Package org.biojava.nbio.core.alignment.template

Interface AlignedSequence<S extends Sequence<C>,C extends Compound>

Type Parameters:
C - each element of the Sequence is a Compound of type C
All Superinterfaces:
Accessioned, Iterable<C>, Sequence<C>
All Known Subinterfaces:
MutableAlignedSequence<S,C>
All Known Implementing Classes:
SimpleAlignedSequence
public interface AlignedSequence<S extends Sequence<C>,C extends Compound> extends Sequence<C>
Defines a data structure for a Sequence within an alignment.
Author:
Mark Chapman, Paolo Pavan

  • Method Details

    • clearCache

      void clearCache()
      Nullifies cached arrays/objects.

    • getAlignmentFromSequence

      int[] getAlignmentFromSequence()
      Returns the alignment.
      Returns:
      the alignment

    • getSequenceFromAlignment

      int[] getSequenceFromAlignment()
      Returns the sequence positions at each alignment index
      Returns:
      array of the sequence positions

    • getAlignmentIndexAt

      int getAlignmentIndexAt(int sequenceIndex)
      Returns the column index within an alignment corresponding to the given index in the original Sequence. Both indices are 1-indexed and inclusive.
      Parameters:
      sequenceIndex - index in the original Sequence
      Returns:
      column index within an alignment
      Throws:
      IndexOutOfBoundsException - if sequenceIndex < 1 or sequenceIndex > getOriginalSequence().Sequence.getLength()

    • getEnd

      Point getEnd()
      Returns the Point within an alignment of the last element of the original Sequence.
      Returns:
      position within an alignment of final original Sequence element

    • getLocationInAlignment

      Location getLocationInAlignment()
      Returns the Location of the original Sequence within an alignment. This provides access to additional substructure beyond start and end points.
      Returns:
      location within an alignment

    • getNumGaps

      int getNumGaps()
      Returns number of gaps in the sequence. This could be determined from the Location information or from gap Compounds, which may not necessarily result in the same number.
      Returns:
      number of gaps in the sequence

    • getOriginalSequence

      S getOriginalSequence()
      Returns the original Sequence before alignment.
      Returns:
      the original sequence

    • getOverlapCount

      int getOverlapCount()
      Returns the maximum number of elements contributed to a column of an alignment by this Sequence. If this Sequence is circular, this number is >= 1. If not, this overlap count is definitely 1.
      Returns:
      the most elements contributed to any alignment column

    • getSequenceIndexAt

      int getSequenceIndexAt(int alignmentIndex)
      Returns the index in the original Sequence corresponding to the given index within an alignment. Both indices are 1-indexed and inclusive.
      Parameters:
      alignmentIndex - column index within an alignment
      Returns:
      index in the original Sequence
      Throws:
      IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Sequence.getLength()

    • getStart

      Point getStart()
      Returns the Point within an alignment of the first element of the original Sequence.
      Returns:
      position within an alignment of first original Sequence element

    • isCircular

      boolean isCircular()
      Returns true if this Sequence wraps around from the last alignment column back to the first. This makes overlap possible, but does not require an overlap count > 1.
      Returns:
      true for circular alignment elements

    • isGap

      boolean isGap(int alignmentIndex)
      Returns true if this Sequence has a gap at a particular alignment column.
      Parameters:
      alignmentIndex - column index within an alignment
      Returns:
      true if this column has a gap
      Throws:
      IndexOutOfBoundsException - if alignmentIndex < 1 or alignmentIndex > Sequence.getLength()

    • getNumGapPositions

      int getNumGapPositions()
      Returns number of gap positions (gap openings and extensions) in the sequence. This could be determined from the Location information or from gap Compounds, which may not necessarily result in the same number.
      Returns:
      number of gap positions in the sequence

    • getCoverage

      double getCoverage()
      Returns the coverage, as a fraction between 0 and 1, of this AlignedSequence with respect to the original sequence. This is equivalent to (Sequence.getLength() - getNumGapPositions()) / getOriginalSequence().getLength().
      Returns:
      coverage of the original sequence by the aligned sequence