Package de.julielab.genemapper.mappingcores

Class DypsisGeneSelector

java.lang.Object

de.julielab.genemapper.mappingcores.DypsisGeneSelector

public class DypsisGeneSelector
extends Object

Constructor Summary

Constructors

Constructor	Description
DypsisGeneSelector()

Method Summary

Modifier and Type	Method	Description
static void	addSynonyms(de.julielab.geneexpbase.genemodel.GeneDocument document)
static void	clipAsterisksFromGeneNames(de.julielab.geneexpbase.genemodel.GeneDocument document)	Call BEFORE selecting genes.
static void	mergeContinuousGeneAnnotations(de.julielab.geneexpbase.genemodel.GeneDocument document)	Call BEFORE selecting genes.
static void	removeGenesWithVerbs(de.julielab.geneexpbase.genemodel.GeneDocument document)	Call AFTER selecting genes.
static void	removeSpeciesMention(com.fulmicoton.multiregexp.MultiPatternSearcher searcher, de.julielab.geneexpbase.genemodel.GeneDocument document)	Removes all prefixes belonging to a species, e.g.
static void	removeSpeciesMention(de.julielab.geneexpbase.genemodel.GeneDocument document)
static void	removeSpeciesPrefixesFromGenes(de.julielab.geneexpbase.genemodel.GeneDocument document)
static void	selectLongerGazetteerMatchesOverFlair(de.julielab.geneexpbase.genemodel.GeneDocument document)	Call BEFORE selecting genes.
static void	splitDashGenes(de.julielab.geneexpbase.genemodel.GeneDocument document, CandidateRetrieval candidateRetrieval)	Call AFTER selecting genes.

Methods inherited from class java.lang.Object

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

Constructor Detail

DypsisGeneSelector

public DypsisGeneSelector()

Method Detail

selectLongerGazetteerMatchesOverFlair

public static void selectLongerGazetteerMatchesOverFlair(de.julielab.geneexpbase.genemodel.GeneDocument document)

Call BEFORE selecting genes. From the "all genes" field in the document, remove flair genes with gazetteer genes that include the flair gene but are larger.

Parameters:

document -

splitDashGenes

public static void splitDashGenes(de.julielab.geneexpbase.genemodel.GeneDocument document,
                                  CandidateRetrieval candidateRetrieval)

Call AFTER selecting genes.

Parameters:

document -

candidateRetrieval -

mergeContinuousGeneAnnotations

public static void mergeContinuousGeneAnnotations(de.julielab.geneexpbase.genemodel.GeneDocument document)

Call BEFORE selecting genes.

Parameters:

document -

clipAsterisksFromGeneNames

public static void clipAsterisksFromGeneNames(de.julielab.geneexpbase.genemodel.GeneDocument document)

Call BEFORE selecting genes.

addSynonyms

public static void addSynonyms(de.julielab.geneexpbase.genemodel.GeneDocument document)

removeGenesWithVerbs

public static void removeGenesWithVerbs(de.julielab.geneexpbase.genemodel.GeneDocument document)

Call AFTER selecting genes.

Parameters:

document -

removeSpeciesPrefixesFromGenes

public static void removeSpeciesPrefixesFromGenes(de.julielab.geneexpbase.genemodel.GeneDocument document)

removeSpeciesMention

public static void removeSpeciesMention(de.julielab.geneexpbase.genemodel.GeneDocument document)

removeSpeciesMention

public static void removeSpeciesMention(com.fulmicoton.multiregexp.MultiPatternSearcher searcher,
                                        de.julielab.geneexpbase.genemodel.GeneDocument document)

Removes all prefixes belonging to a species, e.g. "human FGF-22" will be turned into "FGF-22"

Parameters:

searcher - A MultiPatternSearcher containing a compiled multi-regex of all species to be considered.

document -