com.milaboratory.core.motif

Class BitapPattern

java.lang.Object

com.milaboratory.core.motif.BitapPattern

All Implemented Interfaces:

Serializable

public final class BitapPattern
extends Object
implements Serializable

Use Motif.getBitapPattern() to create bitap pattern.

See Also:

Serialized Form

Method Summary

Methods

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

exactSearch

public int exactSearch(Sequence sequence)

exactSearch

public int exactSearch(Sequence sequence,
              int from)

exactSearch

public int exactSearch(Sequence sequence,
              int from,
              int to)

exactMatcher

public BitapMatcher exactMatcher(Sequence sequence,
                        int from,
                        int to)

substitutionOnlyMatcherFirst

public BitapMatcher substitutionOnlyMatcherFirst(int substitutions,
                                        Sequence sequence)

Returns a BitapMatcher preforming a fuzzy search in a whole sequence. Search allows no more than substitutions number of substitutions. Matcher will return positions of first matched letter in the motif in ascending order.

Parameters:

substitutions - maximal number of allowed substitutions

sequence - target sequence

Returns:

matcher which will return positions of first matched letter in the motif in ascending order

substitutionOnlyMatcherFirst

public BitapMatcher substitutionOnlyMatcherFirst(int substitutions,
                                        Sequence sequence,
                                        int from,
                                        int to)

Returns a BitapMatcher preforming a fuzzy search in a subsequence of 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.

Parameters:

substitutions - maximal number of allowed substitutions

sequence - target sequence

from - left boundary of search range (inclusive)

to - right boundary of search range (exclusive)

Returns:

matcher which will return positions of first matched letter in the motif in ascending order

substitutionAndIndelMatcherLast

public BitapMatcher substitutionAndIndelMatcherLast(int maxNumberOfErrors,
                                           Sequence sequence)

Returns a BitapMatcher preforming a fuzzy search in a whole 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.

Parameters:

maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletions

sequence - target sequence

Returns:

matcher which will return positions of last matched letter in the motif

substitutionAndIndelMatcherLast

public BitapMatcher substitutionAndIndelMatcherLast(int maxNumberOfErrors,
                                           Sequence sequence,
                                           int from,
                                           int to)

Returns a BitapMatcher preforming a fuzzy search in a subsequence of 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.

Parameters:

maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletions

sequence - target sequence

from - left boundary of search range (inclusive)

to - right boundary of search range (exclusive)

Returns:

matcher which will return positions of last matched letter in the motif in ascending order

substitutionAndIndelMatcherFirst

public BitapMatcher substitutionAndIndelMatcherFirst(int maxNumberOfErrors,
                                            Sequence sequence)

Returns a BitapMatcher preforming a fuzzy search in a whole 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.

Parameters:

maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletions

sequence - target sequence

Returns:

matcher which will return positions of first matched letter in the motif in descending order

substitutionAndIndelMatcherFirst

public BitapMatcher substitutionAndIndelMatcherFirst(int maxNumberOfErrors,
                                            Sequence sequence,
                                            int from,
                                            int to)

Returns a BitapMatcher preforming a fuzzy search in a subsequence of 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.

Parameters:

maxNumberOfErrors - maximal number of allowed substitutions/insertions/deletions

sequence - target sequence

from - left boundary of search range (inclusive)

to - right boundary of search range (exclusive)

Returns:

matcher which will return positions of first matched letter in the motif in descending order