| Modifier and Type | Method and Description |
|---|---|
Mutations<S> |
Alignment.getAbsoluteMutations()
Returns mutations in absolute (global)
sequence1 coordinates. |
Mutations<S> |
Alignment.getRelativeMutations()
Returns mutations in local coordinates, relative to
sequence1range. |
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Mutations<S> mutations,
AlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
AffineGapAlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
AlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.calculateScore(S seq1,
Range seq1Range,
Mutations<S> mutations,
LinearGapAlignmentScoring<S> scoring)
Calculates score of alignment
|
static <S extends Sequence<S>> |
AlignmentUtils.toStringSimple(S initialSequence,
Mutations<S> mutations) |
| Constructor and Description |
|---|
Alignment(S sequence1,
Mutations<S> mutations,
AlignmentScoring<S> scoring) |
Alignment(S sequence1,
Mutations<S> mutations,
float score) |
Alignment(S sequence1,
Mutations<S> mutations,
Range sequence1Range,
Range sequence2Range,
AlignmentScoring<S> scoring) |
Alignment(S sequence1,
Mutations<S> mutations,
Range sequence1Range,
Range sequence2Range,
float score) |
AlignmentIteratorForward(Mutations<S> mutations,
Range seq1Range)
Create alignment iterator
|
AlignmentIteratorForward(Mutations<S> mutations,
Range seq1Range,
int seq2Position)
Create alignment iterator
|
AlignmentIteratorReverse(Mutations<S> mutations,
Range seq1Range)
Create alignment iterator
|
AlignmentIteratorReverse(Mutations<S> mutations,
Range seq1Range,
int seq2Position)
Create alignment iterator
|
| Modifier and Type | Field and Description |
|---|---|
List<Mutations<NucleotideSequence>> |
KAlignerQuery.mutationsInTarget |
| Constructor and Description |
|---|
KAlignerQuery(int targetId,
List<Range> queryClusters,
List<Range> targetClusters,
List<Mutations<NucleotideSequence>> mutationsInTarget,
NucleotideSequence query,
Alignment<NucleotideSequence> expectedAlignment) |
| Modifier and Type | Field and Description |
|---|---|
static Mutations<AminoAcidSequence> |
Mutations.EMPTY_AMINO_ACID_MUTATIONS
Identity mutations object for amino acid sequences.
|
static Mutations<NucleotideSequence> |
Mutations.EMPTY_NUCLEOTIDE_MUTATIONS
Identity mutations object for nucleotide sequences.
|
Mutations<AminoAcidSequence> |
MutationsUtil.MutationsWitMapping.mutations |
| Modifier and Type | Method and Description |
|---|---|
<S extends Sequence<S>> |
MutationsCounter.build(Alphabet<S> alphabet,
MutationsCounter.Filter filter) |
Mutations<S> |
Mutations.combineWith(Mutations<S> other)
Returns combined mutations array (
this applied before other). |
Mutations<S> |
Mutations.concat(Mutations<S> other)
Concatenates this and other
|
Mutations<S> |
MutationsBuilder.createAndDestroy() |
static <S extends Sequence<S>> |
Mutations.decode(String string,
Alphabet<S> alphabet) |
static Mutations<AminoAcidSequence> |
Mutations.decodeAA(String string) |
static Mutations<NucleotideSequence> |
Mutations.decodeNuc(String string) |
static <S extends Sequence<S>> |
Mutations.empty(Alphabet<S> alphabet) |
Mutations<S> |
Mutations.extractAbsoluteMutationsForRange(int from,
int to)
Extracts mutations for a range of positions in the original sequence.
|
Mutations<S> |
Mutations.extractAbsoluteMutationsForRange(Range range)
Extracts mutations for a range of positions in the original sequence.
|
Mutations<S> |
Mutations.extractRelativeMutationsForRange(int from,
int to)
Extracts mutations for a range of positions in the original sequence and performs shift of corresponding
positions (moves them to
-from). |
Mutations<S> |
Mutations.extractRelativeMutationsForRange(Range range)
Extracts mutations for a range of positions in the original sequence and performs shift of corresponding
positions (moves them to
-range.from). |
Mutations<S> |
Mutations.getRange(int from,
int to)
Extracts sub mutations by
from-to mutation indices. |
Mutations<S> |
Mutations.invert()
Inverts mutations, so that they reflect difference from seq2 to seq1.
