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

Uses of AlignmentElement in org.biojava.bio.alignment

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

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

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

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

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

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

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

Modifier	Constructor	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.