStore.commit()
Sequence	SwissprotSequenceDB.getSequence(String id)
Sequence	SubSequenceDB.getSequence(String id)
Sequence	SequenceDBLite.getSequence(String id) Retrieve a single sequence by its id.
void	SequenceDBLite.addSequence(Sequence seq) Adds a sequence to the database.
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	IndexStore.store(Index indx) Add the Index to the store.
void	IndexStore.commit() Commit the stored indices to permanent storage.
Index	IndexStore.fetch(String id) Fetch an Index based upon an ID.
void	IndexedSequenceDB.addFile(File seqFile) Add sequences from a file to the sequence database.
Sequence	IndexedSequenceDB.getSequence(String id)
void	HashSequenceDB.removeSequence(String id)
Sequence	GenpeptSequenceDB.getSequence(String id)
SequenceDB	GenbankSequenceDB.getSequences(Set list) Retrieve sequences from a Genbank
SequenceDB	GenbankSequenceDB.getSequences(Set list, SequenceDB database) Retrieve sequences from a Genbank
void	EmblCDROMIndexStore.store(Index index) store adds an Index to the store.
void	EmblCDROMIndexStore.commit() commit commits changes.
Index	EmblCDROMIndexStore.fetch(String id)
Sequence	DummySequenceDB.getSequence(String id)
void	DummySequenceDB.addSequence(Sequence seq)
void	DummySequenceDB.removeSequence(String id)
Sequence	CachingSequenceDB.getSequence(String id)
Index	BioIndex.fetch(String id)
void	BioIndex.commit()
Sequence	AnnotatedSequenceDB.getSequence(String id)
protected Sequence	AnnotatedSequenceDB.doAnnotation(Sequence seq) Apply the annotation to a sequence.
void	AbstractSequenceDB.addSequence(Sequence seq)
void	AbstractSequenceDB.removeSequence(String id)

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

TabIndexStore(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)
Create a new TabIndexStore.

SubSequenceDB(SequenceDB parent, Set ids)

BioIndex(File indexDirectory, String namespace, int idLength)

BioIndex(File indexDirectory)
Load an existing index file.

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

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

SequenceDBLite	BioFetchSequenceDBProvider.getSequenceDB(Map config)
Sequence	BioFetchSequenceDB.getSequence(String id)

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

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

SequenceDBLite	BioSQLSequenceDBProvider.getSequenceDB(Map config)
void	BioSQLSequenceDB.createDummySequence(String id, Alphabet alphabet, int length)
void	BioSQLSequenceDB.addSequence(Sequence seq)
Sequence	BioSQLSequenceDB.getSequence(String id)
void	BioSQLSequenceDB.removeSequence(String id)

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

BioSQLSequenceDB(String dbDriver, String dbURL, String dbUser, String dbPass, String biodatabase, boolean create)
Connect to a BioSQL database.

BioSQLSequenceDB(String dbURL, String dbUser, String dbPass, String biodatabase, boolean create)
Connect to a BioSQL database.

BioSQLSequenceDB(DataSource ds, String biodatabase, boolean create)

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

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

SequenceDBLite	FlatSequenceDBProvider.getSequenceDB(Map config)
Sequence	FlatSequenceDB.getSequence(String id)

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

FlatSequenceDB(String location, String dbName)

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

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

boolean	SequenceDBDataSource.hasSequence(String id)
boolean	SequenceDBDataSource.hasFeatures(String id)
FeatureHolder	SequenceDBDataSource.getFeatures(FeatureFilter ff)
FeatureHolder	SequenceDBDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
Sequence	SequenceDBDataSource.getSequence(String id)
Set	SequenceDBDataSource.ids(boolean topLevel)
boolean	GFFDataSource.hasSequence(String id)
boolean	GFFDataSource.hasFeatures(String id)
FeatureHolder	GFFDataSource.getFeatures(FeatureFilter ff)
FeatureHolder	GFFDataSource.getFeatures(String id, FeatureFilter ff, boolean recurse)
Sequence	GFFDataSource.getSequence(String id)
Set	GFFDataSource.ids(boolean topLevel)
Sequence	DistributedSequenceDB.getSequence(String id)
boolean	DistDataSource.hasSequence(String id) Find out if this DistDataSource provides the sequence information for a sequence ID.
boolean	DistDataSource.hasFeatures(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(String id, FeatureFilter ff, boolean recurse) Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
Sequence	DistDataSource.getSequence(String id) Get a Sequence object for an ID.
Set	DistDataSource.ids(boolean topLevel) Get the complete set of sequence IDs provided by this DistDataSource.

