gov::lbl::genome::common::features::ChromSegments Class Reference

List of all members.

Public Member Functions
	ChromSegments ()
	ChromSegments (int size)
ChromSegment	removeChromSegment (int index)
void	Add_ChromSegment (ChromSegment reg)
void	Add_ChromSegment (ChromSegment reg, long start, long end)
ChromSegment	Get_ChromSegment (int n)
void	Set_ChromSegment (ChromSegment reg, int n)
String	toString ()
void	Sort ()
ChromSegments	Difference (ChromSegments other)
ChromSegments	Overlap (ChromSegments other)
String	Overlapped ()
ChromSegments	Union (ChromSegments other)
ChromSegments	MergeWith (ChromSegments other)
int	Count_Overlapped (ChromSegments other)
void	Decrement_All (int n)
void	Increment_All (int n)

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Detailed Description

Title: ChromSegments

Description: Add some segment functionality

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

Company: LBNL

Version:

2.0

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Constructor & Destructor Documentation

gov::lbl::genome::common::features::ChromSegments::ChromSegments (   )  [inline]

ChromSegments

gov::lbl::genome::common::features::ChromSegments::ChromSegments (  int  size  )  [inline]

ChromSegments Parameters: size  int

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Member Function Documentation

void gov::lbl::genome::common::features::ChromSegments::Add_ChromSegment (  ChromSegment  reg, long  start, long  end )  [inline]

Add ChromSegment Parameters: reg  ChromSegment start  long end  long

void gov::lbl::genome::common::features::ChromSegments::Add_ChromSegment (  ChromSegment  reg  )  [inline]

Add ChromSegment Parameters: reg  ChromSegment

void gov::lbl::genome::common::features::ChromSegments::Decrement_All (  int  n  )  [inline]

shift all segments Parameters: n  int

ChromSegments gov::lbl::genome::common::features::ChromSegments::Difference (  ChromSegments  other  )  [inline]

return Difference of two segment collections Parameters: other  ChromSegments Returns: ChromSegments

ChromSegment gov::lbl::genome::common::features::ChromSegments::Get_ChromSegment (  int  n  )  [inline]

Get ChromSegment Parameters: n  int Returns: ChromSegment

void gov::lbl::genome::common::features::ChromSegments::Increment_All (  int  n  )  [inline]

shift all segments Parameters: n  int

ChromSegments gov::lbl::genome::common::features::ChromSegments::MergeWith (  ChromSegments  other  )  [inline]

return new collection, combined from 2 collections Parameters: other  ChromSegments Returns: ChromSegments

ChromSegments gov::lbl::genome::common::features::ChromSegments::Overlap (  ChromSegments  other  )  [inline]

return Overlap of two collections Parameters: other  ChromSegments Returns: ChromSegments

ChromSegment gov::lbl::genome::common::features::ChromSegments::removeChromSegment (  int  index  )  [inline]

remove ChromSegment in the position Parameters: index  int Returns: ChromSegment

void gov::lbl::genome::common::features::ChromSegments::Set_ChromSegment (  ChromSegment  reg, int  n )  [inline]

Set ChromSegment Parameters: reg  ChromSegment n  int

ChromSegments gov::lbl::genome::common::features::ChromSegments::Union (  ChromSegments  other  )  [inline]

return Union of two segment collections Parameters: other  ChromSegments Returns: ChromSegments

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The documentation for this class was generated from the following file:

• /home/teplitski/Projects/vgb2/src/gov/lbl/genome/common/features/ChromSegments.java

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