Package pal.alignment

Class IndelAlignment

  • All Implemented Interfaces:
    java.io.Serializable, Alignment, IdGroup, Report
    Direct Known Subclasses:
    IndelAnnotatedAlignment

    public class IndelAlignment
    extends AbstractAlignment
    This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms. It uses the NumericDataType, so that the length of each indel is recorded in the alignment. If anchored is true, then SSR-like (microsatellites) indels will be identified as the same indel locus. If anchored is false, then the same indel start and end at the exact same position.
    Version:
    $Id: IndelAlignment.java,v 1.4 2002/10/14 06:54:24 matt Exp $
    Author:
    Ed Buckler
    See Also:
    Serialized Form
    • Constructor Detail

      • IndelAlignment

        public IndelAlignment​(Alignment a,
                              boolean anchored)
        Basic constructor.
        Parameters:
        anchored - sets to score anchored indels as same position