org.opencb.cellbase.core.variant.annotation.hgvs

Class HgvsDeletionCalculator

java.lang.Object

org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator

org.opencb.cellbase.core.variant.annotation.hgvs.HgvsDeletionCalculator

public class HgvsDeletionCalculator
extends HgvsCalculator

Created by fjlopez on 15/06/17.

Field Summary

Fields inherited from class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator

genomeDBAdaptor, NEIGHBOURING_SEQUENCE_SIZE

Constructor Summary

Constructors

Constructor and Description
HgvsDeletionCalculator(GenomeDBAdaptor genomeDBAdaptor)

Method Summary

Modifier and Type	Method and Description
protected List<String>	run(org.opencb.biodata.models.variant.Variant variant, org.opencb.biodata.models.core.Transcript transcript, String geneId, boolean normalize)

Methods inherited from class org.opencb.cellbase.core.variant.annotation.hgvs.HgvsCalculator

genomicToCdnaCoord, isCoding, justify, normalize, run, run, run, run, setRangeCoordsAndAlleles

Methods inherited from class java.lang.Object

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

Constructor Detail

HgvsDeletionCalculator

public HgvsDeletionCalculator(GenomeDBAdaptor genomeDBAdaptor)

Method Detail

run

protected List<String> run(org.opencb.biodata.models.variant.Variant variant,
                           org.opencb.biodata.models.core.Transcript transcript,
                           String geneId,
                           boolean normalize)

Overrides:

run in class HgvsCalculator