public final class BitapPattern extends Object implements Serializable
Motif.getBitapPattern() to create bitap pattern.| Modifier and Type | Method and Description |
|---|---|
BitapMatcher |
exactMatcher(Sequence sequence,
int from,
int to) |
int |
exactSearch(Sequence sequence) |
int |
exactSearch(Sequence sequence,
int from) |
int |
exactSearch(Sequence sequence,
int from,
int to) |
BitapMatcher |
substitutionAndIndelMatcherFirst(int maxNumberOfErrors,
Sequence sequence)
Returns a BitapMatcher preforming a fuzzy search in a whole
sequence. |
BitapMatcher |
substitutionAndIndelMatcherFirst(int maxNumberOfErrors,
Sequence sequence,
int from,
int to)
Returns a BitapMatcher preforming a fuzzy search in a subsequence of
sequence. |
BitapMatcher |
substitutionAndIndelMatcherLast(int maxNumberOfErrors,
Sequence sequence)
Returns a BitapMatcher preforming a fuzzy search in a whole
sequence. |
BitapMatcher |
substitutionAndIndelMatcherLast(int maxNumberOfErrors,
Sequence sequence,
int from,
int to)
Returns a BitapMatcher preforming a fuzzy search in a subsequence of
sequence. |
BitapMatcher |
substitutionOnlyMatcherFirst(int substitutions,
Sequence sequence)
Returns a BitapMatcher preforming a fuzzy search in a whole
sequence. |
BitapMatcher |
substitutionOnlyMatcherFirst(int substitutions,
Sequence sequence,
int from,
int to)
Returns a BitapMatcher preforming a fuzzy search in a subsequence of
sequence. |
public int exactSearch(Sequence sequence)
public int exactSearch(Sequence sequence, int from)
public int exactSearch(Sequence sequence, int from, int to)
public BitapMatcher exactMatcher(Sequence sequence, int from, int to)
public BitapMatcher substitutionOnlyMatcherFirst(int substitutions, Sequence sequence)
sequence. Search allows no more than substitutions number of substitutions. Matcher will return positions of first matched letter in the motif in
ascending order.substitutions - maximal number of allowed substitutionssequence - target sequencepublic BitapMatcher substitutionOnlyMatcherFirst(int substitutions, Sequence sequence, int from, int to)
sequence. Search range starts from
from (inclusive) and ends at to (exclusive). Search allows no more than substitutions
number of substitutions. Matcher will return positions of first matched letter in the motif in ascending order.substitutions - maximal number of allowed substitutionssequence - target sequencefrom - left boundary of search range (inclusive)to - right boundary of search range (exclusive)public BitapMatcher substitutionAndIndelMatcherLast(int maxNumberOfErrors, Sequence sequence)
sequence. Search allows no more than maxNumberOfErrors number of substitutions/insertions/deletions. Matcher will return positions of last matched
letter in the motif in ascending order.maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletionssequence - target sequencepublic BitapMatcher substitutionAndIndelMatcherLast(int maxNumberOfErrors, Sequence sequence, int from, int to)
sequence. Search range starts from
from (inclusive) and ends at to (exclusive). Search allows no more than maxNumberOfErrors
number of substitutions/insertions/deletions. Matcher will return positions of last matched letter in the motif
in ascending order.maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletionssequence - target sequencefrom - left boundary of search range (inclusive)to - right boundary of search range (exclusive)public BitapMatcher substitutionAndIndelMatcherFirst(int maxNumberOfErrors, Sequence sequence)
sequence. Search allows no more than maxNumberOfErrors number of substitutions/insertions/deletions. Matcher will return positions of first matched
letter in the motif in descending order.maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletionssequence - target sequencepublic BitapMatcher substitutionAndIndelMatcherFirst(int maxNumberOfErrors, Sequence sequence, int from, int to)
sequence. Search range starts from
from (inclusive) and ends at to (exclusive). Search allows no more than maxNumberOfErrors number of substitutions/insertions/deletions. Matcher will return positions of first matched
letter in the motif in descending order.maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletionssequence - target sequencefrom - left boundary of search range (inclusive)to - right boundary of search range (exclusive)Copyright © 2018. All rights reserved.