Package pal.datatype
Class GapBalanced
- java.lang.Object
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- pal.datatype.SimpleDataType
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- pal.datatype.GapBalanced
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
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Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType
MolecularDataType.Utils
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Field Summary
Fields Modifier and Type Field Description static GapBalanced
DEFAULT_INSTANCE
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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
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Constructor Summary
Constructors Constructor Description GapBalanced(CodonTable translationTable)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected char
getCharImpl(int state)
java.lang.String
getDescription()
description of data typeint[]
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 statesint
getStateImpl(char c)
For sub classes to implement main functionality of getState.int
getTypeID()
get numerical code describing the data typeboolean
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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.datatype.DataType
getAmbiguousVersion, getChar, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState
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Field Detail
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DEFAULT_INSTANCE
public static final GapBalanced DEFAULT_INSTANCE
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Constructor Detail
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GapBalanced
public GapBalanced(CodonTable translationTable)
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Method Detail
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getNumStates
public int getNumStates()
Description copied from interface:DataType
get number of unique states- Specified by:
getNumStates
in interfaceDataType
- Returns:
- number of unique states
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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 classSimpleDataType
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getCharImpl
protected char getCharImpl(int state)
- Specified by:
getCharImpl
in classSimpleDataType
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isUnknownStateImpl
protected final boolean isUnknownStateImpl(int state)
Description copied from class:SimpleDataType
For subclasses to handle, without regard for gaps- Specified by:
isUnknownStateImpl
in classSimpleDataType
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getDescription
public java.lang.String getDescription()
Description copied from interface:DataType
description of data type- Specified by:
getDescription
in interfaceDataType
- Returns:
- string describing the data type
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getTypeID
public int getTypeID()
Description copied from interface:DataType
get numerical code describing the data type
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getNucleotideStates
public int[] getNucleotideStates(int[] residueStates)
- Specified by:
getNucleotideStates
in interfaceMolecularDataType
- Parameters:
residueStates
- an array of states corresponding to states ofthis datatype- Returns:
- the corresponding IUPAC states
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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 interfaceMolecularDataType
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getMolecularStatesFromSimpleNucleotides
public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
- Specified by:
getMolecularStatesFromSimpleNucleotides
in interfaceMolecularDataType
- Returns:
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isCreatesIUPACNuecleotides
public boolean isCreatesIUPACNuecleotides()
- Specified by:
isCreatesIUPACNuecleotides
in interfaceMolecularDataType
- Returns:
- true
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getNucleotideLength
public final int getNucleotideLength()
- Specified by:
getNucleotideLength
in interfaceMolecularDataType
- Returns:
- 1
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