pal.datatype
Interface AmbiguousDataType
- All Superinterfaces:
- DataType, java.io.Serializable
- All Known Implementing Classes:
- IUPACNucleotides
public interface AmbiguousDataType
- extends DataType
Additional interface information for data types which represent ambiguity in
sub types.
- Version:
- $Id: AmbiguousDataType.java,v 1.1 2002/11/25 05:38:40 matt Exp $
- Author:
- Matthew Goode
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 |
Method Summary |
void |
getAmbiguity(int ambiguousState,
boolean[] specificInclusion)
Attempts to "resolve" the ambiguity in a state with regard to the specific data type. |
void |
getAmbiguity(int ambiguousState,
double[] specificInclusion)
A more accurate attempt to "resolve" the ambiguity in a state with regard to the specific data type. |
DataType |
getSpecificDataType()
|
int[] |
getSpecificStates(int ambiguousState)
returns an array containing the non-ambiguous states that this state represents. |
Methods inherited from interface pal.datatype.DataType |
getAmbiguousVersion, getChar, getDescription, getNumStates, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, getTypeID, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState |
getSpecificStates
int[] getSpecificStates(int ambiguousState)
- returns an array containing the non-ambiguous states that this state represents.
getSpecificDataType
DataType getSpecificDataType()
- Returns:
- the DataType that this datatype is the Ambiguous Version of.
getAmbiguity
void getAmbiguity(int ambiguousState,
boolean[] specificInclusion)
- Attempts to "resolve" the ambiguity in a state with regard to the specific data type.
- Parameters:
ambiguousState
- the state of this data type (the ambiguous one!)specificInclusion
- An array of length equal to or greater than the number of states of
the specific DataType. Each state of the specific data type is represented by the corresponding
element in this array. The result of this method will be to set the states that the ambiguous state cannot
represent to false, and those states that the ambiguous state might represent to true.
getAmbiguity
void getAmbiguity(int ambiguousState,
double[] specificInclusion)
- A more accurate attempt to "resolve" the ambiguity in a state with regard to the specific data type.
- Parameters:
ambiguousState
- the state of this data type (the ambiguous one!)specificInclusion
- An array of length equal to or greater than the number of states of
the specific DataType. Each state of the specific data type is represented by the corresponding
element in this array. The result of this method will be to set the states that the ambiguous state cannot
represent to zero, and those states that the ambiguous state might represent to a value representing the frequency that the ambiguous state is actually that specific state. In general this should be one for
each specific state covered by the ambiguous state (result should be suitable for use in likelihood calculations).