AminoAcidSet (com.hfg API Documentation)

java.lang.Object
- com.hfg.bio.AminoAcidSet

All Implemented Interfaces:

Cloneable, Iterable<AminoAcid>, Collection<AminoAcid>, Set<AminoAcid>
```
public class AminoAcidSet
extends Object
implements Set<AminoAcid>, Cloneable
```
Mapping of sequence characters to AminoAcids.

Field Summary

Fields
Modifier and Type	Field and Description
`static AminoAcidSet`	`EXTENDED` Contains both upper and lowercase standard mappings plus B, J, and Z ambiguity codes.
`static AminoAcidSet`	`STANDARD` Contains both upper and lowercase standard mappings.
`static AminoAcidSet`	`STANDARD_LC`
`static AminoAcidSet`	`STANDARD_UC`

Constructor Summary

Constructors
Constructor and Description

AminoAcidSet()

AminoAcidSet(AminoAcidSet inAASet)

Constructors
Constructor and Description
`AminoAcidSet()`
`AminoAcidSet(AminoAcidSet inAASet)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`add(AminoAcid inAminoAcid)`
`boolean`	`addAll(Collection<? extends AminoAcid> inCollection)`
`void`	`clear()`
`AminoAcidSet`	`clone()`
`boolean`	`contains(Object inObject)`
`boolean`	`containsAll(Collection<?> inCollection)`
`boolean`	`equals(Object inObj2)`
`AminoAcid`	`getAA(char inResidue)`
`AminoAcid`	`getAA(Character inResidue)`
`Collection<AminoAcid>`	`getAminoAcids()`
`CTerminalGroup`	`getCTerminalGroup()`
`Set<Character>`	`getMapping(AminoAcid inAA)`
`String`	`getName()`
`NTerminalGroup`	`getNTerminalGroup()`
`Set<Character>`	`getResidueChars()`
`int`	`hashCode()`
`static AminoAcidSet`	`instantiate(XMLNode inXMLNode)`
`boolean`	`isEmpty()`
`boolean`	`isLocked()`
`Iterator<AminoAcid>`	`iterator()`
`void`	`lock()`
`Iterator<Character>`	`mapIterator()` Returns an iteration of the Characters mapped to amino acids
`AminoAcid`	`remove(Character inChar)`
`boolean`	`remove(Object inObj)`
`boolean`	`removeAll(Collection<?> inCollection)`
`boolean`	`retainAll(Collection<?> inCollection)`
`AminoAcidSet`	`setCTerminalGroup(CTerminalGroup inValue)`
`boolean`	`setMapping(char inChar, AminoAcid inAA)`
`void`	`setMappings(AminoAcidSet inAASet)`
`AminoAcidSet`	`setName(String inValue)`
`AminoAcidSet`	`setNTerminalGroup(NTerminalGroup inValue)`
`int`	`size()`
`AminoAcidSet`	`subtract(AminoAcidSet inAminoAcidSet2)`
`Object[]`	`toArray()`
`<T> T[]`	`toArray(T[] inArray)`
`XMLNode`	`toXMLNode()`

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

Methods inherited from interface java.util.Set
spliterator

Methods inherited from interface java.util.Collection
parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable
forEach

- Field Detail
  - STANDARD_LC
```
public static final AminoAcidSet STANDARD_LC
```
  - STANDARD_UC
```
public static final AminoAcidSet STANDARD_UC
```
  - STANDARD
```
public static final AminoAcidSet STANDARD
```
    Contains both upper and lowercase standard mappings.
  - EXTENDED
```
public static final AminoAcidSet EXTENDED
```
    Contains both upper and lowercase standard mappings plus B, J, and Z ambiguity codes.
- Constructor Detail
  - AminoAcidSet
```
public AminoAcidSet()
```
  - AminoAcidSet
```
public AminoAcidSet(AminoAcidSet inAASet)
```
- Method Detail
  - instantiate
```
public static AminoAcidSet instantiate(XMLNode inXMLNode)
```
  - toXMLNode
```
public XMLNode toXMLNode()
```
  - clone
```
public AminoAcidSet clone()
```
    Overrides:
    
    clone in class Object
  - isLocked
```
public boolean isLocked()
```
  - lock
```
public void lock()
```
  - setName
```
public AminoAcidSet setName(String inValue)
```
  - getName
```
public String getName()
```
  - setNTerminalGroup
```
public AminoAcidSet setNTerminalGroup(NTerminalGroup inValue)
```
  - getNTerminalGroup
```
public NTerminalGroup getNTerminalGroup()
```
  - setCTerminalGroup
```
public AminoAcidSet setCTerminalGroup(CTerminalGroup inValue)
```
  - getCTerminalGroup
```
public CTerminalGroup getCTerminalGroup()
```
  - setMapping
```
public boolean setMapping(char inChar,
                          AminoAcid inAA)
```
  - setMappings
```
public void setMappings(AminoAcidSet inAASet)
```
  - getAminoAcids
```
public Collection<AminoAcid> getAminoAcids()
```
  - mapIterator
```
public Iterator<Character> mapIterator()
```
    Returns an iteration of the Characters mapped to amino acids
    
