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

Interface Sequence<C extends Compound>

Type Parameters:
C - Compound a Sequence holds
All Superinterfaces:
Accessioned, Iterable<C>
All Known Subinterfaces:
AlignedSequence<S,C>, MutableAlignedSequence<S,C>, ProxySequenceReader<C>, SequenceReader<C>, SequenceView<C>
All Known Implementing Classes:
AbstractSequence, ArrayListProxySequenceReader, ArrayListSequenceReader, BasicSequence, BitSequenceReader, CDSSequence, ChromosomeSequence, ComplementSequenceView, DNASequence, ExonSequence, FourBitSequenceReader, GenbankProxySequenceReader, GeneSequence, IntronSequence, JoiningSequenceReader, ProteinSequence, ReversedSequenceView, RNASequence, RnaSequenceView, SequenceFileProxyLoader, SequenceProxyView, SimpleAlignedSequence, SingleCompoundSequenceReader, StartCodonSequence, StopCodonSequence, StringProxySequenceReader, TranscriptSequence, TwoBitSequenceReader, UniprotProxySequenceReader
public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned
Main interface for defining a collection of Compounds and accessing them using biological indexes
Author:
Richard Holland, Andy Yates, Scooter Willis

  • Method Details

    • getLength

      int getLength()
      Returns the length of the Sequence

    • getCompoundAt

      C getCompoundAt(int position)
      Returns the Compound at the given biological index
      Parameters:
      position - Biological index (1 to n)
      Returns:
      Compound at the specified position

    • getIndexOf

      int getIndexOf(C compound)
      Scans through the Sequence looking for the first occurrence of the given compound
      Parameters:
      compound - Compounds to look for
      Returns:
      Index of the first position of the compound in the sequence (1 to n)

    • getLastIndexOf

      int getLastIndexOf(C compound)
      Scans through the Sequence looking for the last occurrence of the given compound
      Parameters:
      compound - Compounds to look for
      Returns:
      Index of the last position of the compound in the sequence (1 to n)

    • getSequenceAsString

      String getSequenceAsString()
      Returns the String representation of the Sequence

    • getAsList

      List<C> getAsList()
      Returns the Sequence as a List of compounds

    • getSubSequence

      SequenceView<C> getSubSequence(Integer start, Integer end)
      Returns a portion of the sequence from the different positions. This is indexed from 1
      Parameters:
      start - Biological index start; must be greater than 0
      end - Biological end; must be less than length + 1
      Returns:
      A SequenceView of the offset

    • getCompoundSet

      CompoundSet<C> getCompoundSet()
      Gets the compound set used to back this Sequence

    • countCompounds

      int countCompounds(C... compounds)
      Returns the number of times we found a compound in the Sequence
      Parameters:
      compounds - Vargs of the compounds to count
      Returns:
      Number of times a compound was found

    • getInverse

      SequenceView<C> getInverse()
      Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.