Package pal.alignment

Class IndelAlignment

All Implemented Interfaces:
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:
  • Constructor Details

    • IndelAlignment

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