Uses of Class
org.biojava.bio.symbol.Edit

Packages that use Edit

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
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.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.

Uses of Edit in org.biojava.bio.alignment

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

Modifier and Type	Method and Description
void	FlexibleAlignment.edit(Object label, Edit edit)
void	EditableAlignment.edit(Object label, Edit edit) edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.

Uses of Edit in org.biojava.bio.dp

Methods in org.biojava.bio.dp with parameters of type Edit

Modifier and Type	Method and Description
void	SimpleStatePath.edit(Edit edit)

Uses of Edit in org.biojava.bio.seq

Methods in org.biojava.bio.seq with parameters of type Edit

Modifier and Type	Method and Description
void	SimpleAssembly.edit(Edit e)
void	NewSimpleAssembly.edit(Edit e)

Uses of Edit in org.biojava.bio.seq.homol

Methods in org.biojava.bio.seq.homol with parameters of type Edit

Modifier and Type	Method and Description
void	SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)

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

Methods in org.biojava.bio.seq.impl with parameters of type Edit

Modifier and Type	Method and Description
void	ViewSequence.edit(Edit edit)
void	SubSequence.edit(Edit edit)
void	SimpleSequence.edit(Edit edit)
void	RevCompSequence.edit(Edit e) edit() will try to edit the underlying Sequence.
void	DummySequence.edit(Edit edit)

Uses of Edit in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol with parameters of type Edit

Modifier and Type	Method and Description
void	SymbolList.edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
void	SimpleSymbolList.edit(Edit edit) Apply and edit to the SymbolList as specified by Edit.
void	RelabeledAlignment.edit(Edit edit)
void	AbstractSymbolList.edit(Edit edit)

Uses of Edit in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql with parameters of type Edit

Modifier and Type	Method and Description
void	BioSQLRichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.

Uses of Edit in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq with parameters of type Edit

Modifier and Type	Method and Description
void	ThinRichSequence.edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
void	InfinitelyAmbiguousSymbolList.edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
void	RichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.
void	DummyRichSequenceHandler.edit(RichSequence seq, Edit edit) Apply an edit to the Sequence as specified by the edit object.