org.biojava3.core.sequence
Class BasicSequence<C extends Compound>

java.lang.Object
  org.biojava3.core.sequence.template.AbstractSequence<C>
      org.biojava3.core.sequence.BasicSequence<C>

All Implemented Interfaces:

java.lang.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.biojava3.core.sequence.template.AbstractSequence

AbstractSequence.AnnotationType

Constructor Summary

BasicSequence(ProxySequenceReader<C> reader)

BasicSequence(java.lang.String sequence, CompoundSet<C> compoundSet)

Method Summary

Methods inherited from class org.biojava3.core.sequence.template.AbstractSequence

addFeature, addFeature, addNote, countCompounds, getAccession, getAnnotationType, getAsList, getBioBegin, getBioEnd, getCompoundAt, getCompoundSet, getDatabaseReferences, getDescription, 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, setFeaturesKeyWord, setNotesList, setOriginalHeader, setParentSequence, setProxySequenceReader, setSequenceScore, setSource, setTaxonomy, setUserCollection, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BasicSequence

public BasicSequence(java.lang.String sequence,
                     CompoundSet<C> compoundSet)

BasicSequence

public BasicSequence(ProxySequenceReader<C> reader)