ExtractEnd Class Reference

List of all members.

Public Member Functions
	ExtractEnd (Ace db, String outf)
void	setup (String gn, int len)
void	extract ()
void	close ()
Static Public Member Functions
static void	main (String[] args)
Public Attributes
final int	TAIL_LIMIT = 5000
Private Attributes
String	gseq
int	DNALength
TreeMap	name2regv
Vector	locsorted
Ace	ace
PrintWriter	out

---

Detailed Description

ExtractEnd class extract the 3'-end of those sequences whose 3'-end of CDS and mRNA are the same. each object should be based on one genome sequence. The main method iterate through the main query result. The genomic sequence is too long in this case. Combined with the multiple threads running and the poor java efficiency (The unocode is one factor. The subsequence extraction cannot be done from this computer. The output of this program is the instruction files as to how to obtain the subsequences. Then I need to write a separate perl program (exend.pl) to extract the subsequences.

---

Constructor & Destructor Documentation

ExtractEnd::ExtractEnd	(	Ace	db,
		String	outf
	)			[inline]

basic set up, not ready for action yet.

References ace, locsorted, name2regv, and out.

Referenced by main().

---

Member Function Documentation

void ExtractEnd::setup	(	String	gn,
		int	len
	)			[inline]

set up this object for extraction. It first clears the internal map and vector member.

References ace, DNALength, gseq, locsorted, and name2regv.

Referenced by main().

void ExtractEnd::extract

(

)

[inline]

References ace, Region::differentEnd(), Region::distance(), DNALength, Region::forward(), Region::getEnd(), Region::getLargeEnd(), gseq, locsorted, name2regv, out, Region::overlap(), and TAIL_LIMIT.

Referenced by main().

void ExtractEnd::close

(

)

[inline]

References ace, and out.

Referenced by main().

static void ExtractEnd::main

(

String[]

args

)

[inline, static]

References close(), extract(), ExtractEnd(), and setup().

---

Member Data Documentation

String ExtractEnd::gseq [private]

Referenced by extract(), and setup().

int ExtractEnd::DNALength [private]

Referenced by extract(), and setup().

TreeMap ExtractEnd::name2regv [private]

Referenced by extract(), ExtractEnd(), and setup().

Vector ExtractEnd::locsorted [private]

Referenced by extract(), ExtractEnd(), and setup().

Ace ExtractEnd::ace [private]

Referenced by close(), extract(), ExtractEnd(), and setup().

PrintWriter ExtractEnd::out [private]

Referenced by close(), extract(), and ExtractEnd().

final int ExtractEnd::TAIL_LIMIT = 5000

Referenced by extract().

---

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

• seqana/ExtractEnd.java