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
    GAP
    character used to designate gaps
    static final String
    GAP_TLA
    A three letter acronym version of a gap.
    static final String
    GAPS
    Characters that might be used as gaps
    static final char
    UNKNOWN
    character used to designate unknown characters
    static final String
    UNKNOWN_TLA
    character used to designate unknown characters

  • Method Summary

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

    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.