dumpClusterPrt Class Reference

List of all members.

Public Member Functions
	dumpClusterPrt (String pgQuery) throws ClassNotFoundException, SQLException
String	getPrt (String div, String prtName) throws AceException
String	getDef (String div, String prtName) throws AceException
void	dumpClusterDef (int filesize)
void	threadedTitleDump (int filesize)
Static Public Member Functions
static void	main (String[] args)
Static Public Attributes
static File	dir = null
Static Package Functions
static PrintWriter	createPR (int cnt, String ext) throws IOException
Package Attributes
ResultSet	clusters = null
Private Attributes
HashMap	div2db = new HashMap()
Static Private Attributes
static String	user = "kzhou"
static String	passwd = "fugufish"
static String	pgPasswd = ""
static String	aceHost = "localhost"
static int[]	ports = {3001, 3002, 3003, 3004, 3005, 3006, 3007, 3008, 3009}
static String[]	dbs = {"amp", "fr", "hs", "mam", "mm", "pri", "rod", "sau", "vrt"}
static String	pgdb = "jdbc:postgresql://localhost/parortho"

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Detailed Description

This program will dump all the proteins within one cluster into each file. All the clusters from orpara database stored in the cds table will be dumped.

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Constructor & Destructor Documentation

dumpClusterPrt::dumpClusterPrt

(

String

pgQuery

)

throws ClassNotFoundException, SQLException [inline]

initialize the 9 Acedb on localhost. They could be on different machines for parallel processing

References aceHost, clusters, dbs, div2db, passwd, pgdb, pgPasswd, ports, stmt, and user.

Referenced by main().

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Member Function Documentation

String dumpClusterPrt::getPrt	(	String	div,
		String	prtName
	)			throws AceException [inline]

obtains the fastaFormated protein sequence.

References div2db.

Referenced by main().

String dumpClusterPrt::getDef	(	String	div,
		String	prtName
	)			throws AceException [inline]

Get the title or definition for protein prtName.

Returns:

null if prrName has no Title.

References acedb::Aceobj::at(), div2db, acedb::Aceobj::right(), and acedb::Aceobj::toString().

Referenced by dumpClusterDef().

void dumpClusterPrt::dumpClusterDef

(

int

filesize

)

[inline]

dump all clusters into files with filesize clusters in each file. Files will be named 1.def 2.def ...

References clusters, and getDef().

Referenced by dumpClusterTitle::main().

void dumpClusterPrt::threadedTitleDump

(

int

filesize

)

[inline]

dump the title of each protein sequence into files with filesize clusters in each file. Default filesize=2000.

References clusters, and div2db.

Referenced by dumpClusterTitle::main().

static PrintWriter dumpClusterPrt::createPR	(	int	cnt,
		String	ext
	)			throws IOException [inline, static, package]

a helper function to manage files and directories.

References dir.

Referenced by main().

static void dumpClusterPrt::main

(

String[]

args

)

[inline, static]

the trim(division) is essential to remove to whitespaces

References clusters, createPR(), dumpClusterPrt(), getPrt(), passwd, pgPasswd, and user.

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Member Data Documentation

String dumpClusterPrt::user = "kzhou" [static, private]

Referenced by dumpClusterPrt(), and main().

String dumpClusterPrt::passwd = "fugufish" [static, private]

Referenced by dumpClusterPrt(), and main().

String dumpClusterPrt::pgPasswd = "" [static, private]

Referenced by dumpClusterPrt(), and main().

String dumpClusterPrt::aceHost = "localhost" [static, private]

Referenced by dumpClusterPrt().

int [] dumpClusterPrt::ports = {3001, 3002, 3003, 3004, 3005, 3006, 3007, 3008, 3009} [static, private]

Referenced by dumpClusterPrt().

String [] dumpClusterPrt::dbs = {"amp", "fr", "hs", "mam", "mm", "pri", "rod", "sau", "vrt"} [static, private]

inside the postgresdb division is char(30), so they must be trimmed in the query, otherwise the HashMap div2db will not find it!.

Referenced by dumpClusterPrt().

File dumpClusterPrt::dir = null [static]

Referenced by createPR().

HashMap dumpClusterPrt::div2db = new HashMap() [private]

Referenced by dumpClusterPrt(), getDef(), getPrt(), and threadedTitleDump().

String dumpClusterPrt::pgdb = "jdbc:postgresql://localhost/parortho" [static, private]

Referenced by dumpClusterPrt().

ResultSet dumpClusterPrt::clusters = null [package]

Referenced by dumpClusterDef(), dumpClusterPrt(), main(), and threadedTitleDump().

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

• cluster/dumpClusterPrt.java