public class HgvsCalculator extends Object
Modifier and Type | Field and Description |
---|---|
protected GenomeDBAdaptor |
genomeDBAdaptor |
protected static int |
NEIGHBOURING_SEQUENCE_SIZE |
Constructor and Description |
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HgvsCalculator(GenomeDBAdaptor genomeDBAdaptor) |
Modifier and Type | Method and Description |
---|---|
protected CdnaCoord |
genomicToCdnaCoord(org.opencb.biodata.models.core.Transcript transcript,
int genomicPosition) |
protected boolean |
isCoding(org.opencb.biodata.models.core.Transcript transcript) |
protected void |
justify(org.opencb.biodata.models.variant.Variant variant,
int startOffset,
int endOffset,
String allele,
String genomicSequence,
String strand)
Justify an indel to the left or right along a sequence 'seq'.
|
protected org.opencb.biodata.models.variant.Variant |
normalize(org.opencb.biodata.models.variant.Variant variant,
boolean normalize) |
List<String> |
run(org.opencb.biodata.models.variant.Variant variant,
org.opencb.biodata.models.core.Gene gene) |
List<String> |
run(org.opencb.biodata.models.variant.Variant variant,
org.opencb.biodata.models.core.Gene gene,
boolean normalize) |
List<String> |
run(org.opencb.biodata.models.variant.Variant variant,
List<org.opencb.biodata.models.core.Gene> geneList) |
List<String> |
run(org.opencb.biodata.models.variant.Variant variant,
List<org.opencb.biodata.models.core.Gene> geneList,
boolean normalize) |
protected List<String> |
run(org.opencb.biodata.models.variant.Variant variant,
org.opencb.biodata.models.core.Transcript transcript,
String geneId,
boolean normalize) |
protected void |
setRangeCoordsAndAlleles(int genomicStart,
int genomicEnd,
String genomicReference,
String genomicAlternate,
org.opencb.biodata.models.core.Transcript transcript,
HgvsStringBuilder hgvsStringBuilder) |
protected static final int NEIGHBOURING_SEQUENCE_SIZE
protected GenomeDBAdaptor genomeDBAdaptor
public HgvsCalculator(GenomeDBAdaptor genomeDBAdaptor)
public List<String> run(org.opencb.biodata.models.variant.Variant variant, List<org.opencb.biodata.models.core.Gene> geneList)
public List<String> run(org.opencb.biodata.models.variant.Variant variant, List<org.opencb.biodata.models.core.Gene> geneList, boolean normalize)
public List<String> run(org.opencb.biodata.models.variant.Variant variant, org.opencb.biodata.models.core.Gene gene)
public List<String> run(org.opencb.biodata.models.variant.Variant variant, org.opencb.biodata.models.core.Gene gene, boolean normalize)
protected List<String> run(org.opencb.biodata.models.variant.Variant variant, org.opencb.biodata.models.core.Transcript transcript, String geneId, boolean normalize)
protected org.opencb.biodata.models.variant.Variant normalize(org.opencb.biodata.models.variant.Variant variant, boolean normalize)
protected boolean isCoding(org.opencb.biodata.models.core.Transcript transcript)
protected void setRangeCoordsAndAlleles(int genomicStart, int genomicEnd, String genomicReference, String genomicAlternate, org.opencb.biodata.models.core.Transcript transcript, HgvsStringBuilder hgvsStringBuilder)
protected void justify(org.opencb.biodata.models.variant.Variant variant, int startOffset, int endOffset, String allele, String genomicSequence, String strand)
variant
- Variant object that needs to be justified. It will get modified accordingly.startOffset
- relative start position of the variant within genomicSequence (0-based).endOffset
- relative end position of the variant within genomicSequence (0-based, startOffset=endOffset
for insertions).allele
- String containing the allele that needs to be justified.genomicSequence
- String containing the genomic sequence around the variant.getStart() position
(+-NEIGHBOURING_SEQUENCE_SIZE).strand
- String {"+", "-"}.protected CdnaCoord genomicToCdnaCoord(org.opencb.biodata.models.core.Transcript transcript, int genomicPosition)
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