Uses of Class
org.bridgedb.IDMapperException

Packages that use IDMapperException

Package	Description
org.bridgedb	BridgeDb is a java library intended for dealing with identifiers for biological entities such as genes, proteins, metabolites.
org.bridgedb.file	Driver and helper classes for using simple files as an identifier mapping service.
org.bridgedb.impl

Uses of IDMapperException in org.bridgedb

Methods in org.bridgedb that throw IDMapperException

Modifier and Type	Method and Description
IDMapper	IDMapperStack.addIDMapper(String connectionString) Create a fresh IDMapper from a connectionString and add it to the stack.
void	IDMapperStack.close() closes all child databases.
void	IDMapper.close() dispose any resources (such as open database connections) associated with this IDMapper.
IDMapper	Driver.connect(String locationString) Never call this method directly, use BridgeDb.connect(java.lang.String) instead.
static IDMapper	BridgeDb.connect(String connectionString) Finds the correct implementation of the IDMapper interface and instantiates it.
Map<Xref,String>	IDMapperStack.freeAttributeSearch(String query, String attrType, int limit) free text search for matching attributes.
Map<Xref,String>	AttributeMapper.freeAttributeSearch(String query, String attrType, int limit) free text search for matching attributes.
Map<Xref,Set<String>>	IDMapperStack.freeAttributeSearchEx(String query, String attrType, int limit)
Map<Xref,Set<String>>	AttributeMapper.freeAttributeSearchEx(String query, String attrType, int limit) Improved version of free text search for matching attributes.
Set<Xref>	IDMapperStack.freeSearch(String text, int limit) free text search for matching symbols or identifiers.
Set<Xref>	IDMapper.freeSearch(String text, int limit) free text search for matching symbols or identifiers.
Map<String,Set<String>>	IDMapperStack.getAttributes(Xref ref) Get all attributes for an entity.
Map<String,Set<String>>	AttributeMapper.getAttributes(Xref ref) Get all attributes for an entity.
Set<String>	IDMapperStack.getAttributes(Xref ref, String attrname) Get attributes for an entity, such as gene Symbol.
Set<String>	AttributeMapper.getAttributes(Xref ref, String attrType) Get attributes for an entity, such as gene Symbol.
Set<String>	IDMapperStack.getAttributeSet() Set of attributes provided by this AttributeMapper.
Set<String>	AttributeMapper.getAttributeSet() Set of attributes provided by this AttributeMapper.
Map<String,Set<String>>	IDMapperStack.getAttributesForAllMappings(Xref ref, DataSource... dataSources)
Set<String>	IDMapperStack.getAttributesForAllMappings(Xref ref, String attrname, DataSource... dataSources)
Iterable<Xref>	XrefIterator.getIterator() Create an iterator that iterates over all Xrefs defined by this IDMapper.
Iterable<Xref>	XrefIterator.getIterator(DataSource ds) Create an iterator that iterates over all Xrefs of a certain DataSource defined by this IDMapper.
Set<DataSource>	AbstractIDMapperCapabilities.getSupportedSrcDataSources()
Set<DataSource>	IDMapperCapabilities.getSupportedSrcDataSources()
Set<DataSource>	AbstractIDMapperCapabilities.getSupportedTgtDataSources()
Set<DataSource>	IDMapperCapabilities.getSupportedTgtDataSources()
boolean	AbstractIDMapperCapabilities.isMappingSupported(DataSource src, DataSource tgt)
boolean	IDMapperCapabilities.isMappingSupported(DataSource src, DataSource tgt)
Map<Xref,Set<Xref>>	IDMapperStack.mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources) Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
Map<Xref,Set<Xref>>	IDMapper.mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources) Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
Set<Xref>	IDMapperStack.mapID(Xref ref, DataSource... resultDs) Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
Set<Xref>	IDMapper.mapID(Xref ref, DataSource... tgtDataSources) Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
Set<Xref>	AbstractIDMapper.mapID(Xref srcRef, DataSource... tgtDataSources) Default implementation of mapID.
boolean	IDMapperStack.xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.
boolean	IDMapper.xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.

