uk.ac.ebi.pridemod.io.slimmod.model

Class SlimModCollection

java.lang.Object

uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

All Implemented Interfaces:

Iterable<SlimModification>, Collection<SlimModification>, List<SlimModification>

public class SlimModCollection
extends Object
implements List<SlimModification>

Class that contains a List and methods to retrieve the information from a List of Slim Modifications.

Constructor Summary

Constructors

Constructor and Description
SlimModCollection() Constructor that create a new List of Slim modifications
SlimModCollection(List<SlimModification> modCollection) Constructor that create an instance of the SlimModCollection class and initializes the collection of slim modification with the parameter.

Method Summary

Methods

Modifier and Type	Method and Description
void	add(int index, SlimModification element) Add an Slim Modification in the list in an specific position (index)
boolean	add(SlimModification mod) Add an slim modification to the list of modifications
boolean	addAll(Collection<? extends SlimModification> c) Add a collection of slim modifications to the current list of slim modifications.
boolean	addAll(int index, Collection<? extends SlimModification> c) Add a collection of slim modifications from the index integer
void	clear() Clear the List of modifications
boolean	contains(Object o) Verified if a Modification exist in the List of the current modifications.
boolean	containsAll(Collection<?> c) Compare if a list of slim modifications are included in the List of modifications
SlimModification	get(int index) Get a modification in the list.
SlimModCollection	getbyDelta(double deltaMass, double difference) This method return an object of SlimCollection with a list of the slim modifications by a given mass and small windows or error between the delta mass of the modifications and the parameter deltaMass.
SlimModification	getbyName(String name) Get the list of slim modifications compare only with the default specificity of each modification.
SlimModCollection	getbySpecificity(Specificity.AminoAcid specificity) This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities.
SlimModCollection	getbySpecificity(Specificity.AminoAcid specificity, double mass, double difference) This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.
SlimModCollection	getbySpecificity(String nameSpecificity) This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities.
SlimModCollection	getbySpecificity(String nameSpecificity, double mass, double difference) This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.
int	indexOf(Object o) Index of the Object slim modification in the List of modifications
boolean	isEmpty() Get if the modification list is Empty.
Iterator<SlimModification>	iterator() An iterator through the modification List
int	lastIndexOf(Object o) Index after the element passed by parameters in the list
ListIterator<SlimModification>	listIterator() Get List of Iterator of the List of modifications
ListIterator<SlimModification>	listIterator(int index) Get List of Iterator of the List of modifications from specific position
SlimModification	remove(int index) Remove an slim object from the list of slim modification by index.
boolean	remove(Object o) Remove an modification passed by parameters from the List of modifications
boolean	removeAll(Collection<?> c) Remove a collection of slim modifications from the current List of slim modifications
boolean	retainAll(Collection<?> c)
SlimModification	set(int index, SlimModification element) Set slim modification with the value passed by parameter element in the position index of the list.
int	size() Get the size of the modification List.
List<SlimModification>	subList(int fromIndex, int toIndex) Get a collection of modification between to indexes.
Object[]	toArray() Convert the current List to an Array of Objects
<T> T[]	toArray(T[] a)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

equals, hashCode

Constructor Detail

SlimModCollection

public SlimModCollection()

Constructor that create a new List of Slim modifications

SlimModCollection

public SlimModCollection(List<SlimModification> modCollection)

Constructor that create an instance of the SlimModCollection class and initializes the collection of slim modification with the parameter.

Parameters:

modCollection -

Method Detail

getbyDelta

public SlimModCollection getbyDelta(double deltaMass,
                           double difference)

This method return an object of SlimCollection with a list of the slim modifications by a given mass and small windows or error between the delta mass of the modifications and the parameter deltaMass.

Parameters:

deltaMass - the value of the delta mass to filter modifications.

difference - an small error allowed between the mass and the param deltaMass.

Returns:

an object SlimModCollection with all of the modification that pass the filter.

getbySpecificity

public SlimModCollection getbySpecificity(Specificity.AminoAcid specificity)

This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities.

Parameters:

specificity - the specificity to looking in the List of specificities in each modification

Returns:

an object SlimModCollection with all of the modification that pass the filter.

getbySpecificity

public SlimModCollection getbySpecificity(String nameSpecificity)

This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities. The parameter used is the string representation in one character of the amino acids (K or R or H..).

Parameters:

nameSpecificity - String one character representation of Amino Acids.

Returns:

an object SlimModCollection with all of the modification that pass the filter.

getbySpecificity

public SlimModCollection getbySpecificity(Specificity.AminoAcid specificity,
                                 double mass,
                                 double difference)

This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.

Parameters:

specificity - an specificity in the form of class Specificity

mass - the delta mass

difference - the difference or error between the parameter mass and the delta mas of each modification.

Returns:

an object SlimModCollection with all of the modification that pass the filter.

getbySpecificity

public SlimModCollection getbySpecificity(String nameSpecificity,
                                 double mass,
                                 double difference)

This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.

Parameters:

nameSpecificity - an specificity in the form of String.

mass - the delta mass

difference - the difference or error between the parameter mass and the delta mas of each modification.

