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

Packages that use BioSequenceType

Package	Description
com.hfg.bio.seq
com.hfg.bio.seq.alignment
com.hfg.bio.seq.alignment.blast
com.hfg.bio.seq.pattern

Uses of BioSequenceType in com.hfg.bio.seq

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

Modifier and Type	Method and Description
BioSequenceType	BioSequence.getType()
BioSequenceType	BioSequenceImpl.getType()
BioSequenceType	NucleicAcid.getType()
BioSequenceType	Protein.getType()
static BioSequenceType	SeqUtil.guessBioSequenceType(String inSequence) Guesses the BioSequenceType for the specified sequence.
static BioSequenceType	BioSequenceType.valueOf(char inAbbrev)
static BioSequenceType	BioSequenceType.valueOf(String name) Returns the enum constant of this type with the specified name.
static BioSequenceType[]	BioSequenceType.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

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

Modifier and Type	Method and Description
BioSequenceType	KMerBitSet.getBioSequenceType()
BioSequenceType	MultipleSequenceAlignment.getBioSequenceType()

Methods in com.hfg.bio.seq.alignment with parameters of type BioSequenceType

Modifier and Type	Method and Description
SubstitutionMatrix	MSA_Settings.getSubstitutionMatrix(BioSequenceType inSeqType)
SubstitutionMatrix	PairwiseSettings.getSubstitutionMatrix(BioSequenceType inSeqType)

Constructors in com.hfg.bio.seq.alignment with parameters of type BioSequenceType

Constructor and Description
KMerBitSet(BioSequenceType inSeqType, int inKMerSize)

Uses of BioSequenceType in com.hfg.bio.seq.alignment.blast

Methods in com.hfg.bio.seq.alignment.blast that return BioSequenceType

Modifier and Type	Method and Description
BioSequenceType	BLAST_Program.getDatabaseBioSequenceType()
BioSequenceType	BLAST_Program.getQueryBioSequenceType()
BioSequenceType	BLAST_Database.getSeqType()
BioSequenceType	BLAST_DatabaseGroup.getSeqType()

Methods in com.hfg.bio.seq.alignment.blast with parameters of type BioSequenceType

Modifier and Type	Method and Description
List<BLAST_DatabaseGroup>	BLAST_DatabaseMgr.getGroups(BioSequenceType inType)
BLAST_Database	BLAST_Database.setSeqType(BioSequenceType inValue)

Constructors in com.hfg.bio.seq.alignment.blast with parameters of type BioSequenceType

Constructor and Description
BLAST_DatabaseGroup(String inName, BioSequenceType inType)

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

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

Modifier and Type	Method and Description
BioSequenceType	NucleotidePattern.getBioSequenceType()
BioSequenceType	ProteinPattern.getBioSequenceType()
abstract BioSequenceType	SeqPattern.getBioSequenceType()