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

    • Method Detail

      • clearCache

        void clearCache()
        Nullifies cached arrays/objects.
      • getSequenceFromAlignment

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