gov.lbl.genome.common.features
Class ChromSegments

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.Vector
              gov.lbl.genome.common.features.ChromSegments

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

public class ChromSegments
extends java.util.Vector

Title: ChromSegments

Description: Add some segment functionality

Copyright: Copyright (c) 2002 Ernst Orlando Lawrence Berkeley National Laboratory

Company: LBNL

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ChromSegments()
ChromSegments

ChromSegments(int size)
ChromSegments

Method Summary

void	Add_ChromSegment(ChromSegment reg) Add ChromSegment
void	Add_ChromSegment(ChromSegment reg, long start, long end) Add ChromSegment
int	Count_Overlapped(ChromSegments other)
void	Decrement_All(int n) shift all segments
ChromSegments	Difference(ChromSegments other) return Difference of two segment collections
ChromSegment	Get_ChromSegment(int n) Get ChromSegment
void	Increment_All(int n) shift all segments
ChromSegments	MergeWith(ChromSegments other) return new collection, combined from 2 collections
ChromSegments	Overlap(ChromSegments other) return Overlap of two collections
java.lang.String	Overlapped()
ChromSegment	removeChromSegment(int index) remove ChromSegment in the position
void	Set_ChromSegment(ChromSegment reg, int n) Set ChromSegment
void	Sort()
java.lang.String	toString()
ChromSegments	Union(ChromSegments other) return Union of two segment collections

Methods inherited from class java.util.Vector

add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

iterator, listIterator, listIterator

Constructor Detail

ChromSegments

public ChromSegments()

ChromSegments

ChromSegments

public ChromSegments(int size)

ChromSegments

Parameters:

size - int

Method Detail

removeChromSegment

public ChromSegment removeChromSegment(int index)

remove ChromSegment in the position

Parameters:

index - int

Returns:

ChromSegment

Add_ChromSegment

public void Add_ChromSegment(ChromSegment reg)

Add ChromSegment

Parameters:

reg - ChromSegment

Add_ChromSegment

public void Add_ChromSegment(ChromSegment reg,
                             long start,
                             long end)

Add ChromSegment

Parameters:

reg - ChromSegment

start - long

end - long

Get_ChromSegment

public ChromSegment Get_ChromSegment(int n)

Get ChromSegment

Parameters:

n - int

Returns:

ChromSegment

Set_ChromSegment

public void Set_ChromSegment(ChromSegment reg,
                             int n)

Set ChromSegment

Parameters:

reg - ChromSegment

n - int

toString

public java.lang.String toString()

Overrides:

toString in class java.util.Vector

Sort

public void Sort()

Difference

public ChromSegments Difference(ChromSegments other)

return Difference of two segment collections

Parameters:

other - ChromSegments

Returns:

ChromSegments

Overlap

public ChromSegments Overlap(ChromSegments other)

return Overlap of two collections

Parameters:

other - ChromSegments

Returns:

ChromSegments

Overlapped

public java.lang.String Overlapped()

Union

public ChromSegments Union(ChromSegments other)

return Union of two segment collections

Parameters:

other - ChromSegments

Returns:

ChromSegments

MergeWith

public ChromSegments MergeWith(ChromSegments other)

return new collection, combined from 2 collections

Parameters:

other - ChromSegments

Returns:

ChromSegments

Count_Overlapped

public int Count_Overlapped(ChromSegments other)

Decrement_All

public void Decrement_All(int n)

shift all segments

Parameters:

n - int

Increment_All

public void Increment_All(int n)

shift all segments

Parameters:

n - int