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java.lang.Objectpal.datatype.SimpleDataType
pal.datatype.GapBalanced
public class GapBalanced
implements a ResidueDataType for GapBalanced notation. The terminate character IS included as a state
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.datatype.MolecularDataType |
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MolecularDataType.Utils |
Field Summary | |
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static GapBalanced |
DEFAULT_INSTANCE
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Constructor Summary | |
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GapBalanced(CodonTable translationTable)
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Method Summary | |
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protected char |
getCharImpl(int state)
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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)
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int |
getNucleotideLength()
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int[] |
getNucleotideStates(int[] residueStates)
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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()
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protected boolean |
isUnknownStateImpl(int state)
For subclasses to handle, without regard for gaps |
Methods inherited from class pal.datatype.SimpleDataType |
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getAmbiguousVersion, getChar, getPreferredChar, getPreferredCharImpl, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState, toString |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.datatype.DataType |
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getAmbiguousVersion, getChar, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState |
Field Detail |
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public static final GapBalanced DEFAULT_INSTANCE
Constructor Detail |
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public GapBalanced(CodonTable translationTable)
Method Detail |
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public int getNumStates()
DataType
getNumStates
in interface DataType
public int getStateImpl(char c)
SimpleDataType
getStateImpl
in class SimpleDataType
protected char getCharImpl(int state)
getCharImpl
in class SimpleDataType
protected final boolean isUnknownStateImpl(int state)
SimpleDataType
isUnknownStateImpl
in class SimpleDataType
public java.lang.String getDescription()
DataType
getDescription
in interface DataType
public int getTypeID()
DataType
getTypeID
in interface DataType
public int[] getNucleotideStates(int[] residueStates)
getNucleotideStates
in interface MolecularDataType
residueStates
- an array of states corresponding to states of public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
getMolecularStatesFromIUPACNucleotides
in interface MolecularDataType
public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
getMolecularStatesFromSimpleNucleotides
in interface MolecularDataType
public boolean isCreatesIUPACNuecleotides()
isCreatesIUPACNuecleotides
in interface MolecularDataType
public final int getNucleotideLength()
getNucleotideLength
in interface MolecularDataType
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