com.hfg.bio.seq.pattern

Class NucleotidePattern<T extends NucleotidePatternMatch>

java.lang.Object

com.hfg.bio.seq.pattern.SeqPattern<NucleicAcid,T>

com.hfg.bio.seq.pattern.NucleotidePattern<T>

All Implemented Interfaces:

Cloneable

Direct Known Subclasses:

RestrictionEnzyme

public class NucleotidePattern<T extends NucleotidePatternMatch>
extends SeqPattern<NucleicAcid,T>

Container for a nucleotide pattern (motif).

Field Summary

Fields inherited from class com.hfg.bio.seq.pattern.SeqPattern

PROSITE_COUNT_PATTERN

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	NucleotidePattern()
	NucleotidePattern(String inPatternString)

Method Summary

Modifier and Type	Method and Description
NucleotidePattern	clone()
protected String	convertStringToRegExp(String inPrositePattern)
protected T	createMatch(String inSeq, SeqLocation inLocation)
BioSequenceType	getBioSequenceType()
Collection<Strand>	getStrandsToSearch()
NucleotidePattern	setIgnoreGaps(boolean inValue)
NucleotidePattern	setMaxMismatches(int inValue)
NucleotidePattern	setStrandsToSearch(Strand inValue)
NucleotidePattern	setStrandsToSearch(Strand[] inValues)

Methods inherited from class com.hfg.bio.seq.pattern.SeqPattern

containsMismatchRestrictions, containsPositionAmbiguity, containsRanges, getIgnoreGaps, getMaxLength, getMaxMismatches, getPrositePattern, getPrositePatternPositions, isCaseSensitive, isLocked, isRestrictedToSeqEnd, isRestrictedToSeqStart, lock, matcher, matcher, name, setIsCaseSensitive, setName, setPrositePattern, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

NucleotidePattern

protected NucleotidePattern()

NucleotidePattern

public NucleotidePattern(String inPatternString)

Method Detail

clone

public NucleotidePattern clone()

Overrides:

clone in class SeqPattern<NucleicAcid,T extends NucleotidePatternMatch>

getBioSequenceType

public BioSequenceType getBioSequenceType()

Specified by:

getBioSequenceType in class SeqPattern<NucleicAcid,T extends NucleotidePatternMatch>

setIgnoreGaps

public NucleotidePattern setIgnoreGaps(boolean inValue)

Overrides:

setIgnoreGaps in class SeqPattern<NucleicAcid,T extends NucleotidePatternMatch>

setMaxMismatches

public NucleotidePattern setMaxMismatches(int inValue)

Overrides:

setMaxMismatches in class SeqPattern<NucleicAcid,T extends NucleotidePatternMatch>

setStrandsToSearch

public NucleotidePattern setStrandsToSearch(Strand inValue)

setStrandsToSearch

public NucleotidePattern setStrandsToSearch(Strand[] inValues)

getStrandsToSearch

public Collection<Strand> getStrandsToSearch()

createMatch

protected T createMatch(String inSeq,
                        SeqLocation inLocation)

Specified by:

createMatch in class SeqPattern<NucleicAcid,T extends NucleotidePatternMatch>

convertStringToRegExp

protected String convertStringToRegExp(String inPrositePattern)