Package pal.alignment

Interface CharacterAlignment

  • All Superinterfaces:
    IdGroup, Report, java.io.Serializable, TableReport
    All Known Implementing Classes:
    SimpleCharacterAlignment

    public interface CharacterAlignment
    extends java.io.Serializable, IdGroup, Report, TableReport
    This interface is designed to hold quantitative character states. Each trait (a quantitative character) has two sets of labels. One is the traitName, and the second is the environmentName. Obviously any descriptor could be placed in these two labels, however for printing purposes traitName is printed first. Double.NaN is assumed to be the missing value.
    Version:
    $Id: CharacterAlignment.java,v 1.2 2001/09/02 13:19:41 korbinian Exp $
    Author:
    Ed Buckler
    • Method Detail

      • getTraitName

        java.lang.String getTraitName​(int trait)
        Return name of the trait for this trait number
      • getEnvironmentName

        java.lang.String getEnvironmentName​(int trait)
        Return name of the environments for this trait number
      • getTrait

        double getTrait​(int seq,
                        int trait)
        Return the trait value for a given sequence (taxon) and trait number
      • getSequenceCount

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

        int getTraitCount()
        Return number of traits for each sequence in this alignment