Uses of Class
org.biojava.bio.BioException

Packages that use BioException
org.biojava.bio.alignment Classes to generate and describe sequence alignments. 
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.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.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 protein structure (PDB). 
org.biojava.bio.structure.io Input and Output of Structures 
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.db Interactions between biojavax objects and a DB. 
org.biojavax.bio.db.biosql Interface between biojava and biosql databases 
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.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)
           
 List NeedlemanWunsch.alignAll(SequenceIterator source, SequenceDB subjectDB)
           
 String NeedlemanWunsch.getAlignmentString()
           
 int SubstitutionMatrix.getValueAt(Symbol row, Symbol col)
          There are some substitution matrices containing more columns than lines.
protected  int[][] SubstitutionMatrix.parseMatrix(String matString)
          Reads a String representing the contents of a substitution matrix file.
 

Constructors in org.biojava.bio.alignment that throw BioException
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).
SimpleAlignmentElement(Object label, SymbolList seq, Location loc)
           
SubstitutionMatrix(FiniteAlphabet alpha, File matrixFile)
          This constructs a SubstitutionMatrix-object that contains two Map data structures having biojava symbols as key and the value being the index of the matrix containing the substitution score.
SubstitutionMatrix(FiniteAlphabet alpha, String matrixString, String name)
          With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.
 

Uses of BioException in org.biojava.bio.annodb
 

Constructors in org.biojava.bio.annodb that throw 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 distribution arrays.
static 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
 class IllegalTransitionException
          This exception indicates that there is no transition between two states.
 

Methods in org.biojava.bio.dp that throw BioException
 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 WMAsMM.registerWithTrainer(ModelTrainer modelTrainer)
           
 void Trainable.registerWithTrainer(ModelTrainer mt)
          Perform any registration that is necessary with mt.
 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.
 

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

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
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
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
 class DuplicateTaxonException
           
 

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

Methods in org.biojava.bio.program.indexdb that throw BioException
 BioStore BioStoreFactory.createBioStore()
          createBioStore creates a BioStore reflecting the current state of the factory and returns a reference to it.
 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.
 List BioStore.get(String id, String namespace)
           
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
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
 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 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 CompactedDataStoreFactory.buildDataStore(File storeFile, SequenceStreamer streamer, Packing packing, int wordLength, int stepSize, int threshold)
           
 void SequenceStreamer.reset()
           
 void SequenceStreamer.streamNext(SeqIOListener listener)
           
 void SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener)
           
 void SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener)
           
 

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)
           
 SeqSimilaritySearchResult BlastLikeSearchBuilder.makeSearchResult()
           
protected  Sequence ViewSequenceFactory.makeSubjectViewSequence(String subjectID)
           
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
 UnigeneCluster UnigeneDB.addCluster(UnigeneCluster cluster)
          Add a cluster to a database.
 UnigeneDB FlatFileUnigeneFactory.createUnigene(URL unigeneLoc)
           
 UnigeneDB UnigeneFactory.createUnigene(URL unigeneURL)
           
static UnigeneDB UnigeneTools.createUnigene(URL dbURL)
          Create a new UnigeneDB instance referred to by a URL.
 UnigeneDB SQLUnigeneFactory.createUnigene(URL dbURL)
           
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 UnigeneFactory.loadUnigene(URL unigeneURL)
           
static UnigeneDB UnigeneTools.loadUnigene(URL dbURL)
          Load a UnigeneDB instance referred to by a URL.
 UnigeneDB SQLUnigeneFactory.loadUnigene(URL dbURL)
           
 

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)
           
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
 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.
 double IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)
          Computes isoelectric point of specified peptide.
static 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
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
 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
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
 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
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
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 SimpleAssembly.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 AbstractFeatureHolder.createFeature(Feature.Template temp)
           
 Feature NewSimpleAssembly.createFeature(Feature.Template temp)
           
 Feature LazyFeatureHolder.createFeature(Feature.Template template)
           
 Feature FeatureHolder.createFeature(Feature.Template ft)
          Create a new Feature, and add it to this FeatureHolder.
 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 SimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
           
 Feature NewSimpleAssembly.realizeFeature(FeatureHolder fh, Feature.Template temp)
           
