Package pal.alignment

Interface Alignment

All Superinterfaces:
IdGroup, Serializable
All Known Subinterfaces:
AnnotationAlignment
All Known Implementing Classes:
AbstractAlignment, AlignmentReaders.PhylipClustalAlignment, AlignmentReaders.UnalignedAlignment, BootstrappedAlignment, ConcatenatedAlignment, ConcatenatedAnnotatedAlignment, GapBalancedAlignment, IndelAlignment, IndelAnnotatedAlignment, JumbledAlignment, MultiLocusAnnotatedAlignment, ReadAlignment, ReadAlignmentOld, SimpleAlignment, SimpleAnnotatedAlignment, SimulatedAlignment, SitePattern, StrippedAlignment, StrippedAnnotatedAlignment

public interface Alignment extends Serializable, IdGroup
interface for any alignment data.
Version:
$Id: Alignment.java,v 1.15 2003/03/23 00:12:57 matt Exp $
Author:
Alexei Drummond, Korbinian Strimmer
  • Nested Class Summary

    Nested classes/interfaces inherited from interface pal.misc.IdGroup

    IdGroup.Utils
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final char
    character used to designate gaps
    static final String
    A three letter acronym version of a gap.
    static final String
    Characters that might be used as gaps
    static final char
    character used to designate unknown characters
    static final String
    character used to designate unknown characters
  • Method Summary

    Modifier and Type
    Method
    Description
    Returns string representation of single sequence in alignment with gap characters included.
    char
    getData(int seq, int site)
    sequence alignment at (sequence, site)
    Return DataType of this alignment.
    int
    Return number of sequences in this alignment
    int
     

    Methods inherited from interface pal.misc.IdGroup

    getIdCount, getIdentifier, setIdentifier, whichIdNumber
  • Field Details

  • Method Details

    • getData

      char getData(int seq, int site)
      sequence alignment at (sequence, site)
    • getSiteCount

      int getSiteCount()
      Returns:
      number of sites for each sequence in this alignment
    • getSequenceCount

      int getSequenceCount()
      Return number of sequences in this alignment
    • getDataType

      DataType getDataType()
      Return DataType of this alignment.
    • getAlignedSequenceString

      String getAlignedSequenceString(int sequence)
      Returns string representation of single sequence in alignment with gap characters included.