Package pal.datatype
Interface MolecularDataType
-
- All Superinterfaces:
DataType
,java.io.Serializable
- All Known Implementing Classes:
Codons
,GapBalanced
,IUPACNucleotides
,Nucleotides
,SpecificAminoAcids
public interface MolecularDataType extends DataType
An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).- Version:
- 1.1
- Author:
- Matthew Goode
-
-
Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
MolecularDataType.Utils
Utilities relating to MolecularDataType stuff
-
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
-
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description int[]
getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
int[]
getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
int
getNucleotideLength()
int[]
getNucleotideStates(int[] molecularStates)
boolean
isCreatesIUPACNuecleotides()
-
Methods inherited from interface pal.datatype.DataType
getAmbiguousVersion, getChar, getDescription, getNumStates, getPreferredChar, getRecommendedGapState, getRecommendedUnknownState, getState, getTypeID, hasGap, isAmbiguous, isGapChar, isGapState, isUnknownChar, isUnknownState
-
-
-
-
Method Detail
-
getNucleotideStates
int[] getNucleotideStates(int[] molecularStates)
- Parameters:
molecularStates
- an array of states corresponding to states ofthis datatype- Returns:
- the corresponding IUPAC states
-
getMolecularStatesFromIUPACNucleotides
int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
- Parameters:
the
- IUPAC nucleotidestates
-
getMolecularStatesFromSimpleNucleotides
int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
- Parameters:
the
- Simple nucleotide states (eg 0,1,2,3 or A,C,G,T)
-
isCreatesIUPACNuecleotides
boolean isCreatesIUPACNuecleotides()
- Returns:
- true if this data type will create Nucleotide states using IUPAC states (for example if this DataType is AminoAcid based, IUPAC states are needed to maintain information on different possible values for a state)
-
getNucleotideLength
int getNucleotideLength()
- Returns:
- the number of nucleotides required for a single character of this data typedata
-
-