Package adams.data.container

Class AbstractDataContainer<T extends DataPoint>

java.lang.Object

adams.data.container.AbstractDataContainer<T>

Type Parameters:

T - the type of the container

All Implemented Interfaces:

CloneHandler, Mergeable<DataContainer>, UniqueIDHandler, DataContainer<T>, IDHandler, MutableIDHandler, Serializable, Comparable, Iterable<T>, Collection<T>

Direct Known Subclasses:

Instance, SpreadSheetRow, Timeseries, XYSequence

public abstract class AbstractDataContainer<T extends DataPoint>
extends Object
implements DataContainer<T>, MutableIDHandler

Superclass for all data structures.

Version:

$Revision$

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected String	m_ID	the ID of the sequence.
protected ArrayList<T>	m_Points	the data points.
protected long	m_UUID	the unique ID.

Constructor Summary

Constructors

Constructor	Description
AbstractDataContainer()	Initializes the container.

Method Summary

Modifier and Type	Method	Description
boolean	add(T point)	Adds the point to the list of points.
boolean	addAll(Collection points)	Adds all the points to the list of points.
void	assign(DataContainer<T> other)	Obtains the stored variables from the other data point, but not the actual data points.
void	clear()	Removes all the points.
int	compareTo(Object o)	Compares this object with the specified object for order.
int	compareToData(Object o)	Compares this object with the specified object for order.
int	compareToHeader(Object o)	Compares this object with the specified object for order.
boolean	contains(Object point)	Checks whether the given point is already stored.
boolean	containsAll(Collection points)	Checks whether all the given points are already stored.
void	ensureCapacity(int minCapacity)	Ensures that the capacity is at least the specified minimum.
boolean	equals(Object obj)	Indicates whether some other object is "equal to" this one.
boolean	equalsData(Object obj)	Indicates whether some other container's header is "equal to" this ones.
boolean	equalsHeader(Object obj)	Indicates whether some other chromatogram's header is "equal to" this ones.
Object	getClone()	Returns a clone of itself.
DataContainer	getHeader()	Returns an empty container with the same payload data as this one.
String	getID()	Returns the ID of the sequence.
long	getUniqueID()	Returns the unique ID.
int	hashCode()	Returns the hash code for this DataContainer.
boolean	isEmpty()	Returns whether the DataContainer is empty.
Iterator<T>	iterator()	Returns an iterator over the points.
void	mergeWith(DataContainer other)	Adds copies of all the points from the given container to its own.
protected boolean	modifiedListener(boolean modified)	Method that gets notified about changes in the collection of data points.
static DataContainer	newInstance(DataContainer cont)	Returns a new (empty) instance of the same class as the specified container.
boolean	remove(Object point)	Removes the given point from its list of points.
boolean	removeAll(Collection points)	Removes all the points from the list of points.
boolean	retainAll(Collection points)	Retains all the given points and removes the others.
void	setID(String value)	Sets the ID of the sequence.
int	size()	Returns the number of points stored in the DataContainer.
Object[]	toArray()	Returns the stored points as array.
Object[]	toArray(Object[] array)	Returns the stored points as array.
List<T>	toList()	Returns a list with the points.
List<T>	toList(DataPointComparator comparator)	Returns a list with the points.
String	toString()	Returns a string representation of the DataContainer.
TreeSet<T>	toTreeSet()	Returns a treeset with the points.
TreeSet<T>	toTreeSet(DataPointComparator comparator)	Returns a treeset with the points, sorted according to the given comparator.
void	trimToSize()	Trims the capacity of this container to be the container's current size.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Collection

parallelStream, removeIf, spliterator, stream, toArray

Methods inherited from interface adams.data.container.DataContainer

getComparator, newComparator, newPoint

Methods inherited from interface java.lang.Iterable

forEach

Field Detail

m_ID

protected String m_ID

the ID of the sequence.

m_Points

protected ArrayList<T extends DataPoint> m_Points

the data points.

m_UUID

protected long m_UUID

the unique ID.

