Package org.intermine.bio.web.biojava

Class BioSequence

  • All Implemented Interfaces:
    java.lang.Iterable<org.biojava.nbio.core.sequence.template.Compound>, org.biojava.nbio.core.sequence.template.Accessioned, org.biojava.nbio.core.sequence.template.Sequence<org.biojava.nbio.core.sequence.template.Compound>
    public class BioSequence
extends org.biojava.nbio.core.sequence.template.AbstractSequence<org.biojava.nbio.core.sequence.template.Compound>
    An implementation of the BioJava Sequence interface that uses InterMine objects underneath.

    • Nested Class Summary

      • Nested classes/interfaces inherited from class org.biojava.nbio.core.sequence.template.AbstractSequence

        org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType

    • Constructor Summary

      Constructors 
      Constructor Description
      BioSequence​(org.biojava.nbio.core.sequence.template.AbstractSequence seq, org.intermine.model.bio.BioEntity bioEntity)
      Create a new BioSequence from a BioEntity

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      org.biojava.nbio.ontology.utils.SmallAnnotation getAnnotation()  

      • 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, toString

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator

    • Constructor Detail

      • BioSequence

        public BioSequence​(org.biojava.nbio.core.sequence.template.AbstractSequence seq,
                   org.intermine.model.bio.BioEntity bioEntity)
            throws org.biojava.nbio.core.exceptions.CompoundNotFoundException
        Create a new BioSequence from a BioEntity
        Parameters:
        seq - a biojava sequence
        bioEntity - the BioEntity
        Throws:
        org.biojava.nbio.core.exceptions.CompoundNotFoundException - exception

    • Method Detail

      • getAnnotation

        public org.biojava.nbio.ontology.utils.SmallAnnotation getAnnotation()
        Returns:
        the annotation