info.bioinfweb.commons.collections

Class NonOverlappingIntervalList

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<E>

java.util.TreeSet<SimpleSequenceInterval>

info.bioinfweb.commons.collections.NonOverlappingIntervalList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<SimpleSequenceInterval>, java.util.Collection<SimpleSequenceInterval>, java.util.NavigableSet<SimpleSequenceInterval>, java.util.Set<SimpleSequenceInterval>, java.util.SortedSet<SimpleSequenceInterval>

Direct Known Subclasses:

CharSet

public class NonOverlappingIntervalList
extends java.util.TreeSet<SimpleSequenceInterval>

Stores a set of non overlapping intervals of a sequence. The sequence intervals only mark a subset of all sequence characters and carry no additional information.

Author:

Ben Stöver

See Also:

SequenceIntervalList, Serialized Form

Constructor Summary

Constructors

Constructor and Description
NonOverlappingIntervalList()

Method Summary

Modifier and Type	Method and Description
boolean	add(int pos)
boolean	add(int firstPos, int lastPos)
boolean	add(SimpleSequenceInterval e)
void	addAll(NonOverlappingIntervalList other) Adds all of the intervals contained in another list to this list.
void	addAll(NonOverlappingIntervalList other, int firstIndex, int lastIndex, boolean moveToFront) Adds all or a part of the intervals contained in another list to this list.
boolean	contains(int pos) Checks whether the specified position is marked by this list.
boolean	containsAll(int firstPos, int lastPos) Checks whether all positions in the specified interval are marked by this list.
java.util.SortedSet<SimpleSequenceInterval>	getOverlappingElements(int firstPos, int lastPos)
void	movePositions(int start, int offset)
boolean	remove(int firstPos, int lastPos) Removes the specified interval from this list.
boolean	remove(java.lang.Object o) Removes the specified object from this interval list.

Methods inherited from class java.util.TreeSet

addAll, ceiling, clear, clone, comparator, contains, descendingIterator, descendingSet, first, floor, headSet, headSet, higher, isEmpty, iterator, last, lower, pollFirst, pollLast, size, spliterator, subSet, subSet, tailSet, tailSet

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

containsAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Set

containsAll, equals, hashCode, removeAll, retainAll, toArray, toArray

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

NonOverlappingIntervalList

public NonOverlappingIntervalList()

Method Detail

add

public boolean add(SimpleSequenceInterval e)

Specified by:

add in interface java.util.Collection<SimpleSequenceInterval>

Specified by:

add in interface java.util.Set<SimpleSequenceInterval>

Overrides:

add in class java.util.TreeSet<SimpleSequenceInterval>

add

public boolean add(int pos)

add

public boolean add(int firstPos,
                   int lastPos)

remove

public boolean remove(java.lang.Object o)

Removes the specified object from this interval list. If o in an instance of SimpleSequenceInterval but this exact interval is not contained in this list, this method will delegate to remove(int, int), which may then modify overlapping interval entries.

Specified by:

remove in interface java.util.Collection<SimpleSequenceInterval>

Specified by:

remove in interface java.util.Set<SimpleSequenceInterval>

Overrides:

remove in class java.util.TreeSet<SimpleSequenceInterval>

Returns:

true if an object was removed or intervals have been modified.

See Also:

TreeSet.remove(java.lang.Object)

remove

public boolean remove(int firstPos,
                      int lastPos)

Removes the specified interval from this list. (Overlapping interval objects will be modified.)

Parameters:

firstPos - the first index of the interval to be removed (must be >= 0)

lastPos - the index after the last position to be removed (must be > firstIndex).

Returns:

true if any changes were made to the list

addAll

public void addAll(NonOverlappingIntervalList other,
                   int firstIndex,
                   int lastIndex,
                   boolean moveToFront)

Adds all or a part of the intervals contained in another list to this list.

Parameters:

other - the other list instance

firstIndex - the first position from where to start the import (must be >= 0)

lastIndex - the index after the last position to be imported (must be > firstIndex).

moveToFront - Specify true here, if you want to move the imported intervals to the front of the target list. (An interval starting at firstIndex would than start at 0 in the target list.)

addAll

public void addAll(NonOverlappingIntervalList other)

Adds all of the intervals contained in another list to this list. Calling this method is equivalent to calling addAll(other, 0, other.last().getLastPos() + 1, false).

Parameters:

other - the other list instance

movePositions

public void movePositions(int start,
                          int offset)

contains

public boolean contains(int pos)

Checks whether the specified position is marked by this list.

Parameters:

pos - the position to be checked

Returns:

true if the specified position is marked by this list, false otherwise.

containsAll

public boolean containsAll(int firstPos,
                           int lastPos)

Checks whether all positions in the specified interval are marked by this list.

Parameters:

firstPos - the first position of the interval to be checked

lastPos - the last position of the interval to be checked (inclusive)

Returns:

true if all specified positions are marked by this list, false otherwise.

getOverlappingElements

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