de.unibi.techfak.jpredictor.motifs
Interface MotifSearchWithError

All Superinterfaces:

MotifSearcher

All Known Implementing Classes:

RegularExpressionMotif, SequenceMotif

interface MotifSearchWithError
extends MotifSearcher

The Interface MotifSearchWithError should be implemented by classes that wants to define methods for searching motifs on sequences, where errors in the match are allowed.

Field Summary

Fields inherited from interface de.unibi.techfak.jpredictor.motifs.MotifSearcher

SEARCH_ALL_ORIENTATIONS, SEARCH_DIRECTION_MAX, SEARCH_DIRECTION_MINUS, SEARCH_DIRECTION_PLUS

Method Summary

int	getErrorNumberAllowedForMatch()
void	setErrorNumberAllowedForMatch(int errorNumber) Sets the number of mismatch errors allowed in one single alignment of motif against another sequence

Methods inherited from interface de.unibi.techfak.jpredictor.motifs.MotifSearcher

getSearchMode, initSearch, search, searchAll, setSearchMode

Method Detail

getErrorNumberAllowedForMatch

int getErrorNumberAllowedForMatch()

Returns:

The number of mismatch errors allowed in one single alignment of motif against sequence.

See Also:

MotifSearcher.search(int, int)

setErrorNumberAllowedForMatch

void setErrorNumberAllowedForMatch(int errorNumber)

Sets the number of mismatch errors allowed in one single alignment of motif against another sequence

Parameters:

errorNumber - The number of mismatches allowed.

See Also:

MotifSearcher.search(int, int)