org.biopax.paxtools.controller

Class IdFetcher

java.lang.Object

org.biopax.paxtools.controller.IdFetcher

public class IdFetcher
extends Object

Tries to get preferred type IDs of an entity reference. Could be used, e.g., as part of a BioPAX to plain text (or SIF, GMT) converter.

Constructor Summary

Constructors

Constructor and Description
IdFetcher() Constructor.

Method Summary

Modifier and Type	Method and Description
IdFetcher	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)
List<String>	getChemDbStartsWithOrEquals()
List<String>	getSeqDbStartsWithOrEquals()
IdFetcher	seqDbStartsWithOrEquals(String dbStartsWithOrEquals) Set to prefer collecting gene/sequence IDs of such Xrefs where the db starts with or equals given string, ignoring case.
IdFetcher	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

IdFetcher

public IdFetcher()

Constructor.

Method Detail

seqDbStartsWithOrEquals

public IdFetcher 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 IdFetcher 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 IdFetcher 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)