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 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.
 

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.