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

java.lang.Object
  extended by org.biojava3.core.sequence.template.AbstractSequence<C>
      extended by org.biojava3.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 specialised 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(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(String sequence,
                     CompoundSet<C> compoundSet)

BasicSequence

public BasicSequence(ProxySequenceReader<C> reader)