pal.datatype
Class GapBalanced

java.lang.Object
  pal.datatype.SimpleDataType
      pal.datatype.GapBalanced

All Implemented Interfaces:

java.io.Serializable, DataType, MolecularDataType

public class GapBalanced
extends SimpleDataType
implements MolecularDataType

implements a ResidueDataType for GapBalanced notation. The terminate character IS included as a state

Version:

$Id: GapBalanced.java,v 1.6 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.MolecularDataType

MolecularDataType.Utils

Field Summary

static GapBalanced

DEFAULT_INSTANCE

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

GapBalanced(CodonTable translationTable)

Method Summary

protected char	getCharImpl(int state)
java.lang.String	getDescription() description of data type
int[]	getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex) Currently converts ambiguous states to a simple version (IE takes the first possible simple state for the ambiguous state)
int[]	getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
int	getNucleotideLength()
int[]	getNucleotideStates(int[] residueStates)
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
boolean	isCreatesIUPACNuecleotides()
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

Methods inherited from interface pal.datatype.DataType

getAmbiguousVersion, getChar, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState

Field Detail

DEFAULT_INSTANCE

public static final GapBalanced DEFAULT_INSTANCE

Constructor Detail

GapBalanced

public GapBalanced(CodonTable translationTable)

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

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

getCharImpl

protected char getCharImpl(int state)

Specified by:

getCharImpl 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

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

getNucleotideStates

public int[] getNucleotideStates(int[] residueStates)

Specified by:

getNucleotideStates in interface MolecularDataType

Parameters:

residueStates - an array of states corresponding to states of this datatype

Returns:

the corresponding IUPAC states

getMolecularStatesFromIUPACNucleotides

public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates,
                                                          int startingIndex)

Currently converts ambiguous states to a simple version (IE takes the first possible simple state for the ambiguous state)

Specified by:

getMolecularStatesFromIUPACNucleotides in interface MolecularDataType

getMolecularStatesFromSimpleNucleotides

public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates,
                                                           int startingIndex)

Specified by:

getMolecularStatesFromSimpleNucleotides in interface MolecularDataType

Returns:

isCreatesIUPACNuecleotides

public boolean isCreatesIUPACNuecleotides()

Specified by:

isCreatesIUPACNuecleotides in interface MolecularDataType

Returns:

true

getNucleotideLength

public final int getNucleotideLength()

Specified by:

getNucleotideLength in interface MolecularDataType

Returns:

1