Package jebl.evolution.sequences

Class FilteredSequence

  • All Implemented Interfaces:
    java.lang.Comparable, Sequence, Attributable
    Direct Known Subclasses:
    GaplessSequence, TranslatedSequence
    public abstract class FilteredSequence
extends java.lang.Object
implements Sequence
    Version:
    $Id: FilteredSequence.java 641 2007-02-16 11:56:21Z rambaut $
    Author:
    rambaut, Alexei Drummond

    • Constructor Detail

      • FilteredSequence

        public FilteredSequence​(Sequence source)
        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

      • getTaxon

        public Taxon getTaxon()
        Specified by:
        getTaxon in interface Sequence
        Returns:
        that taxon that this sequence represents

      • compareTo

        public int compareTo​(java.lang.Object o)
        Specified by:
        compareTo in interface java.lang.Comparable

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • 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