Nucleotide (com.hfg API Documentation)

java.lang.Object
- com.hfg.chem.Molecule
- - com.hfg.bio.Nucleotide

All Implemented Interfaces:

Matter, HfgXMLSerializable, Cloneable, Comparable
```
public class Nucleotide
extends Molecule
```
Nucleotide.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Nucleotide.BaseType

Nested Classes
Modifier and Type	Class and Description
`static class`	`Nucleotide.BaseType`

Field Summary

Fields
Modifier and Type	Field and Description
`static Nucleotide`	`ADENINE`
`static Nucleotide`	`B`
`static Nucleotide`	`CYTOSINE`
`static Nucleotide`	`D`
`static Nucleotide`	`GUANINE`
`static Nucleotide`	`H`
`static Nucleotide`	`K`
`static Nucleotide`	`M`
`static Nucleotide`	`N`
`static Nucleotide`	`R`
`static Nucleotide`	`S`
`static Nucleotide`	`THYMINE`
`static Nucleotide`	`URACIL`
`static Nucleotide`	`V`
`static Nucleotide`	`W`
`static Nucleotide`	`Y`

Fields inherited from class com.hfg.chem.Molecule
H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors
Constructor and Description
`Nucleotide(String inName)`
`Nucleotide(String inName, char in1LetterCode)`
`Nucleotide(String inName, char in1LetterCode, Nucleotide.BaseType inBaseType)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Nucleotide`	`addDegeneracy(Nucleotide inValue)`
`Nucleotide`	`clone()` Returns an unlocked copy of the Nucleotide.
`static Nucleotide[]`	`degenerateValues()`
`Nucleotide.BaseType`	`getBaseType()`
`Nucleotide`	`getComplement()`
`Collection<Nucleotide>`	`getDegeneracy()`
`String`	`getDegeneracyAsString()`
`Character`	`getOneLetterCode()`
`boolean`	`isAmbiguous()`
`Nucleotide`	`lock()`
`Nucleotide`	`register()` Puts the Nucleotide into the Set of unique Nucleotides returned by Nucleotide.values().
`static Nucleotide`	`valueOf(char inChar)` Returns the Nucleotide whose 1-letter code matches the specified String.
`static Nucleotide`	`valueOf(String inString)` Returns the Nucleotide whose name or 1-letter code matches the specified String.
`static Nucleotide[]`	`values()`

Methods inherited from class com.hfg.chem.Molecule
add, add, addAtom, addAtoms, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearCalculatedProperties, clearElementalComposition, compareTo, equals, formatMassString, getAtoms, getAttribute, getAttributeNames, getAverageMass, getChemicalFormula, getChemicalFormulaWithSubscripts, getElementalComposition, getKas, getLastAtom, getMonoisotopicMass, getOrganicAverageMass, getPhysicalProperty, hasAttribute, hasAttributes, hashCode, isLocked, massesAreUserSet, name, remove, remove, removeAttribute, setAttribute, setAverageMass, setChemicalFormula, setElementalComposition, setMonoisotopicMass, setName, setOrganicAverageMass, setPhysicalProperty, toString, toXMLNode

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

ADENINE
```
public static final Nucleotide ADENINE
```

GUANINE
```
public static final Nucleotide GUANINE
```

CYTOSINE

public static final Nucleotide CYTOSINE

THYMINE
```
public static final Nucleotide THYMINE
```

URACIL
```
public static final Nucleotide URACIL
```

W
```
public static final Nucleotide W
```

S
```
public static final Nucleotide S
```

M
```
public static final Nucleotide M
```

K
```
public static final Nucleotide K
```

R
```
public static final Nucleotide R
```

Y
```
public static final Nucleotide Y
```

B
```
public static final Nucleotide B
```

D
```
public static final Nucleotide D
```

H
```
public static final Nucleotide H
```

V
```
public static final Nucleotide V
```

N
```
public static final Nucleotide N
```

Constructor Detail

Nucleotide
```
public Nucleotide(String inName)
```

Nucleotide

public Nucleotide(String inName,
                  char in1LetterCode)

Nucleotide

public Nucleotide(String inName,
                  char in1LetterCode,
                  Nucleotide.BaseType inBaseType)

Method Detail
- lock
```
public Nucleotide lock()
```
  Overrides:
  
  lock in class Molecule
- register
```
public Nucleotide register()
```
  Puts the Nucleotide into the Set of unique Nucleotides returned by Nucleotide.values().
- valueOf
```
public static Nucleotide valueOf(String inString)
```
  Returns the Nucleotide whose name or 1-letter code matches the specified String.
  
  Parameters:
  
  inString - the name or 1-letter code for the Nucleotide to retrieve
  
  Returns:
  
  the Nucleotide whose name or 1-letter code matches the specified String
- valueOf
```
public static Nucleotide valueOf(char inChar)
```
  Returns the Nucleotide whose 1-letter code matches the specified String.
  
  Parameters:
  
  inChar - the 1-letter code for the Nucleotide to retrieve
  
  Returns:
  
  the Nucleotide whose 1-letter code matches the specified String
- values
```
public static Nucleotide[] values()
```
- degenerateValues
```
public static Nucleotide[] degenerateValues()
```
- clone
```
public Nucleotide clone()
```
  Returns an unlocked copy of the Nucleotide.
  
  Overrides:
  
  clone in class Molecule
  
  Returns:
  
  an unlocked copy of the Molecule
- getBaseType
```
public Nucleotide.BaseType getBaseType()
```
- getOneLetterCode
```
public Character getOneLetterCode()
```
- getComplement
```
public Nucleotide getComplement()
```
- addDegeneracy
```
public Nucleotide addDegeneracy(Nucleotide inValue)
```
- getDegeneracy
```
public Collection<Nucleotide> getDegeneracy()
```
- getDegeneracyAsString
```
public String getDegeneracyAsString()
```
- isAmbiguous
```
public boolean isAmbiguous()
```

Class Nucleotide

Nested Class Summary

Field Summary

Fields inherited from class com.hfg.chem.Molecule

Constructor Summary

Method Summary

Methods inherited from class com.hfg.chem.Molecule

Methods inherited from class java.lang.Object

Field Detail

ADENINE

GUANINE

CYTOSINE

THYMINE

URACIL

W

S

M

K

R

Y

B

D

H

V

N

Constructor Detail

Nucleotide

Nucleotide

Nucleotide

Method Detail

lock

register

valueOf

valueOf

values

degenerateValues

clone

getBaseType

getOneLetterCode

getComplement

addDegeneracy

getDegeneracy

getDegeneracyAsString

isAmbiguous