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