Returns:

an object SlimModCollection with all of the modification that pass the filter.

getbyName

public SlimModification getbyName(String name)

Get the list of slim modifications compare only with the default specificity of each modification.

Parameters:

name - the name of the modification.

Returns:

an object SlimModification.

add

public boolean add(SlimModification mod)

Add an slim modification to the list of modifications

Specified by:

add in interface Collection<SlimModification>

Specified by:

add in interface List<SlimModification>

Parameters:

mod - new modification

Returns:

size

public int size()

Get the size of the modification List.

Specified by:

size in interface Collection<SlimModification>

Specified by:

size in interface List<SlimModification>

Returns:

isEmpty

public boolean isEmpty()

Get if the modification list is Empty.

Specified by:

isEmpty in interface Collection<SlimModification>

Specified by:

isEmpty in interface List<SlimModification>

Returns:

contains

public boolean contains(Object o)

Verified if a Modification exist in the List of the current modifications.

Specified by:

contains in interface Collection<SlimModification>

Specified by:

contains in interface List<SlimModification>

Parameters:

o - generic slim modification object

Returns:

iterator

public Iterator<SlimModification> iterator()

An iterator through the modification List

Specified by:

iterator in interface Iterable<SlimModification>

Specified by:

iterator in interface Collection<SlimModification>

Specified by:

iterator in interface List<SlimModification>

Returns:

toArray

public Object[] toArray()

Convert the current List to an Array of Objects

Specified by:

toArray in interface Collection<SlimModification>

Specified by:

toArray in interface List<SlimModification>

Returns:

toArray

public <T> T[] toArray(T[] a)

Specified by:

toArray in interface Collection<SlimModification>

Specified by:

toArray in interface List<SlimModification>

Type Parameters:

T -

Parameters:

a -

Returns:

remove

public boolean remove(Object o)

Remove an modification passed by parameters from the List of modifications

Specified by:

remove in interface Collection<SlimModification>

Specified by:

remove in interface List<SlimModification>

Parameters:

o - modification

Returns:

containsAll

public boolean containsAll(Collection<?> c)

Compare if a list of slim modifications are included in the List of modifications

Specified by:

containsAll in interface Collection<SlimModification>

Specified by:

containsAll in interface List<SlimModification>

Parameters:

c - a collection of objects

Returns:

addAll

public boolean addAll(Collection<? extends SlimModification> c)

Add a collection of slim modifications to the current list of slim modifications.

Specified by:

addAll in interface Collection<SlimModification>

Specified by:

addAll in interface List<SlimModification>

Parameters:

c - collection of slim modifications

Returns:

removeAll

public boolean removeAll(Collection<?> c)

Remove a collection of slim modifications from the current List of slim modifications

Specified by:

removeAll in interface Collection<SlimModification>

Specified by:

removeAll in interface List<SlimModification>

Parameters:

c - collection of slim modifications

Returns:

retainAll

public boolean retainAll(Collection<?> c)

Specified by:

retainAll in interface Collection<SlimModification>

Specified by:

retainAll in interface List<SlimModification>

Parameters:

c -

Returns:

clear

public void clear()

Clear the List of modifications

Specified by:

clear in interface Collection<SlimModification>

Specified by:

clear in interface List<SlimModification>

addAll

public boolean addAll(int index,
             Collection<? extends SlimModification> c)

Add a collection of slim modifications from the index integer

Specified by:

addAll in interface List<SlimModification>

Parameters:

index - an index of the first position to add slim modifications.

c - a collection of the slim modifications to add to the list.

Returns:

get

public SlimModification get(int index)

Get a modification in the list.

Specified by:

get in interface List<SlimModification>

Parameters:

index - the position of the slim modification to return

Returns:

set

public SlimModification set(int index,
                   SlimModification element)

Set slim modification with the value passed by parameter element in the position index of the list.

Specified by:

set in interface List<SlimModification>

Parameters:

index -

element -

Returns:

add

public void add(int index,
       SlimModification element)

Add an Slim Modification in the list in an specific position (index)

Specified by:

add in interface List<SlimModification>

Parameters:

index - position to add the slim modification in the list.

element - an slim modification

remove

public SlimModification remove(int index)

Remove an slim object from the list of slim modification by index.

Specified by:

remove in interface List<SlimModification>

Parameters:

index -

Returns:

indexOf

public int indexOf(Object o)

Index of the Object slim modification in the List of modifications

Specified by:

indexOf in interface List<SlimModification>

Parameters:

o -

Returns:

lastIndexOf

public int lastIndexOf(Object o)

Index after the element passed by parameters in the list

Specified by:

lastIndexOf in interface List<SlimModification>

Parameters:

o -

Returns:

listIterator

public ListIterator<SlimModification> listIterator()

Get List of Iterator of the List of modifications

Specified by:

listIterator in interface List<SlimModification>

Returns:

listIterator

public ListIterator<SlimModification> listIterator(int index)

Get List of Iterator of the List of modifications from specific position

Specified by:

listIterator in interface List<SlimModification>

Parameters:

index -

Returns:

subList

public List<SlimModification> subList(int fromIndex,
                             int toIndex)

Get a collection of modification between to indexes.

Specified by:

subList in interface List<SlimModification>

Parameters:

fromIndex -

toIndex -

Returns: