Uses of Class
de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange
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Packages that use ProteinChange Package Description de.charite.compbio.jannovar.hgvs.protein.change de.charite.compbio.jannovar.hgvs.protein.variant -
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Uses of ProteinChange in de.charite.compbio.jannovar.hgvs.protein.change
Subclasses of ProteinChange in de.charite.compbio.jannovar.hgvs.protein.change Modifier and Type Class Description class
ProteinDeletion
In-frame deletion of a protein (i.e., without frameshift, but can destroy codons).class
ProteinDuplication
class
ProteinExtension
class
ProteinFrameshift
Protein frame shift change.class
ProteinIndel
In-frame substitution on the protein level with more than one base.class
ProteinInsertion
Insertion into a protein sequence.class
ProteinMiscChange
Represents a silent protein-level change, i.e., "p.=".class
ProteinShortSequenceRepeatVariability
Describes short sequence repeat (SSR) variability.class
ProteinSubstitution
Represents a missense protein substitution, for example "Trp2Ala" or "T2A".class
ProteinUnchanged
Unchanged mark inside protein.Methods in de.charite.compbio.jannovar.hgvs.protein.change that return ProteinChange Modifier and Type Method Description abstract ProteinChange
ProteinChange. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinDeletion. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinDuplication. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinExtension. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinFrameshift. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinIndel. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinInsertion. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinMiscChange. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinShortSequenceRepeatVariability. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinSubstitution. withOnlyPredicted(boolean onlyPredicted)
ProteinChange
ProteinUnchanged. withOnlyPredicted(boolean onlyPredicted)
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Uses of ProteinChange in de.charite.compbio.jannovar.hgvs.protein.variant
Methods in de.charite.compbio.jannovar.hgvs.protein.variant that return ProteinChange Modifier and Type Method Description ProteinChange
ProteinChangeAllele. get(int index)
ProteinChange
SingleAlleleProteinVariant. getChange()
ProteinChange
ProteinChangeAllele. remove(int index)
Deprecated.ProteinChange
ProteinChangeAllele. set(int index, ProteinChange element)
Deprecated.Methods in de.charite.compbio.jannovar.hgvs.protein.variant that return types with arguments of type ProteinChange Modifier and Type Method Description com.google.common.collect.ImmutableList<ProteinChange>
ProteinChangeAllele. getChanges()
Iterator<ProteinChange>
ProteinChangeAllele. iterator()
ListIterator<ProteinChange>
ProteinChangeAllele. listIterator()
ListIterator<ProteinChange>
ProteinChangeAllele. listIterator(int index)
List<ProteinChange>
ProteinChangeAllele. subList(int fromIndex, int toIndex)
Methods in de.charite.compbio.jannovar.hgvs.protein.variant with parameters of type ProteinChange Modifier and Type Method Description void
ProteinChangeAllele. add(int index, ProteinChange element)
Deprecated.boolean
ProteinChangeAllele. add(ProteinChange e)
Deprecated.static ProteinChangeAllele
ProteinChangeAllele. build(VariantConfiguration varConfig, ProteinChange... changes)
static SingleAlleleProteinVariant
SingleAlleleProteinVariant. build(String proteinID, VariantConfiguration varConfig, ProteinChange... changes)
static SingleAlleleProteinVariant
SingleAlleleProteinVariant. makeSingleChangeVariant(String proteinID, ProteinChange change)
ProteinChange
ProteinChangeAllele. set(int index, ProteinChange element)
Deprecated.static ProteinChangeAllele
ProteinChangeAllele. singleChangeAllele(ProteinChange change)
Method parameters in de.charite.compbio.jannovar.hgvs.protein.variant with type arguments of type ProteinChange Modifier and Type Method Description boolean
ProteinChangeAllele. addAll(int index, Collection<? extends ProteinChange> c)
Deprecated.boolean
ProteinChangeAllele. addAll(Collection<? extends ProteinChange> c)
Deprecated.Constructor parameters in de.charite.compbio.jannovar.hgvs.protein.variant with type arguments of type ProteinChange Constructor Description ProteinChangeAllele(VariantConfiguration varConfig, Collection<? extends ProteinChange> changes)
Construct allele with the given a variantVariantConfiguration
andProteinChange
s.SingleAlleleProteinVariant(String proteinID, VariantConfiguration varConfig, Collection<? extends ProteinChange> changes)
ConstructSingleAlleleProteinVariant
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