pal.datatype
Class SimpleDataType
java.lang.Object
|
+--pal.datatype.SimpleDataType
- All Implemented Interfaces:
- DataType, java.io.Serializable
- Direct Known Subclasses:
- AminoAcids, Codons, GeneralizedCodons, Nucleotides, NumericDataType, StateRemover, TwoStates
- public abstract class SimpleDataType
- extends java.lang.Object
- implements DataType
interface for sequence data types
- See Also:
- Serialized Form
Fields inherited from interface pal.datatype.DataType |
AMINO_ACID_DESCRIPTION, AMINOACIDS, CODON_DESCRIPTION, CODONS, GENERALIZED_CODONS_DESCRIPTION, GENERALIZEDCODONS, IUPAC_NUCELOTIDES_DESCRIPTION, IUPACNUCLEOTIDES, NUCLEOTIDE_DESCRIPTION, NUCLEOTIDES, TWO_STATE_DESCRIPTION, TWOSTATES, UNKNOWN_CHARACTER |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SimpleDataType
public SimpleDataType()
isAmbiguousState
public final boolean isAmbiguousState(int state)
- returns true if this state is an ambiguous state.
- Specified by:
isAmbiguousState
in interface DataType
getSimpleStates
public final int[] getSimpleStates(int state)
- returns an array containing the non-ambiguous states that this state represents.
- Specified by:
getSimpleStates
in interface DataType
getNumSimpleStates
public final int getNumSimpleStates()
- get number of unique non-ambiguous states
- Specified by:
getNumSimpleStates
in interface DataType
- Returns:
- number of unique states
isGapChar
public boolean isGapChar(char c)
- Returns:
- true if this state is a gap
isUnknownChar
public boolean isUnknownChar(char c)
- Specified by:
isUnknownChar
in interface DataType
- Returns:
- true if this state is a gap
isUnknownState
public boolean isUnknownState(int state)
- Specified by:
isUnknownState
in interface DataType
- Following copied from interface:
pal.datatype.DataType
- Returns:
- true if this state is an unknown state
(the same as check if a state is >= the number of states... but neater)