Package org.biojava.nbio.core.sequence
Class BasicSequence<C extends Compound>
java.lang.Object
org.biojava.nbio.core.sequence.template.AbstractSequence<C>
org.biojava.nbio.core.sequence.BasicSequence<C>
- All Implemented Interfaces:
Iterable<C>,Accessioned,Sequence<C>
Bare bones version of the Sequence object to be used sparingly. You should
really use a specialized version of
Sequence which describes
your domain.-
Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence
AbstractSequence.AnnotationType -
Constructor Summary
ConstructorsConstructorDescriptionBasicSequence(String sequence, CompoundSet<C> compoundSet) BasicSequence(ProxySequenceReader<C> reader) -
Method Summary
Methods inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence
addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, getFeatureRetriever, getFeatures, getFeatures, getFeatures, getFeaturesByType, getFeaturesKeyWord, getIndexOf, getInverse, getLastIndexOf, getLength, getNotesList, getOriginalHeader, getParentSequence, getProxySequenceReader, getSequenceAsString, getSequenceAsString, getSequenceScore, getSource, getSubSequence, getTaxonomy, getUserCollection, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setCompoundSet, setDatabaseReferences, setDescription, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection, toStringMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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BasicSequence
- Throws:
CompoundNotFoundException
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BasicSequence
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