Uses of Class
jaligner.Sequence

Packages that use Sequence

jaligner	Core classes for the implementation of Smith-Waterman-Gotoh algorithm
jaligner.formats	Group of formats for output alignments.
jaligner.util	Utility classes for helping core and GUI classes.

Uses of Sequence in jaligner

Methods in jaligner that return Sequence

Sequence	Alignment.getOriginalSequence1() Returns original Sequence #1
Sequence	Alignment.getOriginalSequence2() Returns original Sequence #2

Methods in jaligner with parameters of type Sequence

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)
void	Alignment.setOriginalSequence1(Sequence originalSequence1)
void	Alignment.setOriginalSequence2(Sequence originalSequence2)

Uses of Sequence in jaligner.formats

Methods in jaligner.formats with parameters of type Sequence

java.lang.String

FASTA.format(Sequence sequence) Returns the name, description and sequence combined in one string.

Uses of Sequence in jaligner.util

Methods in jaligner.util that return Sequence

static Sequence	SequenceParser.parse(java.lang.String sequence) Returns a parsed Sequence from a string.
static Sequence	SequenceParser.parse(java.io.File file) Returns a Sequence parsed and loaded from a file