public final class AminoAcidChangeNormalizer extends Object
Constructor and Description |
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AminoAcidChangeNormalizer() |
Modifier and Type | Method and Description |
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static AminoAcidChange |
normalizeDeletion(String ref,
AminoAcidChange change)
Normalize deletion
AminoAcidChange for amino acid string
Return change if it is not a clean deletion. |
static AminoAcidChange |
shiftInsertion(AminoAcidChange aaChange,
String wtAASeq)
Shift insertion
AminoAcidChange to the right in WT AA sequence. |
static AminoAcidChange |
truncateAltAfterStopCodon(AminoAcidChange change)
Search for stop codon in
change.alt and truncate afterwards. |
static AminoAcidChange |
truncateBothSides(AminoAcidChange aaChange)
Truncate
AminoAcidChange from both sides for matching ref/alt prefixes/suffixes. |
public static AminoAcidChange truncateAltAfterStopCodon(AminoAcidChange change)
change.alt
and truncate afterwards.change
- the AminoAcidChange
to normalizeAminoAcidChange
public static AminoAcidChange normalizeDeletion(String ref, AminoAcidChange change)
AminoAcidChange
for amino acid string
Return change
if it is not a clean deletion.ref
- reference amino acid string to changechange
- the AminoAcidChange
to normalizepublic static AminoAcidChange truncateBothSides(AminoAcidChange aaChange)
AminoAcidChange
from both sides for matching ref/alt prefixes/suffixes.
Truncating of the prefixes is given higher priority to conform with the HGVS notation (you have to call
shiftInsertion(de.charite.compbio.jannovar.reference.AminoAcidChange, java.lang.String)
) afterwards.aaChange
- AminoAcidChange
to truncateAminoAcidChange
public static AminoAcidChange shiftInsertion(AminoAcidChange aaChange, String wtAASeq)
AminoAcidChange
to the right in WT AA sequence.
Returns aaChange
if aaChange.ref
is not the empty string.aaChange
- AminoAcidChange
to normalizewtAASeq
- WT AA sequence to use for shiftingAminoAcidChange
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