org.biopax.paxtools.pattern.miner

Class ConfigurableIDFetcher

java.lang.Object

org.biopax.paxtools.pattern.miner.ConfigurableIDFetcher

All Implemented Interfaces:

IDFetcher

public class ConfigurableIDFetcher
extends Object
implements IDFetcher

Tries to get preferred type IDs of an entity reference. This id-fetcher can be optionally used when converting (reducing) BioPAX to the binary SIF format.

Constructor Summary

Constructors

Constructor and Description
ConfigurableIDFetcher() Constructor.

Method Summary

Modifier and Type	Method and Description
ConfigurableIDFetcher	chemDbStartsWithOrEquals(String dbStartsWithOrEquals) Set to prefer collecting chemical IDs of such Xrefs where the small molecules db starts with or equals given string, ignoring case.
Set<String>	fetchID(BioPAXElement ele) Finds a String ID for the given element.
List<String>	getChemDbStartsWithOrEquals()
List<String>	getSeqDbStartsWithOrEquals()
ConfigurableIDFetcher	seqDbStartsWithOrEquals(String dbStartsWithOrEquals) Set to prefer collecting gene/sequence IDs of such Xrefs where the db starts with or equals given string, ignoring case.
ConfigurableIDFetcher	useNameWhenNoDbMatch(boolean useNameWhenNoDbMatch) Set the flag to use the entity reference's names when no desired ID type can be found (none of xref.db matched before, or there're no xrefs at all).

Methods inherited from class java.lang.Object

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

Constructor Detail

ConfigurableIDFetcher

public ConfigurableIDFetcher()

Constructor.

Method Detail

seqDbStartsWithOrEquals

public ConfigurableIDFetcher seqDbStartsWithOrEquals(String dbStartsWithOrEquals)

Set to prefer collecting gene/sequence IDs of such Xrefs where the db starts with or equals given string, ignoring case. You can chain this method calls like seqDbStartsWithOrEquals(A).seqDbStartsWithOrEquals(B)... - it will try to match a xref.db and collect xref.id in the given order/priority.

Parameters:

dbStartsWithOrEquals - the Xref.db value or prefix (case-insensitive)

Returns:

this id-fetcher instance

getSeqDbStartsWithOrEquals

public List<String> getSeqDbStartsWithOrEquals()

chemDbStartsWithOrEquals

public ConfigurableIDFetcher chemDbStartsWithOrEquals(String dbStartsWithOrEquals)

Set to prefer collecting chemical IDs of such Xrefs where the small molecules db starts with or equals given string, ignoring case. You can chain this method calls like chemDbStartsWithOrEquals(A).chemDbStartsWithOrEquals(B)... - it will try to match a xref.db and collect xref.id in the given order/priority.

Parameters:

dbStartsWithOrEquals - the Xref.db value or prefix (case-insensitive)

Returns:

this id-fetcher instance

getChemDbStartsWithOrEquals

public List<String> getChemDbStartsWithOrEquals()

useNameWhenNoDbMatch

public ConfigurableIDFetcher useNameWhenNoDbMatch(boolean useNameWhenNoDbMatch)

Set the flag to use the entity reference's names when no desired ID type can be found (none of xref.db matched before, or there're no xrefs at all).

Parameters:

useNameWhenNoDbMatch - true/false (default is 'true' - when this method's never been called)

Returns:

this id-fetcher instance

fetchID

public Set<String> fetchID(BioPAXElement ele)

Description copied from interface: IDFetcher

Finds a String ID for the given element.

Specified by:

fetchID in interface IDFetcher

Parameters:

ele - element to fecth the ID from

Returns:

ID