pal.datatype
Class StateRemover

java.lang.Object
  extended by pal.datatype.SimpleDataType
      extended by pal.datatype.StateRemover
All Implemented Interfaces:
java.io.Serializable, DataType

public class StateRemover
extends SimpleDataType
implements java.io.Serializable

A standard data type, but with characters removed

Version:
$Id: StateRemover.java,v 1.14 2003/03/23 00:04:23 matt Exp $
Author:
Matthew Goode
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
 
Field Summary
 
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
StateRemover(DataType toAdjust, int[] statesToRemove)
          A translation array -> originalToAdjusted_["adjusted State"] = "original state"
 
Method Summary
protected  char getCharImpl(int state)
          Get character corresponding to a given 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.
 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
 

Constructor Detail

StateRemover

public StateRemover(DataType toAdjust,
                    int[] statesToRemove)
A translation array -> originalToAdjusted_["adjusted State"] = "original state"

Method Detail

getNumStates

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

Specified by:
getNumStates in interface DataType
Returns:
number of unique states

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

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)
Get character corresponding to a given state

Specified by:
getCharImpl in class SimpleDataType

getDescription

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

Specified by:
getDescription in interface DataType
Returns:
string describing the data type

getTypeID

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

Specified by:
getTypeID in interface DataType
Returns:
numerical code