Package org.biojava.nbio.core.sequence.template

Class AbstractNucleotideCompoundSet<C extends NucleotideCompound>

java.lang.Object

org.biojava.nbio.core.sequence.template.AbstractCompoundSet<C>

org.biojava.nbio.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:

ABITracerCompoundSet, DNACompoundSet, RNACompoundSet

public abstract class AbstractNucleotideCompoundSet<C extends NucleotideCompound>
extends AbstractCompoundSet<C>

Author:

Andy Yates

Constructor Summary

Constructors

Constructor	Description
AbstractNucleotideCompoundSet()

Method Summary

Modifier and Type	Method	Description
protected void	addNucleotideCompound(String base, String complement, 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(String base, String complement, String... equivalents)

Methods inherited from class org.biojava.nbio.core.sequence.template.AbstractCompoundSet

addCompound, addCompound, addCompound, addEquivalent, compoundsEqual, compoundsEquivalent, equals, getAllCompounds, getCompoundForString, getEquivalentCompounds, getMaxSingleCompoundStringLength, getStringForCompound, hasCompound, hashCode, isCompoundStringLengthEqual, isValidSequence

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractNucleotideCompoundSet

public AbstractNucleotideCompoundSet()

Method Detail

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 nucleotides 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>