Package jebl.evolution.alignments

Class ConsensusSequence

  • All Implemented Interfaces:
    java.lang.Comparable, Sequence, Attributable
    public class ConsensusSequence
extends java.lang.Object
implements Sequence
    Version:
    $Id: ConsensusSequence.java 365 2006-06-28 07:34:56Z pepster $
    Author:
    rambaut, Alexei Drummond

    • Constructor Detail

      • ConsensusSequence

        public ConsensusSequence​(Taxon taxon,
                         Alignment source)
        Creates a FilteredSequence wrapper to the given source sequence.
        Parameters:
        source -

      • ConsensusSequence

        public ConsensusSequence​(Taxon taxon,
                         Alignment source,
                         boolean includeAmbiguities)
        Creates a FilteredSequence wrapper to the given source sequence.
        Parameters:
        source -

    • Method Detail

      • getString

        public java.lang.String getString()
        Specified by:
        getString in interface Sequence
        Returns:
        a string representing the sequence of symbols.

      • getStates

        public State[] getStates()
        Specified by:
        getStates in interface Sequence
        Returns:
        an array of state objects.

      • getStateIndices

        public byte[] getStateIndices()
        Specified by:
        getStateIndices in interface Sequence
        Returns:
        an array of state indices.

      • getState

        public State getState​(int site)
        Specified by:
        getState in interface Sequence
        Returns:
        the state at site.

      • getLength

        public int getLength()
        Returns the length of the sequence
        Specified by:
        getLength in interface Sequence
        Returns:
        the length

      • constructConsensus

        public static State[] constructConsensus​(Alignment source,
                                         boolean includeAmbiguities)

      • getTaxon

        public Taxon getTaxon()
        Specified by:
        getTaxon in interface Sequence
        Returns:
        that taxon that this sequence represents (primarily used to match sequences with tree nodes)

      • compareTo

        public int compareTo​(java.lang.Object o)
        Sequences are compared by their taxa
        Specified by:
        compareTo in interface java.lang.Comparable
        Parameters:
        o - another sequence
        Returns:
        an integer

      • setAttribute

        public void setAttribute​(java.lang.String name,
                         java.lang.Object value)
        Description copied from interface: Attributable
        Sets an named attribute for this object.
        Specified by:
        setAttribute in interface Attributable
        Parameters:
        name - the name of the attribute.
        value - the new value of the attribute.

      • getAttribute

        public java.lang.Object getAttribute​(java.lang.String name)
        Specified by:
        getAttribute in interface Attributable
        Parameters:
        name - the name of the attribute of interest, or null if the attribute doesn't exist.
        Returns:
        an object representing the named attributed for this object.

      • removeAttribute

        public void removeAttribute​(java.lang.String name)
        Specified by:
        removeAttribute in interface Attributable
        Parameters:
        name - name of attribute to remove

      • getAttributeNames

        public java.util.Set<java.lang.String> getAttributeNames()
        Specified by:
        getAttributeNames in interface Attributable
        Returns:
        an array of the attributeNames that this object has.

      • getAttributeMap

        public java.util.Map<java.lang.String,​java.lang.Object> getAttributeMap()
        Description copied from interface: Attributable
        Gets the entire attribute map.
        Specified by:
        getAttributeMap in interface Attributable
        Returns:
        an unmodifiable map