Package org.biojava.nbio.core.sequence.template

Class AbstractSequence<C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.template.AbstractSequence<C>
Type Parameters:
C -
All Implemented Interfaces:
Iterable<C>, Accessioned, Sequence<C>
Direct Known Subclasses:
BasicSequence, DNASequence, ProteinSequence, RNASequence
public abstract class AbstractSequence<C extends Compound> extends Object implements Sequence<C>
The base class for DNA, RNA and Protein sequences.

  • Constructor Details

    • AbstractSequence

      public AbstractSequence()

    • AbstractSequence

      public AbstractSequence(String seqString, CompoundSet<C> compoundSet) throws CompoundNotFoundException
      Create a Sequence from a simple string where the values should be found in compoundSet
      Parameters:
      seqString -
      compoundSet -
      Throws:
      CompoundNotFoundException

    • AbstractSequence

      public AbstractSequence(SequenceReader<C> proxyLoader, CompoundSet<C> compoundSet)
      A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data. A variety of use cases are possible. A ProxySequenceReader that knows the offset and of the sequence in a large fasta file. A ProxySequenceReader that can pull Sequence data from UniProt, NCBI or a custom database. If the ProxySequenceReader implements various interfaces then the sequence will set those interfaces so that calls to various methods will be valid.
      Parameters:
      proxyLoader -
      compoundSet -

  • Method Details

    • setProxySequenceReader

      public void setProxySequenceReader(SequenceReader<C> proxyLoader)
      Very important method that allows external mappings of sequence data and features. This method will gain additional interface inspection that allows external data sources with knowledge of features for a sequence to be supported.
      Parameters:
      proxyLoader -

    • getProxySequenceReader

      public SequenceReader<C> getProxySequenceReader()

    • getBioBegin

      public Integer getBioBegin()
      Returns:
      the bioBegin

    • setBioBegin

      public void setBioBegin(Integer begin)
      Parameters:
      bioBegin - the bioBegin to set

    • getBioEnd

      public Integer getBioEnd()
      Returns:
      the bioEnd

    • setBioEnd

      public void setBioEnd(Integer end)
      Parameters:
      bioEnd - the bioEnd to set

    • getUserCollection

      public Collection<Object> getUserCollection()
      Provided for convince if the developer needs to associate data with a sequence
      Returns:

    • setUserCollection

      public void setUserCollection(Collection<Object> userCollection)
      Parameters:
      userCollection -

    • getAnnotationType

      public AbstractSequence.AnnotationType getAnnotationType()
      Returns:
      the annotation

    • setAnnotationType

      public void setAnnotationType(AbstractSequence.AnnotationType annotationType)
      Parameters:
      annotation - the annotation to set

    • getDescription

      public String getDescription()
      Returns:
      the description

    • setDescription

      public void setDescription(String description)
      Parameters:
      description - the description to set

    • getOriginalHeader

      public String getOriginalHeader()
      Returns:
      the originalHeader

    • setOriginalHeader

      public void setOriginalHeader(String originalHeader)
      Parameters:
      originalHeader - the originalHeader to set

    • getParentSequence

      public AbstractSequence<?> getParentSequence()
      Returns:
      the parentSequence

    • setParentSequence

      public void setParentSequence(AbstractSequence<?> parentSequence)
      Parameters:
      parentSequence - the parentSequence to set

    • getSource

      public String getSource()
      Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source
      Returns:
      the source

    • setSource

      public void setSource(String source)
      Added support for the source of this sequence for GFF3 export
      Parameters:
      source - the source to set

    • addNote

      public void addNote(String note)
      Add notes about this sequence that will get exported for GFF3
      Parameters:
      note -

    • removeNote

      public void removeNote(String note)

    • getNotesList

      public ArrayList<String> getNotesList()
      Returns:
      the notesList

    • setNotesList

      public void setNotesList(ArrayList<String> notesList)
      Parameters:
      notesList - the notesList to set

    • getSequenceScore

      public Double getSequenceScore()
      Provide place holder for a metric that indicate a score associated with the sequence
      Returns:
      the sequenceScore

    • setSequenceScore

      public void setSequenceScore(Double sequenceScore)
      Parameters:
      sequenceScore - the sequenceScore to set

    • getFeatures

      public List<FeatureInterface<AbstractSequence<C>,C>> getFeatures(String featureType, int bioSequencePosition)
      Return features at a sequence position by type
      Parameters:
      featureType -
      bioSequencePosition -
      Returns:

    • getFeatures

      public List<FeatureInterface<AbstractSequence<C>,C>> getFeatures(int bioSequencePosition)
      Return features at a sequence position
      Parameters:
      featureType -
      bioSequencePosition -
      Returns:

    • getFeatures

      public List<FeatureInterface<AbstractSequence<C>,C>> getFeatures()
      Returns:

    • addFeature

      public void addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>,C> feature)
      Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
      Parameters:
      bioStart -
      bioEnd -
      feature -

