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public interface GappedSequence
Extension of GappedSymbolList which also projects features into the gapped coordinate system.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
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FeatureHolder.EmptyFeatureHolder |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary |
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Fields inherited from interface org.biojava.bio.symbol.SymbolList |
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EDIT, EMPTY_LIST |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
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EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
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EDIT, EMPTY_LIST |
Method Summary |
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Methods inherited from interface org.biojava.bio.seq.Sequence |
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getName, getURN |
Methods inherited from interface org.biojava.bio.symbol.SymbolList |
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edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.bio.seq.FeatureHolder |
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containsFeature, countFeatures, createFeature, features, filter, filter, getSchema, removeFeature |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.bio.Annotatable |
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getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.bio.symbol.GappedSymbolList |
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addGapInSource, addGapInView, addGapsInSource, addGapsInView, firstNonGap, getSourceSymbolList, getUngappedLocation, lastNonGap, removeGap, removeGaps, sourceToView, viewToSource |
Methods inherited from interface org.biojava.bio.symbol.SymbolList |
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edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
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