Uses of Interface
org.biojava.bio.alignment.AlignmentElement

Packages that use AlignmentElement

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.

Uses of AlignmentElement in org.biojava.bio.alignment

Classes in org.biojava.bio.alignment that implement AlignmentElement

Modifier and Type	Class and Description
class	SimpleAlignmentElement SimpleSimpleAlignment is a simple implementation of AlignmentElement.

Fields in org.biojava.bio.alignment with type parameters of type AlignmentElement

Modifier and Type	Field and Description
protected Map<Object,AlignmentElement>	FlexibleAlignment.data

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

Modifier and Type	Method and Description
protected AlignmentElement	FlexibleAlignment.getAE(Object label)

Methods in org.biojava.bio.alignment with parameters of type AlignmentElement

Modifier and Type	Method and Description
void	FlexibleAlignment.addSequence(AlignmentElement ae) add a new a alignment usings a location to the reference sequence.
void	ARAlignment.addSequence(AlignmentElement ae)

Constructor parameters in org.biojava.bio.alignment with type arguments of type AlignmentElement

Constructor and Description

FlexibleAlignment(List<AlignmentElement> seqList) construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.