org.bridgedb.rdb

Class SimpleGdbImplCommon

java.lang.Object

org.bridgedb.rdb.IDMapperRdb

org.bridgedb.rdb.SimpleGdb

org.bridgedb.rdb.SimpleGdbImplCommon

All Implemented Interfaces:

AttributeMapper, IDMapper, XrefIterator

public abstract class SimpleGdbImplCommon
extends SimpleGdb

Some methods and constants that are shared between SimpleGdbImpl2 and SimpleGdbImpl3

Field Summary

Fields inherited from class org.bridgedb.rdb.SimpleGdb

dbName, NO_LIMIT, NO_TIMEOUT, QUERY_TIMEOUT

Fields inherited from interface org.bridgedb.AttributeMapper

MATCH_ID

Method Summary

Modifier and Type	Method and Description
Map<Xref,String>	freeAttributeSearch(String query, String attrType, int limit) free text search for matching symbols.
Map<Xref,Set<String>>	freeAttributeSearchEx(String query, String attrType, int limit)
Set<Xref>	freeSearch(String text, int limit)
Set<String>	getAttributeSet()
IDMapperCapabilities	getCapabilities()
List<Xref>	getCrossRefsByAttribute(String attrName, String attrValue)
Iterable<Xref>	getIterator()
Iterable<Xref>	getIterator(DataSource ds)
boolean	isFreeAttributeSearchSupported()
Set<Xref>	mapID(Xref idc, DataSource... resultDs)
boolean	xrefExists(Xref xref)

Methods inherited from class org.bridgedb.rdb.SimpleGdb

close, getConnection, getDbName, getGeneCount, getGeneCount, getLinkCount, isConnected

Methods inherited from class org.bridgedb.rdb.IDMapperRdb

mapID, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.bridgedb.AttributeMapper

getAttributes, getAttributes

Method Detail

xrefExists

public boolean xrefExists(Xref xref)
                   throws IDMapperException

Throws:

IDMapperException

mapID

public Set<Xref> mapID(Xref idc,
                       DataSource... resultDs)
                throws IDMapperException

Throws:

IDMapperException

getCrossRefsByAttribute

public List<Xref> getCrossRefsByAttribute(String attrName,
                                          String attrValue)
                                   throws IDMapperException

Throws:

IDMapperException

freeSearch

public Set<Xref> freeSearch(String text,
                            int limit)
                     throws IDMapperException

Throws:

IDMapperException

getCapabilities

public IDMapperCapabilities getCapabilities()

Returns:

the capabilities of this gene database

isFreeAttributeSearchSupported

public boolean isFreeAttributeSearchSupported()

Returns:

true

freeAttributeSearch

public Map<Xref,String> freeAttributeSearch(String query,
                                            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'.

limit - The number of results to limit the search to

Returns:

references that match the query

Throws:

IDMapperException - if the mapping service is (temporarily) unavailable

freeAttributeSearchEx

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

Throws:

IDMapperException

getAttributeSet

public Set<String> getAttributeSet()
                            throws IDMapperException

Throws:

IDMapperException

getIterator

public Iterable<Xref> getIterator()
                           throws IDMapperException

Throws:

IDMapperException

getIterator

public Iterable<Xref> getIterator(DataSource ds)
                           throws IDMapperException

Throws:

IDMapperException