Package de.julielab.genemapper.filtering.families

Class FamilyMatchPipe

java.lang.Object

cc.mallet.pipe.Pipe

de.julielab.genemapper.filtering.families.FamilyMatchPipe

All Implemented Interfaces:

cc.mallet.types.AlphabetCarrying, Serializable

public class FamilyMatchPipe
extends cc.mallet.pipe.Pipe

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
FamilyMatchPipe(de.julielab.geneexpbase.configuration.Parameters parameters)

Method Summary

Modifier and Type	Method	Description
cc.mallet.types.Instance	pipe(cc.mallet.types.Instance inst)
org.apache.commons.lang3.tuple.Pair<Integer,Double>	searchCandidatesForFamilyNames(de.julielab.geneexpbase.genemodel.GeneMention geneMention)	Iterates through all the candidates that belong to the assigned species of the given gene mention.

Methods inherited from class cc.mallet.pipe.Pipe

alphabetsMatch, getAlphabet, getAlphabets, getDataAlphabet, getInstanceId, getTargetAlphabet, instanceFrom, instancesFrom, instancesFrom, isDataAlphabetSet, isTargetProcessing, newIteratorFrom, preceedingPipeDataAlphabetNotification, preceedingPipeTargetAlphabetNotification, precondition, readResolve, setDataAlphabet, setOrCheckDataAlphabet, setOrCheckTargetAlphabet, setTargetAlphabet, setTargetProcessing

Methods inherited from class java.lang.Object

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

Constructor Detail

FamilyMatchPipe

public FamilyMatchPipe(de.julielab.geneexpbase.configuration.Parameters parameters)

Method Detail

pipe

public cc.mallet.types.Instance pipe(cc.mallet.types.Instance inst)

Overrides:

pipe in class cc.mallet.pipe.Pipe

searchCandidatesForFamilyNames

public org.apache.commons.lang3.tuple.Pair<Integer,Double> searchCandidatesForFamilyNames(de.julielab.geneexpbase.genemodel.GeneMention geneMention)

Iterates through all the candidates that belong to the assigned species of the given gene mention. Returns a tuple (a,b) where a is the minimal rank of a family name found in a candidate list and b is the fraction of family names found within the candidates.

Parameters:

geneMention - The gene mention.

Returns:

The minimal rank of a family name in the candidates and the fraction of family names in the candidates.