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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 |
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. |
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. |
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 | |
void |
Commitable.commit()
commit commits pending changes. |
protected abstract void |
FileAsList.generateRecord(byte[] buffer,
java.lang.Object item)
|
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. |
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