Constructor Detail

AbstractDataContainer

public AbstractDataContainer()

Initializes the container.

Method Detail

setID

public void setID(String value)

Sets the ID of the sequence.

Specified by:

setID in interface MutableIDHandler

Parameters:

value - the new ID

getID

public String getID()

Returns the ID of the sequence.

Specified by:

getID in interface IDHandler

Returns:

the ID

getUniqueID

public long getUniqueID()

Returns the unique ID.

Specified by:

getUniqueID in interface UniqueIDHandler

Returns:

the ID

getClone

public Object getClone()

Returns a clone of itself. Note: resets the read-only flag!

Specified by:

getClone in interface CloneHandler<T extends DataPoint>

Specified by:

getClone in interface DataContainer<T extends DataPoint>

Returns:

the clone

assign

public void assign(DataContainer<T> other)

Obtains the stored variables from the other data point, but not the actual data points.

Specified by:

assign in interface DataContainer<T extends DataPoint>

Parameters:

other - the data point to get the values from

getHeader

public DataContainer getHeader()

Returns an empty container with the same payload data as this one.

Specified by:

getHeader in interface DataContainer<T extends DataPoint>

Returns:

a clone of the payload

compareToHeader

public int compareToHeader(Object o)

Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Specified by:

compareToHeader in interface DataContainer<T extends DataPoint>

Parameters:

o - the object to be compared.

Returns:

a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Throws:

ClassCastException - if the specified object's type prevents it from being compared to this object.

compareToData

public int compareToData(Object o)

Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Specified by:

compareToData in interface DataContainer<T extends DataPoint>

Parameters:

o - the object to be compared.

Returns:

a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Throws:

ClassCastException - if the specified object's type prevents it from being compared to this object.

equalsData

public boolean equalsData(Object obj)

Indicates whether some other container's header is "equal to" this ones.

Specified by:

equalsData in interface DataContainer<T extends DataPoint>

Parameters:

obj - the reference object with which to compare.

Returns:

true if this object is the same as the obj argument; false otherwise.

compareTo

public int compareTo(Object o)

Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Specified by:

compareTo in interface Comparable<T extends DataPoint>

Parameters:

o - the object to be compared.

Returns:

a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Throws:

ClassCastException - if the specified object's type prevents it from being compared to this object.

equalsHeader

public boolean equalsHeader(Object obj)

Indicates whether some other chromatogram's header is "equal to" this ones.

Specified by:

equalsHeader in interface DataContainer<T extends DataPoint>

Parameters:

obj - the reference object with which to compare.

Returns:

true if this object is the same as the obj argument; false otherwise.

equals

public boolean equals(Object obj)

Indicates whether some other object is "equal to" this one.

Specified by:

equals in interface Collection<T extends DataPoint>

Overrides:

equals in class Object

Parameters:

obj - the reference object with which to compare.

Returns:

true if this object is the same as the obj argument; false otherwise.

modifiedListener

protected boolean modifiedListener(boolean modified)

Method that gets notified about changes in the collection of data points. Just passes the modified state through.

The default implementation only passes the value through.

Parameters:

modified - whether the action modified the collection

Returns:

the same as the input

clear

public void clear()

Removes all the points.

Specified by:

clear in interface Collection<T extends DataPoint>

isEmpty

public boolean isEmpty()

Returns whether the DataContainer is empty.

Specified by:

isEmpty in interface Collection<T extends DataPoint>

Returns:

true if empty

ensureCapacity

public void ensureCapacity(int minCapacity)

Ensures that the capacity is at least the specified minimum.

Parameters:

minCapacity - the minimum capacity that the container should have for storing data points

trimToSize

public void trimToSize()

Trims the capacity of this container to be the container's current size.

add

public boolean add(T point)

Adds the point to the list of points.

