pal.datatype
Class StateRemover

java.lang.Object
  pal.datatype.SimpleDataType
      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