pal.datatype
Class AminoAcids

java.lang.Object
  extended by pal.datatype.SimpleDataType
      extended by pal.datatype.AminoAcids
All Implemented Interfaces:
java.io.Serializable, DataType
Direct Known Subclasses:
SpecificAminoAcids

public class AminoAcids
extends SimpleDataType

implements DataType for amino acids

Version:
$Id: AminoAcids.java,v 1.19 2003/03/23 00:04:23 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond, Matthew Goode
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
 
Field Summary
static AminoAcids DEFAULT_INSTANCE
           
static char TERMINATE_CHARACTER
           
static int TERMINATE_STATE
           
 
Fields inherited from interface pal.datatype.DataType
AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GAP_BALANCED, GAP_BALANCED_DESCRIPTION, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, NUMERIC, PRIMARY_SUGGESTED_GAP_CHARACTER, SUGGESTED_GAP_CHARACTERS, SUGGESTED_GAP_STATE, SUGGESTED_UNKNOWN_STATE, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN, UNKNOWN_CHARACTER, UNKNOWN_TLA
 
Constructor Summary
AminoAcids()
           
 
Method Summary
protected  char getCharImpl(int state)
           
 java.lang.String getDescription()
          description of data type
 int getNumStates()
          get number of unique states
protected  int getStateImpl(char c)
          For sub classes to implement main functionality of getState.
static java.lang.String getTLA(int state)
           
 int getTypeID()
          get numerical code describing the data type
protected  boolean isUnknownStateImpl(int state)
          For subclasses to handle, without regard for gaps
 
Methods inherited from class pal.datatype.SimpleDataType
getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

DEFAULT_INSTANCE

public static final AminoAcids DEFAULT_INSTANCE

TERMINATE_CHARACTER

public static final char TERMINATE_CHARACTER
See Also:
Constant Field Values

TERMINATE_STATE

public static final int TERMINATE_STATE
See Also:
Constant Field Values
Constructor Detail

AminoAcids

public AminoAcids()
Method Detail

getNumStates

public int getNumStates()
Description copied from interface: DataType
get number of unique states

Returns:
number of unique states

getStateImpl

protected int getStateImpl(char c)
Description copied from class: SimpleDataType
For sub classes to implement main functionality of getState. Gaps do not need to be considered

Specified by:
getStateImpl in class SimpleDataType

getCharImpl

protected char getCharImpl(int state)
Specified by:
getCharImpl in class SimpleDataType

isUnknownStateImpl

protected boolean isUnknownStateImpl(int state)
Description copied from class: SimpleDataType
For subclasses to handle, without regard for gaps

Specified by:
isUnknownStateImpl in class SimpleDataType

getDescription

public java.lang.String getDescription()
Description copied from interface: DataType
description of data type

Returns:
string describing the data type

getTypeID

public int getTypeID()
Description copied from interface: DataType
get numerical code describing the data type

Returns:
numerical code

getTLA

public static final java.lang.String getTLA(int state)
Returns:
a three letter acronym for an AminoAcid, according to state