Fetchaceprt Class Reference

List of all members.

Public Member Functions
	Fetchaceprt (Ace a, String div, Vector list, PrintWriter pw_pep, PrintWriter pw_def)
void	dump () throws AceException
void	run ()
Static Public Member Functions
static Vector	prepareKeyset (Vector prtlist)
Static Public Attributes
static int	threadCount = 0
static final int	LARGE = 10
Private Member Functions
synchronized void	increaseCount ()
synchronized void	decreaseCount ()
synchronized String	getDef (String prtname) throws AceException
synchronized String	getPep (String name) throws AceException, AceObjectNotFoundException
Private Attributes
Ace	acedb = null
Vector	prtlist = new Vector()
String	divname = null
PrintWriter	pepout
PrintWriter	defout

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Detailed Description

fetcheas both the protein part and the title part simultaneously. This class should be used in place of Fetchacedef.

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Constructor & Destructor Documentation

Fetchaceprt::Fetchaceprt	(	Ace	a,
		String	div,
		Vector	list,
		PrintWriter	pw_pep,
		PrintWriter	pw_def
	)			[inline]

Constructor. div is redundant with a. list is the input protein ids. There two outputs pw_pep for protein, pw_def for definition.

References acedb, defout, divname, increaseCount(), pepout, and prtlist.

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Member Function Documentation

synchronized void Fetchaceprt::increaseCount

(

)

[inline, private]

References threadCount.

Referenced by Fetchaceprt().

synchronized void Fetchaceprt::decreaseCount

(

)

[inline, private]

References threadCount.

Referenced by run().

synchronized String Fetchaceprt::getDef

(

String

prtname

)

throws AceException [inline, private]

not used in run but can be used for other purposes.

References acedb, acedb::Aceobj::at(), acedb::Aceobj::right(), and acedb::Aceobj::toString().

synchronized String Fetchaceprt::getPep

(

String

name

)

throws AceException, AceObjectNotFoundException [inline, private]

not used in run but can be used in other methods.

References acedb, and name.

void Fetchaceprt::dump

(

)

throws AceException [inline]

simple dump not to be used under threaded condition. this method is the same except that it is not executed under the thread environment.

References acedb, acedb::Aceobj::at(), defout, divname, name, pepout, prtlist, acedb::Aceobj::right(), and acedb::Aceobj::toString().

static Vector Fetchaceprt::prepareKeyset

(

Vector

prtlist

)

[inline, static]

create several keyset commands if prtlist is too long with each String shorter than Ace.QUERY_LIMIT.

References length.

Referenced by run().

void Fetchaceprt::run

(

)

[inline]

Does both title and sequence fetch and dump.

References acedb, acedb::Aceobj::at(), decreaseCount(), defout, divname, LARGE, pepout, prepareKeyset(), prtlist, acedb::Aceobj::right(), and threadCount.

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Member Data Documentation

Ace Fetchaceprt::acedb = null [private]

Referenced by dump(), Fetchaceprt(), getDef(), getPep(), and run().

Vector Fetchaceprt::prtlist = new Vector() [private]

Referenced by dump(), Fetchaceprt(), and run().

String Fetchaceprt::divname = null [private]

Referenced by dump(), Fetchaceprt(), and run().

PrintWriter Fetchaceprt::pepout [private]

Referenced by dump(), Fetchaceprt(), and run().

PrintWriter Fetchaceprt::defout [private]

Referenced by dump(), Fetchaceprt(), and run().

int Fetchaceprt::threadCount = 0 [static]

Referenced by decreaseCount(), increaseCount(), and run().

final int Fetchaceprt::LARGE = 10 [static]

Referenced by run().

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

• cluster/Clusterdump.java