 Feature RealizingFeatureHolder.realizeFeature(FeatureHolder parent, Feature.Template template)
          Realize a feature template.
 Feature SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)
           
 Feature FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)
          Install a feature on the specified sequence.
 void AbstractFeatureHolder.removeFeature(Feature f)
           
 void LazyFeatureHolder.removeFeature(Feature f)
           
 void FeatureHolder.removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 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
 class IllegalIDException
           
 

Methods in org.biojava.bio.seq.db that throw BioException
 void IndexedSequenceDB.addFile(File seqFile)
          Add sequences from a file to the sequence database.
 void AbstractSequenceDB.addSequence(Sequence seq)
           
 void SequenceDBLite.addSequence(Sequence seq)
          Adds a sequence to the database.
 void DummySequenceDB.addSequence(Sequence seq)
           
 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 WebSequenceDB.getSequence(String id)
          Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
 Sequence SwissprotSequenceDB.getSequence(String id)
           
 Sequence ViewingSequenceDB.getSequence(String id)
           
 Sequence CachingSequenceDB.getSequence(String id)
           
 Sequence IndexedSequenceDB.getSequence(String id)
           
 Sequence AnnotatedSequenceDB.getSequence(String id)
           
 Sequence SequenceDBLite.getSequence(String id)
          Retrieve a single sequence by its id.
 Sequence SubSequenceDB.getSequence(String id)
           
 Sequence GenpeptSequenceDB.getSequence(String id)
           
 Sequence DummySequenceDB.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 HashSequenceDB.removeSequence(String id)
           
 void AbstractSequenceDB.removeSequence(String id)
           
 void SequenceDBLite.removeSequence(String id)
          Remove the sequence associated with an ID from the database.
 void DummySequenceDB.removeSequence(String id)
           
 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
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
 Sequence BioFetchSequenceDB.getSequence(String id)
           
 SequenceDBLite BioFetchSequenceDBProvider.getSequenceDB(Map config)
           
 

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

Methods in org.biojava.bio.seq.db.biosql that throw BioException
static Taxon TaxonSQL.addName(Connection conn, Taxon taxon, String nameClass, String newName)
          Deprecated. Adds a new name of the given nameClass to the taxon.
 void BioSQLSequenceDB.addSequence(Sequence seq)
          Deprecated.  
 void BioSQLSequenceDB.createDummySequence(String id, Alphabet alphabet, int length)
          Deprecated.  
static Stack TaxonSQL.getChildrenOf(Connection conn, String scientificName)
          Deprecated. Returns all children of the specified taxon.
static Stack TaxonSQL.getChildrenOf(Connection conn, Taxon t)
          Deprecated. Returns the children as a Stack of this given taxon.
 Sequence BioSQLSequenceDB.getSequence(int bioentry_id)
          Deprecated.  
 Sequence BioSQLSequenceDB.getSequence(String id)
          Deprecated.  
 SequenceDBLite BioSQLSequenceDBProvider.getSequenceDB(Map config)
          Deprecated.  
static Taxon TaxonSQL.removeName(Connection conn, DBHelper helper, Taxon taxon, String nameClass, String oldName)
          Deprecated. Deletes the specified name from of the taxon from the database.
 void BioSQLSequenceDB.removeSequence(String id)
          Deprecated.  
static Taxon TaxonSQL.removeTaxon(Connection conn, DBHelper helper, String name)
          Deprecated. Deletes a taxon specified by one of it's names with all it's different names, annotations and sequences from the database.
static Taxon TaxonSQL.removeTaxon(Connection conn, int ncbi_id, DBHelper helper)
          Deprecated. Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the removed taxon.
static Taxon TaxonSQL.setCommonName(Connection conn, Taxon taxon, String newName)
          Deprecated. With this method the common name of the given taxon can be changed or created, if there was none before.
 

