org.bridgedb
Interface AttributeMapper

All Known Implementing Classes:

IDMapperStack

public interface AttributeMapper

AttributeMapper knows about attributes for Xrefs.

Field Summary

static java.lang.String

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

Method Summary

java.util.Map<Xref,java.lang.String>	freeAttributeSearch(java.lang.String query, java.lang.String attrType, int limit) free text search for matching symbols.
java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	getAttributes(Xref ref) Get all attributes for an entity.
java.util.Set<java.lang.String>	getAttributes(Xref ref, java.lang.String attrType) Get attributes for an entity, such as gene Symbol.
java.util.Set<java.lang.String>	getAttributeSet() Set of attributes provided by this AttributeMapper.
boolean	isFreeAttributeSearchSupported()

Field Detail

MATCH_ID

static final java.lang.String MATCH_ID

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

See Also:

Constant Field Values

Method Detail

getAttributes

java.util.Set<java.lang.String> getAttributes(Xref ref,
                                              java.lang.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

java.util.Map<java.lang.String,java.util.Set<java.lang.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

java.util.Map<Xref,java.lang.String> freeAttributeSearch(java.lang.String query,
                                                         java.lang.String attrType,
                                                         int limit)
                                                         throws IDMapperException

free text search for matching symbols.

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

getAttributeSet

java.util.Set<java.lang.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