    Returns:
    
    iteration of the Characters mapped to amino acids
  - getResidueChars
```
public Set<Character> getResidueChars()
```
  - getMapping
```
public Set<Character> getMapping(AminoAcid inAA)
```
  - getAA
```
public AminoAcid getAA(char inResidue)
```
  - getAA
```
public AminoAcid getAA(Character inResidue)
```
  - size
```
public int size()
```
    Specified by:
    
    size in interface Collection<AminoAcid>
    
    Specified by:
    
    size in interface Set<AminoAcid>
  - isEmpty
```
public boolean isEmpty()
```
    Specified by:
    
    isEmpty in interface Collection<AminoAcid>
    
    Specified by:
    
    isEmpty in interface Set<AminoAcid>
  - contains
```
public boolean contains(Object inObject)
```
    Specified by:
    
    contains in interface Collection<AminoAcid>
    
    Specified by:
    
    contains in interface Set<AminoAcid>
  - iterator
```
public Iterator<AminoAcid> iterator()
```
    Specified by:
    
    iterator in interface Iterable<AminoAcid>
    
    Specified by:
    
    iterator in interface Collection<AminoAcid>
    
    Specified by:
    
    iterator in interface Set<AminoAcid>
  - toArray
```
public Object[] toArray()
```
    Specified by:
    
    toArray in interface Collection<AminoAcid>
    
    Specified by:
    
    toArray in interface Set<AminoAcid>
  - toArray
```
public <T> T[] toArray(T[] inArray)
```
    Specified by:
    
    toArray in interface Collection<AminoAcid>
    
    Specified by:
    
    toArray in interface Set<AminoAcid>
  - add
```
public boolean add(AminoAcid inAminoAcid)
```
    Specified by:
    
    add in interface Collection<AminoAcid>
    
    Specified by:
    
    add in interface Set<AminoAcid>
  - remove
```
public boolean remove(Object inObj)
```
    Specified by:
    
    remove in interface Collection<AminoAcid>
    
    Specified by:
    
    remove in interface Set<AminoAcid>
  - containsAll
```
public boolean containsAll(Collection<?> inCollection)
```
    Specified by:
    
    containsAll in interface Collection<AminoAcid>
    
    Specified by:
    
    containsAll in interface Set<AminoAcid>
  - addAll
```
public boolean addAll(Collection<? extends AminoAcid> inCollection)
```
    Specified by:
    
    addAll in interface Collection<AminoAcid>
    
    Specified by:
    
    addAll in interface Set<AminoAcid>
  - retainAll
```
public boolean retainAll(Collection<?> inCollection)
```
    Specified by:
    
    retainAll in interface Collection<AminoAcid>
    
    Specified by:
    
    retainAll in interface Set<AminoAcid>
  - removeAll
```
public boolean removeAll(Collection<?> inCollection)
```
    Specified by:
    
    removeAll in interface Collection<AminoAcid>
    
    Specified by:
    
    removeAll in interface Set<AminoAcid>
  - clear
```
public void clear()
```
    Specified by:
    
    clear in interface Collection<AminoAcid>
    
    Specified by:
    
    clear in interface Set<AminoAcid>
  - equals
```
public boolean equals(Object inObj2)
```
    Specified by:
    
    equals in interface Collection<AminoAcid>
    
    Specified by:
    
    equals in interface Set<AminoAcid>
    
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Specified by:
    
    hashCode in interface Collection<AminoAcid>
    
    Specified by:
    
    hashCode in interface Set<AminoAcid>
    
    Overrides:
    
    hashCode in class Object
  - remove
```
public AminoAcid remove(Character inChar)
```
  - subtract
```
public AminoAcidSet subtract(AminoAcidSet inAminoAcidSet2)
```

Class AminoAcidSet

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Set

Methods inherited from interface java.util.Collection

Methods inherited from interface java.lang.Iterable

Field Detail

STANDARD_LC

STANDARD_UC

STANDARD

EXTENDED

Constructor Detail

AminoAcidSet

AminoAcidSet

Method Detail

instantiate

toXMLNode

clone

isLocked

lock

setName

getName

setNTerminalGroup

getNTerminalGroup

setCTerminalGroup

getCTerminalGroup

setMapping

setMappings

getAminoAcids

mapIterator

getResidueChars

getMapping

getAA

getAA

size

isEmpty

contains

iterator

toArray

toArray

add

remove

containsAll

addAll

retainAll

removeAll

clear

equals

hashCode

remove

subtract