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	ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
Feature	ViewSequence.createFeature(Feature.Template template)
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 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.
static Feature.Template	TemplateUtils.makeTemplate(Feature feat)
Feature	SubSequence.createFeature(Feature.Template templ)
void	SubSequence.removeFeature(Feature f)
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.
void	SimpleSequence.removeFeature(Feature f) Remove a feature attached to this sequence.
Feature	SimpleRemoteFeature.getRemoteFeature()
Feature	SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat)
void	SimpleGappedSequence.removeFeature(Feature f)
Feature	SimpleGappedSequence.createFeature(Feature.Template templ)
Feature	SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)
Feature	SimpleFeature.createFeature(Feature.Template temp)
void	RevCompSequence.removeFeature(Feature f)
Feature	RevCompSequence.createFeature(Feature.Template ft) createFeature() will call createFeature() on the underlying Sequence.
Feature	LazyFilterFeatureHolder.createFeature(Feature.Template temp)
void	LazyFilterFeatureHolder.removeFeature(Feature f)
Feature	DummySequence.createFeature(Feature.Template template)
void	DummySequence.removeFeature(Feature feature)

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

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	ReparentContext.createFeature(Feature.Template projTempl)
void	ReparentContext.removeFeature(Feature dyingChild)
Feature	ReparentContext.createFeature(Feature f, Feature.Template projTempl)
void	ReparentContext.removeFeature(Feature f, Feature f2)
Feature	ProjectionContext.createFeature(Feature.Template projTempl) Create a projected feature with properties matching the template.
void	ProjectionContext.removeFeature(Feature dyingChild) Remove the dying child.
Feature	ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl) Create a new projected feature.
void	ProjectionContext.removeFeature(Feature projParent, Feature dyingChild) Remove the dying child.
Feature	ProjectedFeatureHolder.createFeature(Feature.Template templ)
void	ProjectedFeatureHolder.removeFeature(Feature dyingChild)
Feature	ProjectedFeature.createFeature(Feature.Template temp)
void	ProjectedFeature.removeFeature(Feature f)

Uses of BioException in org.biojava.bio.structure

Subclasses of BioException in org.biojava.bio.structure

class

StructureException An exception during the parsing of a PDB file

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

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

class

PDBParseException An exception during the parsing of a PDB file

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	SoftMaskedAlphabet.getTokenization(String type)
static MergeLocation	MergeLocation.mergeLocations(List componentLocations) Static Factory method for getting an instance of a MergeLocation
static MergeLocation	MergeLocation.mergeLocations(Location locA, Location locB)
SymbolTokenization	DoubleAlphabet.SubDoubleAlphabet.getTokenization(String name)
static void	CodonPrefTools.writeToXML(CodonPref codonPref, PrintWriter writer) write out a specified CodonPref object in XML format.
static CodonPref	CodonPrefTools.readFromXML(InputStream prefStream, String name) reads a specified CodonPref from an file.
static CodonPref[]	CodonPrefTools.readFromXML(InputStream prefStream)
static void	CodonPrefTools.readFromXML(InputStream prefStream, CodonPrefFilter filter) read an CodonPref XML stream and handle it with a CodonPrefFilter object.
void	CodonPrefFilter.put(CodonPref codonPref) handles storage of a CodonPref object
void	CodonPrefFilter.ByName.put(CodonPref codonPref)
void	CodonPrefFilter.EverythingToXML.put(CodonPref codonPref)
static void	AlphabetManager.loadAlphabets(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.
SymbolTokenization	Alphabet.getTokenization(String name) Get a SymbolTokenization by name.
SymbolTokenization	AbstractAlphabet.getTokenization(String name)

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(Map config) Get a sequence database.
SequenceDBLite	Registry.getDatabase(String dbName) getDatabase retrieves a database instance known by a name String.

Uses of BioException in org.biojava.utils.automata

Subclasses of BioException in org.biojava.utils.automata

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

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

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

Walker

WalkerFactory.getWalker(Visitor visitor) Get a Walker that is customosed to a particular visitor.