Package jebl.evolution.alignments

Class BasicAlignment

  • All Implemented Interfaces:
    Alignment, Patterns, Sequences
    public class BasicAlignment
extends java.lang.Object
implements Alignment
    A basic implementation of the Alignment interface.
    Version:
    $Id: BasicAlignment.java 1007 2009-07-17 16:01:47Z rambaut $
    Author:
    Andrew Rambaut, Alexei Drummond

    • Constructor Detail

      • BasicAlignment

        public BasicAlignment()
        Constructs a basic alignment with no sequences.

      • BasicAlignment

        public BasicAlignment​(java.util.Collection<? extends Sequence> sequences)
        Constructs a basic alignment from a collection of sequences. The sequence objects are not copied.
        Parameters:
        sequences -

      • BasicAlignment

        public BasicAlignment​(Sequence[] sequences)
        Constructs a basic alignment from an array of sequences. The sequence objects are not copied.
        Parameters:
        sequences -

    • Method Detail

      • getSequences

        public java.util.Set<Sequence> getSequences()
        Specified by:
        getSequences in interface Sequences
        Returns:
        a set containing all the sequences in this alignment.

      • getPatterns

        public java.util.List<Pattern> getPatterns()
        Description copied from interface: Patterns
        Get a list of all the patterns
        Specified by:
        getPatterns in interface Patterns
        Returns:
        the list

      • getTaxa

        public java.util.List<Taxon> getTaxa()
        Specified by:
        getTaxa in interface Patterns
        Returns:
        the list of taxa that the state values correspond to.

      • addSequence

        public void addSequence​(Sequence sequence)
        Adds a sequence to this alignment
        Parameters:
        sequence - the new sequence.