Class State

java.lang.Object
jebl.evolution.sequences.State
All Implemented Interfaces:
Comparable
Direct Known Subclasses:
AminoAcidState, CodonState, NucleotideState

public abstract class State extends Object implements Comparable
Version:
$Id: State.java 1002 2009-05-27 03:33:19Z matt_kearse $
Author:
Andrew Rambaut, Alexei Drummond
  • Method Details

    • getCode

      public String getCode()
      Returns the 1 letter code for this state.
      Returns:
      the 1 letter code for this state.
    • getIndex

      public int getIndex()
    • getFullName

      public String getFullName()
      A descriptive name for this state. e.g. "Phenylalanine" or "Adenine".
      Returns:
      A descriptive name for this state. e.g. "Phenylalanine" or "Adenine".
    • getName

      @Deprecated public String getName()
      Deprecated.
      you probably want to use getFullName() or getCode().
      The 1 letter code (for legacy purposes). Same as getCode()
      Returns:
      The 1 letter code (for legacy purposes). Same as getCode()
      See Also:
    • isAmbiguous

      public boolean isAmbiguous()
    • getCanonicalStates

      public Set<State> getCanonicalStates()
    • possiblyEqual

      public boolean possiblyEqual(State other)
      Parameters:
      other - another state to check for the equality with.
      Returns:
      true if the other state is or possibly is equal to this state, taking ambiguities into account, i.e. if the ambiguity sets of this and the other state intersect.
    • compareTo

      public int compareTo(Object o)
      Specified by:
      compareTo in interface Comparable
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • isGap

      public abstract boolean isGap()
    • getType

      public abstract SequenceType getType()
    • fractionEqual

      public double fractionEqual(State other)
      Determine how much in common these potentially ambigous states have as a fraction between 0 and 1 2 non-ambiguous states will return 0. 2 identical non-ambiguous states will return 1. e.g. for Nucleotides R,A = 0.5 R,G = 0.5 R,M = 0.25
      Parameters:
      other - another state to compare with
      Returns:
      the fraction of canonical states that the 2 potentially ambiguous states have in common between 0 and 1.