## Uses of Class
org.biojava.utils.NestedException

Packages that use NestedException
org.biojava.bibliography: The data structures and interfaces included in this package define an interoperable framework for bibliographic searches.
org.biojava.bio: The core classes that will be used throughout the bio packages.
org.biojava.bio.chromatogram: Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dp: HMM and Dynamic Programming Algorithms.
org.biojava.bio.program.indexdb: A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.ssaha: SSAHA sequence searching API.
org.biojava.bio.seq.db: Collections of biological sequence data.
org.biojava.bio.seq.io: Classes and interfaces for processing and producing flat-file representations of sequences.
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: Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.candy: The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies.

Uses of NestedException in org.biojava.bibliography

Methods in org.biojava.bibliography that throw NestedException
`void` `BibRefQuery.connect()` It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication.
`void` `BibRefQuery.connect(byte[] collectionId)` It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication, and it makes the collection described by `collectionId` the current collection.
`void` `BibRefQuery.destroy()` It frees all resources related to this query collection.
`BibRefQuery` `BibRefQuery.find(java.lang.String[] keywords, java.lang.String[] attrs, java.util.Hashtable properties)` The easiest direct method for querying a repository.
`BibRefQuery` `BibRefQuery.findByAuthor(BiblioProvider author, java.util.Hashtable properties)` This is a convenient method for a common query.
`BibRef` `BibRefQuery.findById(java.lang.String bibRefId)` This is a convenient method returning just one citation.
`BibRef` `BibRefQuery.findById(java.lang.String bibRefId, java.lang.String[] onlyAttrs)` This is a convenient method returning just one citation, perhaps with a limited number of attributes.
`BibRefQuery` `BibRefQuery.query(java.lang.String query, java.util.Hashtable properties)` It queries the current collection using a query language.
`int` `BibRefQuery.getBibRefCount()` It returns the number of citations in the current collection.
`BibRefQuery` `BibRefQuery.sort(java.lang.String[] orderedBy, java.util.Hashtable properties)` It sorts the current collection and returns another collection which is a sorted copy of the current collection.
`BibRef[]` `BibRefQuery.getAllBibRefs()` It returns all citations from the current collection as a (possibly big) array.
`BibRef[]` `BibRefQuery.getAllBibRefs(java.lang.String[] onlyAttrs)` It returns all citations from the current collection as a (possibly big) array, perhaps with a limited number of attributes.
`java.lang.String[]` `BibRefQuery.getAllIDs()` A convenient method returning just identifiers of all current citations.
`java.util.Enumeration` `BibRefQuery.getBibRefs()` It returns an enumeration of all citations from the current collection.
`java.util.Enumeration` `BibRefQuery.getBibRefs(java.lang.String[] onlyAttrs)` It returns an enumeration of all citations from the current collection, perhaps with a limited number of attributes.
`java.io.InputStream` `BibRefQuery.getAllBibRefsAsXML()` It returns all citations from the current collection as an XML stream.
`java.util.Enumeration` `BibRefQuery.getBibRefsAsXML()` It returns an enumeration of all citations from the current collection.
`java.lang.String` `BibRefQuery.getBibRefAsXML(BibRef bibRef)` A convenient utility method converting a given citation to its XML representation.
`void` `BibRefSupport.connect()` It creates a connection to an object providing the supporting utilities, or/and it makes all necessary initialization steps needed for further communication.
`CandyFinder` `BibRefSupport.getVocabularyFinder()` It returns an object representing a central place where all controlled vocabularies can be received from and shared by all users.
`CandyVocabulary` `BibRefSupport.getSupportedValues(java.lang.String resourceType, java.lang.String attrName)` It returns a controlled vocabulary containing all possible values of the attribute given in `attrName` in the context given in `resourceType`.
`BiblioCriterion[]` `BibRefSupport.getSupportedCriteria()` It returns all supported searching and sorting criteria for the whole bibliographic repository.
`BiblioCriterion[]` `BibRefSupport.getSupportedCriteria(java.lang.String repositorySubset)` It returns all supported searching and sorting criteria in the given repository subset.
`BibRefQuery` `BibRefSupport.union(BibRefQuery[] collections, java.util.Hashtable properties)` It merges all given collections together.

