AbstractNucleotideCompoundSet

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:

DNACompoundSet, RNACompoundSet
```
public abstract class AbstractNucleotideCompoundSet<C extends NucleotideCompound>
extends AbstractCompoundSet<C>
```
Author:

Andy Yates

Constructor Summary

Constructors
Constructor Description

AbstractNucleotideCompoundSet()

Constructors
Constructor	Description
`AbstractNucleotideCompoundSet()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
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)`

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(java.lang.String base,
                                     java.lang.String complement,
                                     java.lang.String... equivalents)
```
  - newNucleotideCompound
```
protected abstract C newNucleotideCompound(java.lang.String base,
                                           java.lang.String complement,
                                           java.lang.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>

Class AbstractNucleotideCompoundSet<C extends NucleotideCompound>

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

AbstractNucleotideCompoundSet

Method Detail

addNucleotideCompound

newNucleotideCompound

calculateIndirectAmbiguities

getAmbiguity

isComplementable