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

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

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

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

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 SimpleGappedSequence.createFeature(Feature.Template templ)
           
 Feature RevCompSequence.createFeature(Feature.Template ft)
          createFeature() will call createFeature() on the underlying Sequence.
 Feature SimpleSequence.createFeature(Feature.Template template)
           
 Feature SimpleFeature.createFeature(Feature.Template temp)
           
 Feature DummySequence.createFeature(Feature.Template template)
           
 Feature ViewSequence.createFeature(Feature.Template template)
           
 Feature SubSequence.createFeature(Feature.Template templ)
           
 Feature LazyFilterFeatureHolder.createFeature(Feature.Template temp)
           
 Feature SimpleSequence.createFeature(FeatureHolder fh, Feature.Template template)
          Deprecated. Please use new 1-arg createFeature instead.
 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 SimpleSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
           
 Feature SimpleFeature.realizeFeature(FeatureHolder fh, Feature.Template templ)
           
 Feature ViewSequence.realizeFeature(FeatureHolder parent, Feature.Template template)
           
 void SimpleGappedSequence.removeFeature(Feature f)
           
 void RevCompSequence.removeFeature(Feature f)
           
 void SimpleSequence.removeFeature(Feature f)
          Remove a feature attached to this sequence.
 void DummySequence.removeFeature(Feature feature)
           
 void SubSequence.removeFeature(Feature f)
           
 void LazyFilterFeatureHolder.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
 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
 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 SequenceBuilderFilter.makeSequence()
           
 Sequence SequenceBuilderBase.makeSequence()
           
 Sequence SmartSequenceBuilder.makeSequence()
           
 Sequence SimpleSequenceBuilder.makeSequence()
           
 Sequence SequenceBuilder.makeSequence()
          Return the Sequence object which has been constructed by this builder.
 Sequence SimpleAssemblyBuilder.makeSequence()
           
 Sequence SequenceDBSequenceBuilder.makeSequence()
          create the sequence
 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
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 ReparentContext.createFeature(Feature.Template projTempl)
           
 Feature ProjectionContext.createFeature(Feature.Template projTempl)
          Create a projected feature with properties matching the template.
 Feature ProjectedFeatureHolder.createFeature(Feature.Template templ)
           
 Feature ReparentContext.createFeature(Feature f, Feature.Template projTempl)
           
 Feature ProjectionContext.createFeature(Feature projParent, Feature.Template projTempl)
          Create a new projected feature.
 void ProjectedFeature.removeFeature(Feature f)
           
 void ReparentContext.removeFeature(Feature dyingChild)
           
 void ProjectionContext.removeFeature(Feature dyingChild)
          Remove the dying child.
 void ProjectedFeatureHolder.removeFeature(Feature dyingChild)
           
 void ReparentContext.removeFeature(Feature f, Feature f2)
           
 void ProjectionContext.removeFeature(Feature projParent, Feature dyingChild)
          Remove the dying child.
 

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
static AlphabetIndex AlphabetManager.getAlphabetIndex(Symbol[] syms)
          Get an indexer for an array of symbols.
 SymbolTokenization SoftMaskedAlphabet.getTokenization(String type)
           
 SymbolTokenization Alphabet.getTokenization(String name)
           Get a SymbolTokenization by name.
 SymbolTokenization AbstractAlphabet.getTokenization(String name)
           
 SymbolTokenization DoubleAlphabet.SubDoubleAlphabet.getTokenization(String name)
           
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.put(CodonPref codonPref)
          handles storage of a CodonPref object
 void CodonPrefFilter.ByName.put(CodonPref codonPref)
           
 void CodonPrefFilter.EverythingToXML.put(CodonPref codonPref)
           
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.
static CodonPref CodonPrefTools.readFromXML(InputStream prefStream, String name)
          reads a specified CodonPref from an file.
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
 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
 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
 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.
 

