org.biojava3.core.sequence.template
Class AbstractNucleotideCompoundSet<C extends NucleotideCompound>
java.lang.Object
org.biojava3.core.sequence.template.AbstractCompoundSet<C>
org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet<C>
- Type Parameters:
C
- Type of compound this set will contain but must extend
NucleotideCompound
- All Implemented Interfaces:
- CompoundSet<C>
- Direct Known Subclasses:
- DNACompoundSet, RNACompoundSet
public abstract class AbstractNucleotideCompoundSet<C extends NucleotideCompound>
- extends AbstractCompoundSet<C>
- Author:
- Andy Yates
Methods inherited from class org.biojava3.core.sequence.template.AbstractCompoundSet |
addCompound, addCompound, addCompound, addEquivalent, compoundsEqual, compoundsEquivalent, equals, getAllCompounds, getCompoundForString, getEquivalentCompounds, getMaxSingleCompoundStringLength, getStringForCompound, hasCompound, hashCode, isCompoundStringLengthEqual, verifySequence |
AbstractNucleotideCompoundSet
public AbstractNucleotideCompoundSet()
addNucleotideCompound
protected void addNucleotideCompound(String base,
String complement,
String... equivalents)
newNucleotideCompound
protected abstract C newNucleotideCompound(String base,
String complement,
String... equivalents)
calculateIndirectAmbiguities
protected void calculateIndirectAmbiguities()
- Loops through all known nucelotides and attempts to find which are
equivalent to each other. Also takes into account lower casing
nucleotides as well as upper-cased ones.
getAmbiguity
public NucleotideCompound getAmbiguity(NucleotideCompound... compounds)
- Calculates the best symbol for a collection of compounds. For example
if you gave this method a AC it will return a M which is the ambiguity
symbol for these compounds.
- Parameters:
compounds
- Compounds to calculate ambiguity for
- Returns:
- The ambiguity symbol which represents this set of nucleotides best
isComplementable
public boolean isComplementable()
- NucleotideCompounds can always complement
- Specified by:
isComplementable
in interface CompoundSet<C extends NucleotideCompound>
- Overrides:
isComplementable
in class AbstractCompoundSet<C extends NucleotideCompound>