Uses of Interface
org.biojava.bio.seq.GappedSequence

Packages that use GappedSequence

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.

Uses of GappedSequence in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment that return GappedSequence

Modifier and Type	Method and Description
GappedSequence	AlignmentPair.getQuery() Return the query sequence as a gapped sequence.
GappedSequence	AlignmentPair.getSubject() Return the subject sequence as a gapped sequence.

Uses of GappedSequence in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return GappedSequence

Modifier and Type	Method and Description
static GappedSequence	DNATools.createGappedDNASequence(String dna, String name) Get a new dna as a GappedSequence
static GappedSequence	ProteinTools.createGappedProteinSequence(String theProtein, String name) Get a new protein as a GappedSequence
static GappedSequence	SequenceTools.gappedView(Sequence seq) Create a new gapped sequence for a sequence.

Uses of GappedSequence in org.biojava.bio.seq.impl

Classes in org.biojava.bio.seq.impl that implement GappedSequence

Modifier and Type	Class and Description
class	SimpleGappedSequence Simple implementation of GappedSequence.

Constructors in org.biojava.bio.seq.impl with parameters of type GappedSequence

Constructor and Description
SimpleGappedSequence(GappedSequence seq)