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>

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 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

Constructors

Constructor	Description
BasicSequence(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, 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, initSequenceStorage, iterator, removeFeature, removeNote, setAccession, setAnnotationType, setBioBegin, setBioEnd, setComments, setCompoundSet, setDatabaseReferences, setDescription, setFeatureRetriever, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setReferences, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

BasicSequence

public BasicSequence(String sequence,
                     CompoundSet<C> compoundSet)
              throws CompoundNotFoundException

Throws:

CompoundNotFoundException

BasicSequence

public BasicSequence(ProxySequenceReader<C> reader)