|
Mutations<S> |
Mutations.move(int offset)
Moves positions of mutations by specified offset
|
static Mutations<AminoAcidSequence> |
MutationsUtil.nt2aa(NucleotideSequence seq1,
Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters) |
static Mutations<AminoAcidSequence> |
MutationsUtil.nt2aa(NucleotideSequence seq1,
Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters,
int maxShiftedTriplets) |
Mutations<S> |
Mutations.removeMutationsInRange(int from,
int to)
Removes mutations for a range of positions in the original sequence and performs shift of corresponding
positions of mutations.
|
Mutations<S> |
Mutations.removeMutationsInRange(Range range)
|
Mutations<S> |
Mutations.removeMutationsInRanges(Range... ranges)
|
static <S extends Sequence<S>> |
MutationsUtil.shiftIndelsAtHomopolymers(S seq1,
int seq1From,
Mutations<S> mutations)
This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels
randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
|
static <S extends Sequence<S>> |
MutationsUtil.shiftIndelsAtHomopolymers(S seq1,
Mutations<S> mutations)
This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels
randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
|
| Modifier and Type | Method and Description |
|---|---|
void |
MutationsCounter.adjust(Mutations<?> mutations,
int delta) |
void |
MutationsCounter.adjust(Mutations<?> mutations,
MutationsEnumerator enumerator,
int delta) |
MutationsBuilder<S> |
MutationsBuilder.append(Mutations<S> other) |
MutationsBuilder<S> |
MutationsBuilder.append(Mutations<S> other,
int otherFrom,
int length) |
static boolean |
MutationsUtil.check(Mutations mutations) |
Mutations<S> |
Mutations.combineWith(Mutations<S> other)
Returns combined mutations array (
this applied before other). |
Mutations<S> |
Mutations.concat(Mutations<S> other)
Concatenates this and other
|
static NSequenceWithQuality |
MutationsUtil.mutate(NSequenceWithQuality seq,
Mutations<NucleotideSequence> mutations) |
static Mutations<AminoAcidSequence> |
MutationsUtil.nt2aa(NucleotideSequence seq1,
Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters) |
static Mutations<AminoAcidSequence> |
MutationsUtil.nt2aa(NucleotideSequence seq1,
Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters,
int maxShiftedTriplets) |
static MutationsUtil.MutationNt2AADescriptor[] |
MutationsUtil.nt2aaDetailed(NucleotideSequence seq1,
Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters,
int maxShiftedTriplets)
Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in
corresponding amino acid sequence.
|
static MutationsUtil.MutationsWitMapping |
MutationsUtil.nt2aaWithMapping(NucleotideSequence seq1,
Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters,
int maxShiftedTriplets) |
static int[] |
MutationsUtil.nt2IndividualAA(NucleotideSequence seq1,
Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters) |
static <S extends Sequence<S>> |
MutationsUtil.shiftIndelsAtHomopolymers(S seq1,
int seq1From,
Mutations<S> mutations)
This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels
randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
|
static <S extends Sequence<S>> |
MutationsUtil.shiftIndelsAtHomopolymers(S seq1,
Mutations<S> mutations)
This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels
randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
|
| Constructor and Description |
|---|
MutationsEnumerator(Mutations mutations) |
MutationsUtil.MutationsWitMapping(Mutations<AminoAcidSequence> mutations,
int[] mapping) |
| Modifier and Type | Method and Description |
|---|---|
static <S extends Sequence<S>> |
UniformMutationsGenerator.createUniformMutationAsObject(S sequence,
org.apache.commons.math3.random.RandomGenerator generator) |
static <S extends Sequence<S>> |
UniformMutationsGenerator.createUniformMutationAsObject(S sequence,
org.apache.commons.math3.random.RandomGenerator generator,
MutationType type) |
static Mutations<NucleotideSequence> |
MutationsGenerator.generateMutations(NucleotideSequence sequence,
NucleotideMutationModel model) |
static Mutations<NucleotideSequence> |
MutationsGenerator.generateMutations(NucleotideSequence sequence,
NucleotideMutationModel model,
int from,
int to) |
static Mutations<NucleotideSequence> |
MutationsGenerator.generateMutations(NucleotideSequence sequence,
NucleotideMutationModel model,
Range range) |
| Modifier and Type | Method and Description |
|---|---|
Mutations<S> |
NeighborhoodIterator.getCurrentMutations() |
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