Package de.charite.compbio.jannovar.hgvs.bridge

Class NucleotideLocationConverter

java.lang.Object

de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter

public class NucleotideLocationConverter
extends Object

Helper class for converting NucleotidePointLocations and NucleotideRanges to GenomePositions and GenomeIntervals.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotideLocationConverter()

Method Summary

Modifier and Type	Method	Description
de.charite.compbio.jannovar.reference.GenomePosition	translateNucleotidePointLocation(de.charite.compbio.jannovar.reference.TranscriptModel tm, de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation pos, de.charite.compbio.jannovar.hgvs.SequenceType sequenceType)	Convert NucleotidePointLocation on a TranscriptModel to a GenomePosition
de.charite.compbio.jannovar.reference.GenomeInterval	translateNucleotideRange(de.charite.compbio.jannovar.reference.TranscriptModel tm, de.charite.compbio.jannovar.hgvs.nts.NucleotideRange range, de.charite.compbio.jannovar.hgvs.SequenceType sequenceType)	Convert NucleotideRange on a TranscriptModel to a GenomePosition

Methods inherited from class java.lang.Object

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

Constructor Detail

NucleotideLocationConverter

public NucleotideLocationConverter()

Method Detail

translateNucleotidePointLocation

public de.charite.compbio.jannovar.reference.GenomePosition translateNucleotidePointLocation(de.charite.compbio.jannovar.reference.TranscriptModel tm,
                                                                                             de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation pos,
                                                                                             de.charite.compbio.jannovar.hgvs.SequenceType sequenceType)
                                                                                      throws CannotTranslateHGVSVariant

Convert NucleotidePointLocation on a TranscriptModel to a GenomePosition

Throws:

CannotTranslateHGVSVariant

translateNucleotideRange

public de.charite.compbio.jannovar.reference.GenomeInterval translateNucleotideRange(de.charite.compbio.jannovar.reference.TranscriptModel tm,
                                                                                     de.charite.compbio.jannovar.hgvs.nts.NucleotideRange range,
                                                                                     de.charite.compbio.jannovar.hgvs.SequenceType sequenceType)
                                                                              throws CannotTranslateHGVSVariant

Convert NucleotideRange on a TranscriptModel to a GenomePosition

Throws:

CannotTranslateHGVSVariant