Package org.biojava.bio.seq
Interface GappedSequence
- All Superinterfaces:
Annotatable
,Changeable
,FeatureHolder
,GappedSymbolList
,Sequence
,SymbolList
- All Known Implementing Classes:
SimpleGappedSequence
Extension of GappedSymbolList which also projects features
into the gapped coordinate system.
- Since:
- 1.3
- Author:
- Thomas Down, Matthew Pocock
-
Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
-
Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
-
Method Summary
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, features, filter, filter, getSchema, removeFeature
Methods inherited from interface org.biojava.bio.symbol.GappedSymbolList
addGapInSource, addGapInView, addGapsInSource, addGapsInView, firstNonGap, getSourceSymbolList, getUngappedLocation, lastNonGap, removeGap, removeGaps, sourceToView, viewToSource
Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList