C
- Type of compound this set will contain but must extend
NucleotideCompoundCompoundSet<C>
DNACompoundSet
, RNACompoundSet
public abstract class AbstractNucleotideCompoundSet<C extends NucleotideCompound> extends AbstractCompoundSet<C>
Constructor | Description |
---|---|
AbstractNucleotideCompoundSet() |
Modifier and Type | Method | Description |
---|---|---|
protected void |
addNucleotideCompound(java.lang.String base,
java.lang.String complement,
java.lang.String... equivalents) |
|
protected void |
calculateIndirectAmbiguities() |
Loops through all known nucleotides and attempts to find which are
equivalent to each other.
|
NucleotideCompound |
getAmbiguity(NucleotideCompound... compounds) |
Calculates the best symbol for a collection of compounds.
|
boolean |
isComplementable() |
NucleotideCompounds can always complement
|
protected abstract C |
newNucleotideCompound(java.lang.String base,
java.lang.String complement,
java.lang.String... equivalents) |
addCompound, addCompound, addCompound, addEquivalent, compoundsEqual, compoundsEquivalent, equals, getAllCompounds, getCompoundForString, getEquivalentCompounds, getMaxSingleCompoundStringLength, getStringForCompound, hasCompound, hashCode, isCompoundStringLengthEqual, isValidSequence
protected void addNucleotideCompound(java.lang.String base, java.lang.String complement, java.lang.String... equivalents)
protected abstract C newNucleotideCompound(java.lang.String base, java.lang.String complement, java.lang.String... equivalents)
protected void calculateIndirectAmbiguities()
public NucleotideCompound getAmbiguity(NucleotideCompound... compounds)
compounds
- Compounds to calculate ambiguity forpublic boolean isComplementable()
isComplementable
in interface CompoundSet<C extends NucleotideCompound>
isComplementable
in class AbstractCompoundSet<C extends NucleotideCompound>