Package org.bridgedb

Interface AttributeMapper

All Known Implementing Classes:

IDMapperStack

public interface AttributeMapper

AttributeMapper knows about attributes for Xrefs.

Field Summary

Fields

Modifier and Type	Field	Description
static String	MATCH_ID	use this magic constant as the attrType parameter to also search for identifiers.

Method Summary

Modifier and Type	Method	Description
Map<Xref,String>	freeAttributeSearch(String query, String attrType, int limit)	free text search for matching attributes.
Map<Xref,Set<String>>	freeAttributeSearchEx(String query, String attrType, int limit)	Improved version of free text search for matching attributes.
Map<String,Set<String>>	getAttributes(Xref ref)	Get all attributes for an entity.
Set<String>	getAttributes(Xref ref, String attrType)	Get attributes for an entity, such as gene Symbol.
Set<String>	getAttributeSet()	Set of attributes provided by this AttributeMapper.
boolean	isFreeAttributeSearchSupported()

Field Detail

MATCH_ID

static final String MATCH_ID

use this magic constant as the attrType parameter to also search for identifiers.

See Also:

Constant Field Values

Method Detail

getAttributes

Set<String> getAttributes(Xref ref,
                          String attrType)
                   throws IDMapperException

Get attributes for an entity, such as gene Symbol.

Parameters:

ref - the entity to get the attribute for

attrType - the attribute to look for, e.g. 'Symbol' or 'Description'.

Returns:

the attribute, or null if nothing was found

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable

getAttributes

Map<String,Set<String>> getAttributes(Xref ref)
                                     throws IDMapperException

Get all attributes for an entity. Usually this method is more efficient if you want to query several attributes in a sequence.

Parameters:

ref - the entity to get the attributes for

Returns:

a Map where attribute names are the keys and attribute values are the values.

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable

isFreeAttributeSearchSupported

boolean isFreeAttributeSearchSupported()

Returns:

true if free attribute search is supported, false otherwise.

freeAttributeSearch

Map<Xref,String> freeAttributeSearch(String query,
                                           String attrType,
                                           int limit)
                                    throws IDMapperException

free text search for matching attributes.

Parameters:

query - The text to search for

attrType - the attribute to look for, e.g. 'Symbol' or 'Description'. If you use the special MATCH_ID constant, it will query the identifier instead.

limit - The number of results to limit the search to

Returns:

map references and attribute values that match the query

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable

freeAttributeSearchEx

Map<Xref,Set<String>> freeAttributeSearchEx(String query,
                                                  String attrType,
                                                  int limit)
                                           throws IDMapperException

Improved version of free text search for matching attributes. Unlike freeAttributeSearch, this method may return multiple results per xref.

Parameters:

query - The text to search for

attrType - the attribute to look for, e.g. 'Symbol' or 'Description'. If you use the special MATCH_ID constant, it will query the identifier instead.

limit - The number of results to limit the search to

Returns:

map of references and attribute values that match the query

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable

getAttributeSet

Set<String> getAttributeSet()
                     throws IDMapperException

Set of attributes provided by this AttributeMapper. There is no guarantee that a specific Xref has these attributes.

Returns:

set of available attributes in this AttributeMapper. If there are none available, returns an empty set.

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable