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.