Specified by:

add in interface Collection<T extends DataPoint>

Parameters:

point - the point to add

Returns:

true if the points changed

addAll

public boolean addAll(Collection points)

Adds all the points to the list of points.

Specified by:

addAll in interface Collection<T extends DataPoint>

Parameters:

points - the points to add

Returns:

true if the points changed

remove

public boolean remove(Object point)

Removes the given point from its list of points.

Specified by:

remove in interface Collection<T extends DataPoint>

Parameters:

point - the point to remove

Returns:

true if the points changed

removeAll

public boolean removeAll(Collection points)

Removes all the points from the list of points.

Specified by:

removeAll in interface Collection<T extends DataPoint>

Parameters:

points - the points to remove

Returns:

true if the points changed

contains

public boolean contains(Object point)

Checks whether the given point is already stored.

Specified by:

contains in interface Collection<T extends DataPoint>

Parameters:

point - the point to check

Returns:

true if point already exists in list

containsAll

public boolean containsAll(Collection points)

Checks whether all the given points are already stored.

Specified by:

containsAll in interface Collection<T extends DataPoint>

Parameters:

points - the points to check

Returns:

true if points already exist in list

retainAll

public boolean retainAll(Collection points)

Retains all the given points and removes the others.

Specified by:

retainAll in interface Collection<T extends DataPoint>

Parameters:

points - the points to keep

Returns:

true if points changed

size

public int size()

Returns the number of points stored in the DataContainer.

Specified by:

size in interface Collection<T extends DataPoint>

Returns:

the number of points

mergeWith

public void mergeWith(DataContainer other)

Adds copies of all the points from the given container to its own. No will get overwritten, only added.

Specified by:

mergeWith in interface Mergeable<T extends DataPoint>

Parameters:

other - the container to merge with

iterator

public Iterator<T> iterator()

Returns an iterator over the points.

Specified by:

iterator in interface Collection<T extends DataPoint>

Specified by:

iterator in interface Iterable<T extends DataPoint>

Returns:

the iterator

toArray

public Object[] toArray()

Returns the stored points as array.

Specified by:

toArray in interface Collection<T extends DataPoint>

Returns:

the points as array

toArray

public Object[] toArray(Object[] array)

Returns the stored points as array.

Specified by:

toArray in interface Collection<T extends DataPoint>

Parameters:

array - the array into which the points of this DataContainer are to be stored, if it is big enough; otherwise, a new array of the same runtime type is allocated for this purpose.

Returns:

the points as array

toList

public List<T> toList()

Returns a list with the points. Very fast, as it only returns the internal linked list.

Specified by:

toList in interface DataContainer<T extends DataPoint>

Returns:

a list with all the points

toList

public List<T> toList(DataPointComparator comparator)

Returns a list with the points.

Specified by:

toList in interface DataContainer<T extends DataPoint>

Parameters:

comparator - the comparator to use

Returns:

a list with all the points

toTreeSet

public TreeSet<T> toTreeSet()

Returns a treeset with the points.

Specified by:

toTreeSet in interface DataContainer<T extends DataPoint>

Returns:

a treeset with all the points

toTreeSet

public TreeSet<T> toTreeSet(DataPointComparator comparator)

Returns a treeset with the points, sorted according to the given comparator.

Specified by:

toTreeSet in interface DataContainer<T extends DataPoint>

Parameters:

comparator - the comparator to use

Returns:

a treeset with all the points

hashCode

public int hashCode()

Returns the hash code for this DataContainer.

Specified by:

hashCode in interface Collection<T extends DataPoint>

Overrides:

hashCode in class Object

Returns:

the hash code

toString

public String toString()

Returns a string representation of the DataContainer.

Overrides:

toString in class Object

Returns:

the string representation

newInstance

public static DataContainer newInstance(DataContainer cont)

Returns a new (empty) instance of the same class as the specified container.

Parameters:

cont - the container to use as a class template

Returns:

the instance or null in case of an error