pal.datatype
Class GapBalanced

java.lang.Object
  extended by pal.datatype.SimpleDataType
      extended by 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