Uses of NestedException in org.biojava.bio

Subclasses of NestedException in org.biojava.bio
`class` `BioException` A nestable biological exception.

Uses of NestedException in org.biojava.bio.chromatogram

Subclasses of NestedException in org.biojava.bio.chromatogram
`class` `UnsupportedChromatogramFormatException` Exception indicating that some provided data does not represent a supported chromatogram format.

Uses of NestedException in org.biojava.bio.dp

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

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

Methods in org.biojava.bio.program.indexdb that throw NestedException
`void` `BioStore.commit()` `commit` writes an index to disk.

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

Methods in org.biojava.bio.program.ssaha that throw NestedException
`void` `DataStore.search(java.lang.String id, SymbolList symList, SearchListener listener)` Search the DataStore with a symbol list.
`java.lang.String` `DataStore.seqNameForID(int id)` Resolve an ID to a sequence name.

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

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

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

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

Uses of NestedException in org.biojava.bio.symbol

Subclasses of NestedException 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.

Uses of NestedException in org.biojava.bio.taxa

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

Uses of NestedException in org.biojava.directory

Subclasses of NestedException in org.biojava.directory
`class` `ProviderNotFoundException` `ProviderNotFoundException` is thrown when a sequence database provider can not be located.
`class` `RegistryException` A `RegistryException` thrown when the registry cannot find an implementation of a requested `SequenceDB`.

Uses of NestedException in org.biojava.utils

Subclasses of NestedException in org.biojava.utils
`class` `ChangeVetoException` Exception which is thrown when a ChangeListener does not wish a change to take place.
`class` `ParserException` Exception thrown when an error occurs in document parsing.

Methods in org.biojava.utils that throw NestedException
`protected abstract void` `FileAsList.generateRecord(byte[] buffer, java.lang.Object item)`
`void` `Commitable.commit()` `commit` commits pending changes.

Uses of NestedException in org.biojava.utils.candy

Methods in org.biojava.utils.candy that throw NestedException
`boolean` `CandyVocabulary.contains(java.lang.String name)` It checks if a given entry exists in this vocabulary.
`CandyEntry` `CandyVocabulary.getEntryByName(java.lang.String name)` It returns a selected vocabulary entry.
`java.util.Enumeration` `CandyVocabulary.getAllEntries()` It returns all available vocabulary entries.
`java.util.Enumeration` `CandyVocabulary.getAllNames()` It return all names (entry identifiers) available in this vocabulary.
`void` `CandyVocabulary.destroy()` It frees all resources related to this vocabulary.
`java.lang.String` `CandyVocabulary.getName()` It returns a name of this vocabulary.
`java.lang.String` `CandyVocabulary.getDescription()` It returns a description of this vocabulary.
`java.lang.String` `CandyVocabulary.getVersion()` It returns a vesrion of this vocabulary.
`int` `CandyVocabulary.getCount()` It returns a number of entries contained in this vocabulary.
`boolean` `CandyVocabulary.isCaseSensitive()` It returns `true` if the vocabulary entries should be considered as case-sensitive.
`void` `CandyFinder.connect()` It creates a connection to an object representing a vocabulary finder, or/and it makes all necessary initialization steps needed for further communication.
`java.lang.String[]` `CandyFinder.getAllVocabularyNames()` It returns names of all vocabularies known to this vocabulary finder.
`CandyVocabulary` `CandyFinder.getVocabularyByName(java.lang.String name)` It returns a selected vocabulary.
`CandyVocabulary[]` `CandyFinder.getAllVocabularies()` It returns all available vocabularies.
`int` `CandyFinder.getNumCount()` It returns the number of available vocabularies.
`java.lang.String` `CandyFinder.getFinderName()` It returns a name of this vocabulary finder.