Uses of Class
com.hfg.bio.seq.SeqLocation

Packages that use SeqLocation

Package	Description
com.hfg.bio
com.hfg.bio.molbio
com.hfg.bio.seq
com.hfg.bio.seq.alignment
com.hfg.bio.seq.format
com.hfg.bio.seq.format.feature.genbank
com.hfg.bio.seq.pattern

Uses of SeqLocation in com.hfg.bio

Methods in com.hfg.bio that return SeqLocation

Modifier and Type	Method and Description
SeqLocation	DigestFragment.getSeqLocation()

Uses of SeqLocation in com.hfg.bio.molbio

Methods in com.hfg.bio.molbio with parameters of type SeqLocation

Modifier and Type	Method and Description
protected RestrictionSite	RestrictionEnzyme.createMatch(String inSeq, SeqLocation inLocation)

Constructors in com.hfg.bio.molbio with parameters of type SeqLocation

Constructor and Description
RestrictionSite(RestrictionEnzyme inRestrictionEnzyme, String inSeq, SeqLocation inLocation)

Uses of SeqLocation in com.hfg.bio.seq

Methods in com.hfg.bio.seq that return SeqLocation

Modifier and Type	Method and Description
SeqLocation	NucleicAcidTrimmer.calculateTrimRange(NucleicAcid inSeq)
SeqLocation	SeqLocation.clone()
static SeqLocation	SeqUtil.flipStrandSeqLocation(SeqLocation inSeqLoc, int inNucleotideSeqLength) Creates a new SeqLocation that is relative to the opposite strand.
SeqLocation	SeqLocation.setChainId(String inValue)
SeqLocation	SeqLocation.setEnd(Integer inValue)
SeqLocation	SeqLocation.setStart(Integer inValue)

Methods in com.hfg.bio.seq that return types with arguments of type SeqLocation

Modifier and Type	Method and Description
List<SeqLocation>	Protein.findNLinkedSites()
List<SeqLocation>	SeqLocation.subtract(SeqLocation inLoc2)

Methods in com.hfg.bio.seq with parameters of type SeqLocation

Modifier and Type	Method and Description
static SeqLocation	SeqUtil.flipStrandSeqLocation(SeqLocation inSeqLoc, int inNucleotideSeqLength) Creates a new SeqLocation that is relative to the opposite strand.
String	BioSequence.getSubSequence(SeqLocation inSeqLocation)
String	BioSequenceImpl.getSubSequence(SeqLocation inSeqLocation)
Reader	BioSequence.getSubSequenceReader(SeqLocation inSeqLocation)
Reader	BioSequenceImpl.getSubSequenceReader(SeqLocation inSeqLocation)
List<SeqLocation>	SeqLocation.subtract(SeqLocation inLoc2)

Uses of SeqLocation in com.hfg.bio.seq.alignment

Methods in com.hfg.bio.seq.alignment that return SeqLocation

Modifier and Type	Method and Description
SeqLocation	AlignedSeq.getSeqLocation()

Uses of SeqLocation in com.hfg.bio.seq.format

Methods in com.hfg.bio.seq.format that return SeqLocation

Modifier and Type	Method and Description
SeqLocation	SeqCitation.getSeqLocation()

Methods in com.hfg.bio.seq.format with parameters of type SeqLocation

Modifier and Type	Method and Description
SeqCitation	SeqCitation.setSeqLocation(SeqLocation inValue)

Uses of SeqLocation in com.hfg.bio.seq.format.feature.genbank

Methods in com.hfg.bio.seq.format.feature.genbank that return types with arguments of type SeqLocation

Modifier and Type	Method and Description
List<SeqLocation>	GenBankFeatureLocation.getIntrons()

Uses of SeqLocation in com.hfg.bio.seq.pattern

Methods in com.hfg.bio.seq.pattern that return SeqLocation

Modifier and Type	Method and Description
SeqLocation	SeqPatternMatch.getSeqLocation()
SeqLocation	SeqPatternMatcher.getSeqLocation()

Methods in com.hfg.bio.seq.pattern with parameters of type SeqLocation

Modifier and Type	Method and Description
protected T	NucleotidePattern.createMatch(String inSeq, SeqLocation inLocation)
protected ProteinPatternMatch	ProteinPattern.createMatch(String inSeq, SeqLocation inLocation)
protected abstract T	SeqPattern.createMatch(String inSeq, SeqLocation inLocation)
T	SeqPatternMatcher.find(SeqLocation inSeqLocation)
default List<T>	SeqPatternMatcher.findAll(SeqLocation inSeqLocation)
default T	SeqPatternMatcher.findLast(SeqLocation inSeqLocation)
SeqPatternMatcher<S,T>	SeqPattern.matcher(S inTarget, SeqLocation inSeqLocation)

Constructors in com.hfg.bio.seq.pattern with parameters of type SeqLocation

Constructor and Description
NucleotidePatternMatch(NucleotidePattern inPattern, String inSeq, SeqLocation inLocation)
ProteinPatternMatch(ProteinPattern inPattern, String inSeq, SeqLocation inLocation)
SeqPatternMatch(SeqPattern inPattern, String inSeq, SeqLocation inLocation)