Uses of BioException in org.biojavax.bio
 

Methods in org.biojavax.bio that throw BioException
 BioEntry BioEntryIterator.nextBioEntry()
           
 

Uses of BioException in org.biojavax.bio.db
 

Methods in org.biojavax.bio.db that throw BioException
 void AbstractBioEntryDB.addBioEntry(BioEntry seq)
           
 void AbstractRichSequenceDB.addBioEntry(BioEntry seq)
           
 void BioEntryDBLite.addBioEntry(BioEntry seq)
          Adds a sequence to the database.
 void HashBioEntryDB.addBioEntry(BioEntry seq)
          Add a BioEntry, the name of the BioEntry will be used as the ID
protected  void HashBioEntryDB.addBioEntry(String id, BioEntry seq)
           
 void RichSequenceDBLite.addRichSequence(RichSequence seq)
          Adds a sequence to the database.
 void HashRichSequenceDB.addRichSequence(RichSequence seq)
          Add a sequence.
 void AbstractRichSequenceDB.addRichSequence(RichSequence seq)
           
protected  void HashRichSequenceDB.addRichSequence(String id, RichSequence seq)
           
 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 BioEntryDBLite.getBioEntrys(Set ids)
          Retrieve multiple BioEntry by their ids.
 BioEntryDB HashBioEntryDB.getBioEntrys(Set ids)
           
 BioEntryDB AbstractRichSequenceDB.getBioEntrys(Set ids, BioEntryDB db)
           
 BioEntryDB BioEntryDBLite.getBioEntrys(Set ids, BioEntryDB db)
          Retrieve multiple BioEntry into a specific sequence database.
 BioEntryDB HashBioEntryDB.getBioEntrys(Set ids, BioEntryDB db)
           
 RichSequence RichSequenceDBLite.getRichSequence(String id)
          Retrieve a single RichSequence by its id.
 RichSequence HashRichSequenceDB.getRichSequence(String id)
           
 RichSequenceDB RichSequenceDBLite.getRichSequences(Set ids)
          Retrieve multiple RichSequence by its id.
 RichSequenceDB HashRichSequenceDB.getRichSequences(Set ids)
           
 RichSequenceDB RichSequenceDBLite.getRichSequences(Set ids, RichSequenceDB db)
          Retrieve multiple RichSequence into a specific sequence database.
 RichSequenceDB HashRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)
           
 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 RichSequenceDBLite.removeRichSequence(String id)
          Remove the RichSequence associated with an ID from the database.
 void AbstractRichSequenceDB.removeRichSequence(String id)
           
 void HashRichSequenceDB.removeSequence(String id)
           
 void AbstractRichSequenceDB.removeSequence(String id)
           
 

Uses of BioException in org.biojavax.bio.db.biosql
 

Methods in org.biojavax.bio.db.biosql that throw BioException
 void BioSQLBioEntryDB._addBioEntry(BioEntry seq)
           
 void BioSQLBioEntryDB.addBioEntry(BioEntry seq)
           
 void BioSQLRichSequenceDB.addRichSequence(RichSequence seq)
           
 RichSequence BioSQLRichSequenceDB.fullyLoadRichSequence(RichSequence id)
           
 BioEntry BioSQLBioEntryDB.getBioEntry(String id)
           
 BioEntryDB BioSQLBioEntryDB.getBioEntrys(Set ids)
           
 BioEntryDB BioSQLBioEntryDB.getBioEntrys(Set ids, BioEntryDB db)
           
 RichSequence BioSQLRichSequenceDB.getRichSequence(String id)
           
 RichSequenceDB BioSQLRichSequenceDB.getRichSequences(Set ids)
           
 RichSequenceDB BioSQLRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)
           
 void BioSQLBioEntryDB.removeBioEntry(String id)
           
 void BioSQLRichSequenceDB.removeRichSequence(String id)
           
 

Uses of BioException in org.biojavax.bio.db.ncbi
 

Methods in org.biojavax.bio.db.ncbi that throw BioException
 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.
 RichSequenceDB GenbankRichSequenceDB.getRichSequences(Set list)
          Retrieve rich sequences from a Genbank
 RichSequenceDB GenbankRichSequenceDB.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
 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(Namespace ns, 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(String namespace, String name, String seqString, Alphabet alpha)
          Create a new RichSequence in the specified namespace.
 RichSequence RichSequenceIterator.nextRichSequence()
           
 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
 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. Implementations of this for a RichSequenceBuilder should delegate to makeRichSequence() and return only RichSequence objects.
 Sequence SimpleRichSequenceBuilder.makeSequence()
          Return the Sequence object which has been constructed by this builder.
 BioEntry RichStreamReader.nextBioEntry()
          
 RichSequence RichStreamReader.nextRichSequence()
          
 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.