Package pal.datatype
Class StateRemover
java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.StateRemover
- All Implemented Interfaces:
Serializable
,DataType
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.datatype.DataType
DataType.Utils
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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
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Constructor Summary
ConstructorsConstructorDescriptionStateRemover
(DataType toAdjust, int[] statesToRemove) A translation array -> originalToAdjusted_["adjusted State"] = "original state" -
Method Summary
Modifier and TypeMethodDescriptionprotected char
getCharImpl
(int state) Get character corresponding to a given statedescription of data typeint
get number of unique statesprotected int
getStateImpl
(char c) For sub classes to implement main functionality of getState.int
get numerical code describing the data typeprotected 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
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Constructor Details
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StateRemover
A translation array -> originalToAdjusted_["adjusted State"] = "original state"
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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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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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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 classSimpleDataType
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getCharImpl
protected char getCharImpl(int state) Get character corresponding to a given state- Specified by:
getCharImpl
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
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