Uses of Interface
org.biojava.bio.symbol.GappedSymbolList
Packages that use GappedSymbolList
Package
Description
Classes to generate and describe sequence alignments.
Classes and interfaces for defining biological sequences and informatics
objects.
Standard in-memory implementations of
Sequence
and
Feature
.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 GappedSymbolListModifier and TypeMethodDescriptionvoid
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.seqModifier and TypeInterfaceDescriptioninterface
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 GappedSymbolListModifier and TypeClassDescriptionclass
Simple implementation of GappedSequence. -
Uses of GappedSymbolList in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement GappedSymbolListModifier and TypeClassDescriptionclass
This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.Constructors in org.biojava.bio.symbol with parameters of type GappedSymbolListModifierConstructorDescriptionSimpleGappedSymbolList
(GappedSymbolList gappedSource) Create a new SimpleGappedSymbolList that will view source, inheriting all existing gaps.