pal.datatype
Class TwoStates
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.TwoStates
- All Implemented Interfaces:
- java.io.Serializable, DataType
public class TwoStates
- extends SimpleDataType
implements DataType for two-state data
- Version:
- $Id: TwoStates.java,v 1.9 2003/03/23 00:04:23 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
- Serialized Form
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 |
Method Summary |
protected char |
getCharImpl(int state)
|
java.lang.String |
getDescription()
description of data type |
int |
getNumStates()
get number of unique states |
int |
getStateImpl(char c)
For sub classes to implement main functionality of getState. |
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 |
DEFAULT_INSTANCE
public static final TwoStates DEFAULT_INSTANCE
TwoStates
public TwoStates()
getNumStates
public int getNumStates()
- Description copied from interface:
DataType
- get number of unique states
- Returns:
- number of unique states
getStateImpl
public 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
isUnknownStateImpl
protected final boolean isUnknownStateImpl(int state)
- Description copied from class:
SimpleDataType
- For subclasses to handle, without regard for gaps
- Specified by:
isUnknownStateImpl
in class SimpleDataType
getCharImpl
protected char getCharImpl(int state)
- Specified by:
getCharImpl
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