Uses of Class
jaligner.Alignment

Packages that use Alignment

jaligner	Core classes for the implementation of Smith-Waterman-Gotoh algorithm
jaligner.formats	Group of formats for output alignments.

Uses of Alignment in jaligner

Methods in jaligner that return Alignment

static Alignment	SmithWatermanGotoh.align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) Aligns two sequences by Smith-Waterman (local)
static Alignment	NeedlemanWunschGotoh.align(Sequence s1, Sequence s2, Matrix matrix, float o, float e) Aligns two sequences by Needleman-Wunsch (global)
static Alignment	NeedlemanWunsch.align(Sequence s1, Sequence s2, Matrix matrix, float gap) Aligns two sequences by Needleman-Wunsch (global)

Uses of Alignment in jaligner.formats

Methods in jaligner.formats with parameters of type Alignment

java.lang.String	Pair.format(Alignment alignment) Formats an alignment object to the Pair_FORMAT format
abstract java.lang.String	Format.format(Alignment alignment) Formats alignment
java.lang.String	FASTA.format(Alignment alignment)
java.lang.String	CLUSTAL.format(Alignment alignment) Returns CLUSTAL format of the alignment