| 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 |
| 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.
|
| 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.
|
| 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) |
| 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.
|
| Constructor and Description |
|---|
TransitiveGraph(List<IDMapper> gdbs)
Constructor: immediately starts calculating paths.
|
Copyright © 2006–2021 BridgeDb project. All rights reserved.