info.bioinfweb.commons.collections

Class SequenceIntervalList<E>

java.lang.Object

info.bioinfweb.commons.collections.SequenceIntervalList<E>

Type Parameters:

E - the type of elements that describe a sequence interval (the elements of the collection)

All Implemented Interfaces:

java.lang.Iterable<E>, java.util.Collection<E>

public class SequenceIntervalList<E>
extends java.lang.Object
implements java.util.Collection<E>

Instances of this class are able to manage a set of sequence intervals. The key feature is the efficient calculation of a subset of the stored interval elements that overlap with a defined interval (see getOverlappingElements(int, int)). The actual efficiency depends on the specified interval length (see SequenceIntervalList(SequenceIntervalPositionAdapter, int, int)).

Author:

Ben Stöver

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	SequenceIntervalList.IntervalInformation

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_INITIAL_SEQUENCE_LENGTH
static int	DEFAULT_INTERVAL_LENGTH

Constructor Summary

Constructors

Constructor and Description
SequenceIntervalList(SequenceIntervalPositionAdapter<? super E> positionAdapter) Equivalent to calling SequenceIntervalList(positionAdapter, DEFAULT_INITIAL_SEQUENCE_LENGTH, DEFAULT_INTERVAL_LENGTH).
SequenceIntervalList(SequenceIntervalPositionAdapter<? super E> positionAdapter, int sequenceLength, int intervalLength) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
boolean	add(E element)
boolean	addAll(java.util.Collection<? extends E> collection)
void	clear()
boolean	contains(java.lang.Object o)
boolean	containsAll(java.util.Collection<?> collection)
boolean	containsPosition(int pos)
int	getIntervalLength()
java.util.SortedSet<E>	getOverlappingElements(int firstPos, int lastPos)
SequenceIntervalPositionAdapter<? super E>	getPositionAdapter()
boolean	isEmpty()
java.util.Iterator<E>	iterator() Returns an iterator over the list.
boolean	move(E element, int newFirstPos, int newLastPos) Moves an element of the list to a different position.
boolean	remove(java.lang.Object o)
boolean	removeAll(java.util.Collection<?> collection)
boolean	retainAll(java.util.Collection<?> collection)
void	setPositionAdapter(SequenceIntervalPositionAdapter<? super E> positionAdapter) Calling this methods leads to resorting of all elements in the list.
int	size()
java.lang.Object[]	toArray()
<T> T[]	toArray(T[] array)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Collection

equals, hashCode, parallelStream, removeIf, spliterator, stream

Methods inherited from interface java.lang.Iterable

forEach

Field Detail

DEFAULT_INITIAL_SEQUENCE_LENGTH

public static final int DEFAULT_INITIAL_SEQUENCE_LENGTH

See Also:

Constant Field Values

DEFAULT_INTERVAL_LENGTH

public static final int DEFAULT_INTERVAL_LENGTH

See Also:

Constant Field Values

Constructor Detail

SequenceIntervalList

public SequenceIntervalList(SequenceIntervalPositionAdapter<? super E> positionAdapter)

Equivalent to calling SequenceIntervalList(positionAdapter, DEFAULT_INITIAL_SEQUENCE_LENGTH, DEFAULT_INTERVAL_LENGTH).

Parameters:

positionAdapter -

SequenceIntervalList

public SequenceIntervalList(SequenceIntervalPositionAdapter<? super E> positionAdapter,
                            int sequenceLength,
                            int intervalLength)

Creates a new instance of this class.

Parameters:

sequenceLength - the expected length of the whole sequence, which is populated by the interval elements that are going to be stored in the new instance (it will be extended if necessary)

intervalLength - the interval (number of sequence positions) in which a list of elements overlapping with this interval is stored. (The value specified here has a major influence on the efficiency of this instance. It should depend on how many entries are expected per interval. If you expect e.g. 1 element every 100 sequence positions in average, you should specify a value like 500 or 1000. Alternatively you could make the value dependent on the calls of getOverlappingElements(int, int). If you already know that you are going to call this method with intervals of a certain length, you specify a value here that is in the dimension of that length.)

Method Detail

getIntervalLength

public int getIntervalLength()

getPositionAdapter

public SequenceIntervalPositionAdapter<? super E> getPositionAdapter()

setPositionAdapter

public void setPositionAdapter(SequenceIntervalPositionAdapter<? super E> positionAdapter)

Calling this methods leads to resorting of all elements in the list.

Parameters:

positionAdapter - the new position adapter

add

public boolean add(E element)

Specified by:

add in interface java.util.Collection<E>

remove

public boolean remove(java.lang.Object o)

Specified by:

remove in interface java.util.Collection<E>

move

public boolean move(E element,
                    int newFirstPos,
                    int newLastPos)

Moves an element of the list to a different position. To change positions of elements only this method should be used. If the according properties of the element are set directly, the ordering of this list will not be correct anymore.

Parameters:

element - the element to be moved (with unchanged position values)

newFirstPos - the new start position

newLastPos - the new end position

Returns:

true if the element was moved, false if the element is not contained in the list

getOverlappingElements

public java.util.SortedSet<E> getOverlappingElements(int firstPos,
                                                     int lastPos)

containsPosition

public boolean containsPosition(int pos)

addAll

public boolean addAll(java.util.Collection<? extends E> collection)

Specified by:

addAll in interface java.util.Collection<E>

clear

public void clear()

Specified by:

clear in interface java.util.Collection<E>

contains

public boolean contains(java.lang.Object o)

Specified by:

contains in interface java.util.Collection<E>

containsAll

public boolean containsAll(java.util.Collection<?> collection)

Specified by:

containsAll in interface java.util.Collection<E>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Collection<E>

iterator

public java.util.Iterator<E> iterator()

Returns an iterator over the list. Each element is only returned once, no matter how many intervals it spans. The elements are ordered by their first position.

Specified by:

iterator in interface java.lang.Iterable<E>

Specified by:

iterator in interface java.util.Collection<E>

See Also:

Collection.iterator()

removeAll

public boolean removeAll(java.util.Collection<?> collection)

Specified by:

removeAll in interface java.util.Collection<E>

retainAll

public boolean retainAll(java.util.Collection<?> collection)

Specified by:

retainAll in interface java.util.Collection<E>

size

public int size()

Specified by:

size in interface java.util.Collection<E>

toArray

public java.lang.Object[] toArray()

Specified by:

toArray in interface java.util.Collection<E>

toArray

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

Specified by:

toArray in interface java.util.Collection<E>