Uses of Interface
org.biojava.bio.symbol.GappedSymbolList

Packages that use GappedSymbolList

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.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.

Uses of GappedSymbolList in org.biojava.bio.alignment

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

Modifier and Type	Method and Description
void	FlexibleAlignment.removeGaps(GappedSymbolList seq, int start, int length) because there is a bug in GappedSymbolList

Uses of GappedSymbolList in org.biojava.bio.seq

Subinterfaces of GappedSymbolList in org.biojava.bio.seq

Modifier and Type	Interface and Description
interface	GappedSequence Extension of GappedSymbolList which also projects features into the gapped coordinate system.

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

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

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

Uses of GappedSymbolList in org.biojava.bio.symbol

Classes in org.biojava.bio.symbol that implement GappedSymbolList

Modifier and Type	Class and Description
class	SimpleGappedSymbolList This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.

Constructors in org.biojava.bio.symbol with parameters of type GappedSymbolList

Constructor and Description
SimpleGappedSymbolList(GappedSymbolList gappedSource) Create a new SimpleGappedSymbolList that will view source, inheriting all existing gaps.