pal.datatype
public class StateRemover extends SimpleDataType implements java.io.Serializable
DataType.Utils
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 and Description |
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StateRemover(DataType toAdjust,
int[] statesToRemove)
A translation array -> originalToAdjusted_["adjusted State"] = "original state"
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Modifier and Type | Method and Description |
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protected char |
getCharImpl(int state)
Get character corresponding to a given state
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java.lang.String |
getDescription()
description of data type
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int |
getNumStates()
get number of unique states
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protected int |
getStateImpl(char c)
For sub classes to implement main functionality of getState.
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int |
getTypeID()
get numerical code describing the data type
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protected boolean |
isUnknownStateImpl(int state)
For subclasses to handle, without regard for gaps
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getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, toString
public StateRemover(DataType toAdjust, int[] statesToRemove)
public int getNumStates()
DataType
getNumStates
in interface DataType
protected final boolean isUnknownStateImpl(int state)
SimpleDataType
isUnknownStateImpl
in class SimpleDataType
protected int getStateImpl(char c)
SimpleDataType
getStateImpl
in class SimpleDataType
protected char getCharImpl(int state)
getCharImpl
in class SimpleDataType
public java.lang.String getDescription()
DataType
getDescription
in interface DataType