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java.lang.Objectprocope.tools.namemapping.Synonyms
public class Synonyms
Manages synonyms for protein identifiers. Contains identifier/synonym
pairs. The resolveSynonym(String)
method then maps any incoming
synonyms to their identifiers. Transitive relations will be
followed. That is, if you add the synonym-mappings a => b
and
b => c
then a
will be mapped to c
.
ProteinManager
Constructor Summary | |
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Synonyms()
Creates a new empty set of synonyms |
Method Summary | |
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void |
addMappingNetwork(ProteinNetwork mappings,
boolean targetFirst)
Adds all mappings induced by the edges of a given directed network to the synonyms list. |
void |
addSynonym(String identifier,
String synonym)
Adds a new synonym. |
Set<String> |
getSynonyms(String identifier)
Returns all synonyms associated with a given identifier. |
String |
resolveSynonym(String id)
Returns the identifier a synonym is mapped to or id directly
of no synonym is associated with that string. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Synonyms()
Method Detail |
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public void addSynonym(String identifier, String synonym)
synonym
will be mapped to
identifier
by resolveSynonym(String)
.
identifier
- identifier the synonym is mapped tosynonym
- synonym of the identifierpublic String resolveSynonym(String id)
id
directly
of no synonym is associated with that string.
id
- identifier which is resolved
id
is registered as a synonym or
id
directly otherwisepublic Set<String> getSynonyms(String identifier)
identifier
- identifier for which synonyms are looked up
null
if no
synonyms are associated with the identiferpublic void addMappingNetwork(ProteinNetwork mappings, boolean targetFirst) throws IllegalArgumentException
a => b
the
corresponding synonym mapping will be added with a
being the
synonym and b
its associated identifier or vice versa.
If the networks contains circles or nodes with multiple successors the method's behavious is undefined (but it will not crash).
mappings
- directed mapping network with synonyms to be addedtargetFirst
- true
: the first node of each edge (the source
of the directed edge) is the target protein identifier
where as the second node (the target of the directed
edge) is its synonym; false
: vice versa,
synonym comes first, then the target
IllegalArgumentException
- if the network is undirected
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