Uses of IDMapperException in org.bridgedb.file

Methods in org.bridgedb.file that throw IDMapperException

Modifier and Type	Method and Description
void	IDMapperFile.close() dispose any resources (such as open database connections) associated with this IDMapper.
Set<Xref>	IDMapperText.freeSearch(String text, int limit) Free search is not supported for delimiter-text file.
Set<DataSource>	IDMappingReader.getDataSources() Get DataSources from the file.
Set<DataSource>	IDMappingReaderFromDelimitedReader.getDataSources() Get DataSources from the file.
Map<Xref,Set<Xref>>	IDMappingReader.getIDMappings() Get Xrefs from the file.
Map<Xref,Set<Xref>>	IDMappingReaderFromDelimitedReader.getIDMappings() Get Xrefs from the file.
Map<Xref,Set<Xref>>	IDMapperFile.mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources) Get all cross-references for a set of entities, restricting the result to contain only references from the given set of data sources.
Set<Xref>	IDMapperFile.mapID(Xref srcXref, DataSource... tgtDataSources) Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
protected void	IDMappingReaderFromDelimitedReader.readData(Reader reader) Read data.
boolean	IDMapperFile.xrefExists(Xref xref) Check whether an Xref is known by the given mapping source.

Constructors in org.bridgedb.file that throw IDMapperException

Constructor and Description
IDMapperFile(IDMappingReader reader) Constructor from a IDMappingReader.
IDMapperFile(IDMappingReader reader, boolean freeSearch) Constructor from a IDMappingReader and user-defined free search capacity.
IDMapperText(URL url) Constructor from the URL of a tab-delimited text file.
IDMapperText(URL url, char[] dataSourceDelimiters) Transitivity is unsupported.
IDMapperText(URL url, char[] dataSourceDelimiters, char[] idDelimiters) Transitivity is unsupported.
IDMapperText(URL url, char[] dataSourceDelimiters, char[] idDelimiters, boolean transitivity) Constructor from the URL of a tab-delimited text file, delimiters to separate between different data sources and IDs and transitivity support.
IDMappingReaderFromDelimitedReader(Reader reader, String regExDataSourceDelimiter, String regExIDDelimiter, boolean transitivity)
IDMappingReaderFromText(URL url, char[] dataSourceDelimiters) Transitivity is unsupported.
IDMappingReaderFromText(URL url, char[] dataSourceDelimiters, char[] regExIDDelimiter) Transitivity is unsupported.
IDMappingReaderFromText(URL url, char[] dataSourceDelimiters, char[] regExIDDelimiter, boolean transitivity) Constructor from the URL of a tab-delimited text file, delimiters to separate between different data sources and IDs and transitivity support.
IDMappingReaderFromText(URL url, String regExDataSourceDelimiter) Transitivity is unsupported.
IDMappingReaderFromText(URL url, String regExDataSourceDelimiter, String regExIDDelimiter) Transitivity is unsupported.
IDMappingReaderFromText(URL url, String regExDataSourceDelimiter, String regExIDDelimiter, boolean transitivity)

Uses of IDMapperException in org.bridgedb.impl

Methods in org.bridgedb.impl that throw IDMapperException

Modifier and Type	Method and Description
boolean	TransitiveGraph.isTransitiveMappingSupported(DataSource src, DataSource tgt)
Set<Xref>	TransitiveGraph.mapIDtransitiveTargetted(Xref ref, Set<DataSource> dsFilter)
Set<Xref>	TransitiveGraph.mapIDtransitiveUntargetted(Xref ref)
static Map<Xref,Set<Xref>>	InternalUtils.mapMultiFromSingle(IDMapper mapper, Collection<Xref> srcXrefs, DataSource... tgt) call the "single" mapID (Xref, ...) multiple times to perform mapping of a Set.
static Set<Xref>	InternalUtils.mapSingleFromMulti(IDMapper mapper, Xref src, DataSource... tgt) call the "multi" mapID (Set, ...) using a Set with one item to perform mapping of a single ID.

Constructors in org.bridgedb.impl that throw IDMapperException

Constructor and Description
TransitiveGraph(List<IDMapper> gdbs) Constructor: immediately starts calculating paths.