Package pal.alignment

Interface CharacterAlignment

All Superinterfaces:
IdGroup, Report, Serializable, TableReport
All Known Implementing Classes:
SimpleCharacterAlignment

public interface CharacterAlignment extends 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
  • Field Details

  • Method Details

    • getTraitName

      String getTraitName(int trait)
      Return name of the trait for this trait number
    • getEnvironmentName

      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