    • addFeature

      public void addFeature(FeatureInterface<AbstractSequence<C>,C> feature)
      Add a feature to this sequence. The feature will be added to the collection where the order is start position and if more than one feature at the same start position then longest is added first. This helps on doing feature layout for displaying features in SequenceFeaturePanel
      Parameters:
      feature -

    • removeFeature

      public void removeFeature(FeatureInterface<AbstractSequence<C>,C> feature)
      Remove a feature from the sequence
      Parameters:
      feature -

    • getFeaturesByType

      public List<FeatureInterface<AbstractSequence<C>,C>> getFeaturesByType(String type)
      Parameters:
      type -
      Returns:

    • getFeaturesKeyWord

      public FeaturesKeyWordInterface getFeaturesKeyWord()
      Returns:
      the featuresKeyWord

    • setFeaturesKeyWord

      public void setFeaturesKeyWord(FeaturesKeyWordInterface featuresKeyWord)
      Parameters:
      featuresKeyWord - the featuresKeyWord to set

    • getDatabaseReferences

      public DatabaseReferenceInterface getDatabaseReferences()
      Returns:
      the databaseReferences

    • setDatabaseReferences

      public void setDatabaseReferences(DatabaseReferenceInterface databaseReferences)
      Parameters:
      databaseReferences - the databaseReferences to set

    • getFeatureRetriever

      public FeatureRetriever getFeatureRetriever()

    • setFeatureRetriever

      public void setFeatureRetriever(FeatureRetriever featureRetriever)

    • getAccession

      public AccessionID getAccession()
      Description copied from interface: Accessioned
      Returns the AccessionID this location is currently bound with
      Specified by:
      getAccession in interface Accessioned
      Returns:
      the accession

    • setAccession

      public void setAccession(AccessionID accession)
      Parameters:
      accession - the accession to set

    • getTaxonomy

      public TaxonomyID getTaxonomy()
      Returns:
      the species

    • setTaxonomy

      public void setTaxonomy(TaxonomyID taxonomy)
      Parameters:
      species - the species to set

    • getCompoundSet

      public CompoundSet<C> getCompoundSet()
      Description copied from interface: Sequence
      Gets the compound set used to back this Sequence
      Specified by:
      getCompoundSet in interface Sequence<C extends Compound>

    • setCompoundSet

      public void setCompoundSet(CompoundSet<C> compoundSet)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getSequenceAsString

      public String getSequenceAsString(Integer bioStart, Integer bioEnd, Strand strand)
      Parameters:
      begin -
      end -
      strand -
      Returns:

    • getSequenceAsString

      public String getSequenceAsString()
      Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
      Specified by:
      getSequenceAsString in interface Sequence<C extends Compound>
      Returns:

    • getAsList

      public List<C> getAsList()
      Description copied from interface: Sequence
      Returns the Sequence as a List of compounds
      Specified by:
      getAsList in interface Sequence<C extends Compound>
      Returns:

    • getCompoundAt

      public C getCompoundAt(int position)
      Description copied from interface: Sequence
      Returns the Compound at the given biological index
      Specified by:
      getCompoundAt in interface Sequence<C extends Compound>
      Parameters:
      position - The 1-indexed position of the amino acid
      Returns:

    • getIndexOf

      public int getIndexOf(C compound)
      Description copied from interface: Sequence
      Scans through the Sequence looking for the first occurrence of the given compound
      Specified by:
      getIndexOf in interface Sequence<C extends Compound>
      Parameters:
      compound -
      Returns:
      The first index of compound in this sequence (1-based)

    • getLastIndexOf

      public int getLastIndexOf(C compound)
      Description copied from interface: Sequence
      Scans through the Sequence looking for the last occurrence of the given compound
      Specified by:
      getLastIndexOf in interface Sequence<C extends Compound>
      Parameters:
      compound -
      Returns:
      The last index of compound in this sequence (1-based)

    • getLength

      public int getLength()
      Description copied from interface: Sequence
      Returns the length of the Sequence
      Specified by:
      getLength in interface Sequence<C extends Compound>
      Returns:

    • getSubSequence

      public SequenceView<C> getSubSequence(Integer bioStart, Integer bioEnd)
      Description copied from interface: Sequence
      Returns a portion of the sequence from the different positions. This is indexed from 1
      Specified by:
      getSubSequence in interface Sequence<C extends Compound>
      Parameters:
      bioStart -
      bioEnd -
      Returns:

    • iterator

      public Iterator<C> iterator()
      Specified by:
      iterator in interface Iterable<C extends Compound>
      Returns:

    • countCompounds

      public int countCompounds(C... compounds)
      Description copied from interface: Sequence
      Returns the number of times we found a compound in the Sequence
      Specified by:
      countCompounds in interface Sequence<C extends Compound>
      Parameters:
      compounds -
      Returns:

    • getInverse

      public SequenceView<C> getInverse()
      Description copied from interface: Sequence
      Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.
      Specified by:
      getInverse in interface Sequence<C extends Compound>
      Returns: