Package pal.datatype
Class GapBalanced
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.GapBalanced
- All Implemented Interfaces:
Serializable
,DataType
,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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType
MolecularDataType.Utils
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Field Summary
FieldsFields 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected char
getCharImpl
(int state) description of data typefinal 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)final int[]
getMolecularStatesFromSimpleNucleotides
(int[] nucleotideStates, int startingIndex) final int
int[]
getNucleotideStates
(int[] residueStates) int
get number of unique statesint
getStateImpl
(char c) For sub classes to implement main functionality of getState.int
get numerical code describing the data typeboolean
protected final boolean
isUnknownStateImpl
(int state) For subclasses to handle, without regard for gapsMethods 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
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Field Details
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DEFAULT_INSTANCE
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Constructor Details
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GapBalanced
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Method Details
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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
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 -
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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