jebl.evolution.sequences
Class State

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

public abstract class State
extends java.lang.Object
implements java.lang.Comparable

Version:
$Id: State.java 1002 2009-05-27 03:33:19Z matt_kearse $
Author:
Andrew Rambaut, Alexei Drummond

Method Summary
 int compareTo(java.lang.Object o)
           
 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.
 java.util.Set<State> getCanonicalStates()
           
 java.lang.String getCode()
          Returns the 1 letter code for this state.
 java.lang.String getFullName()
          A descriptive name for this state.
 int getIndex()
           
 java.lang.String getName()
          Deprecated. you probably want to use getFullName() or getCode().
 boolean isAmbiguous()
           
abstract  boolean isGap()
           
 boolean possiblyEqual(State other)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Method Detail

getCode

public java.lang.String getCode()
Returns the 1 letter code for this state.

Returns:
the 1 letter code for this state.

getIndex

public int getIndex()

getFullName

public java.lang.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 java.lang.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:
getFullName()

isAmbiguous

public boolean isAmbiguous()

getCanonicalStates

public java.util.Set<State> getCanonicalStates()

possiblyEqual

public boolean possiblyEqual(State other)
Parameters:
other - another state to check for the quality 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(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

isGap

public abstract boolean isGap()

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-ambigoues states will 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.


http://code.google.com/p/jebl2/