Package de.julielab.genemapper.filtering.families

Class SymbolPrefixPipe

java.lang.Object

cc.mallet.pipe.Pipe

de.julielab.genemapper.filtering.families.SymbolPrefixPipe

All Implemented Interfaces:

cc.mallet.types.AlphabetCarrying, GeneConfigurationDependentPipe, Serializable

public class SymbolPrefixPipe
extends cc.mallet.pipe.Pipe
implements GeneConfigurationDependentPipe

This pipe adds a feature indicated whether the given gene name is a prefix of the official symbol of the gene candidate that was retrieved for the gene name. This would point to the gene name being a family name of the database candidate.

Author:

faessler

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SymbolPrefixPipe(String prefix, Configuration configuration)

Method Summary

Modifier and Type	Method	Description
void	initialize(Configuration configuration)
cc.mallet.types.Instance	pipe(cc.mallet.types.Instance inst)

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

SymbolPrefixPipe

public SymbolPrefixPipe(String prefix,
                        Configuration configuration)
                 throws GeneMapperException

Throws:

GeneMapperException

Method Detail

initialize

public void initialize(Configuration configuration)
                throws GeneMapperException

Specified by:

initialize in interface GeneConfigurationDependentPipe

Throws:

GeneMapperException

pipe

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

Overrides:

pipe in class cc.mallet.pipe.Pipe