gov::lbl::genome::common::CommUnit Class Reference

List of all members.

Public Member Functions
	CommUnit ()
	CommUnit (String s, String cb)
	CommUnit (String s, String cb, boolean dbg)
void	setServletURL (String s)
void	setCodeBaseURL (String cb)
HashMap	getInitInfo ()
HashMap	getInitInfo (String runs, String pos, String show, String bg)
HashMap	getUp2Date (String runs)
Gene[]	getGenes (String gene, String base, String curveid, String genes) throws GeneNotFoundException
String	getVersion ()
String[][]	getAvailCurves ()
String[][]	getAvailCurves (String url)
Vector	getAnno (String base, String src, String pos, String genes, String curveId)
ChromInfo	getChromInfo (String base, String name) throws VGBException
CurveModel	getCurve (CurveInfo curve, String pos, CurveModel cmodel, VistaApp va)
Vector	checkCurves (Vector curves, String pos)
synchronized Document	sendRequest (String src)
Public Attributes
boolean	debug = false
Protected Attributes
String	servletURL
String	codeBaseURL
Static Protected Attributes
final String	GET_CURVE = "get_region"
final String	GET_AVAIL_CURVES = "get_curves"
final String	GET_ANNO = "get_anno"
final String	GET_INIT = "get_init_info"
final String	GET_GENES = "get_genes"
final String	UP2DATE = "up2date"
final String	CHROM_INFO = "chrom_info"
final String	VERSION = "version"
final int	RETRIES = 5

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Detailed Description

Title: CommUnit

Description: Communication Unit

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

Company: LBNL

Author:

Dmitriy Ryaboy

Version:

2.0

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Constructor & Destructor Documentation

gov::lbl::genome::common::CommUnit::CommUnit (   )  [inline]

CommUnit

gov::lbl::genome::common::CommUnit::CommUnit (  String  s, String  cb )  [inline]

CommUnit Parameters: s  String cb  String

gov::lbl::genome::common::CommUnit::CommUnit (  String  s, String  cb, boolean  dbg )  [inline]

CommUnit Parameters: s  String cb  String dbg  boolean

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Member Function Documentation

Vector gov::lbl::genome::common::CommUnit::checkCurves (  Vector  curves, String  pos )  [inline]

check Curves for visibility in the specified position Parameters: curves  Vector pos  String Returns: Vector

Vector gov::lbl::genome::common::CommUnit::getAnno (  String  base, String  src, String  pos, String  genes, String  curveId )  [inline]

getAnno returns a Vector of ChromSegments (use getName() on each segment to find out the type) input: base (hg12, mm2, etc), src (refseq at the moment), position Parameters: base  String src  String pos  String genes  String curveId  String Returns: Vector

String [][] gov::lbl::genome::common::CommUnit::getAvailCurves (  String  url  )  [inline]

getCurves returns a list of curves available at a given url as an array [id][name] Parameters: url  String Returns: String[][]

String [][] gov::lbl::genome::common::CommUnit::getAvailCurves (   )  [inline]

getCurves Returns a list of curves available as an array [id] [name]

ChromInfo gov::lbl::genome::common::CommUnit::getChromInfo (  String  base, String  name )  throws VGBException [inline]

get ChromInfo Parameters: base  String name  String Returns: ChromInfo Exceptions: VGBException

CurveModel gov::lbl::genome::common::CommUnit::getCurve (  CurveInfo  curve, String  pos, CurveModel  cmodel, VistaApp  va )  [inline]

get Curve Parameters: curve  CurveInfo pos  String cmodel  CurveModel va  VistaApp Returns: CurveModel

Gene [] gov::lbl::genome::common::CommUnit::getGenes (  String  gene, String  base, String  curveid, String  genes )  throws GeneNotFoundException [inline]

getGenes returns an array of Genes whose names contain the given string Parameters: gene  String base  String curveid  String genes  String Exceptions: GeneNotFoundException  Returns: Gene[]

HashMap gov::lbl::genome::common::CommUnit::getInitInfo (  String  runs, String  pos, String  show, String  bg )  [inline]

get Init Info Parameters: runs  String pos  String show  String bg  String Returns: HashMap

HashMap gov::lbl::genome::common::CommUnit::getInitInfo (   )  [inline]

getInitInfo returns a hashmap genome id -> GenomeInfo

HashMap gov::lbl::genome::common::CommUnit::getUp2Date (  String  runs  )  [inline]

update init information Parameters: runs  String Returns: HashMap

String gov::lbl::genome::common::CommUnit::getVersion (   )  [inline]

getVersion returns current version

synchronized Document gov::lbl::genome::common::CommUnit::sendRequest (  String  src  )  [inline]

send Request Parameters: src  String Returns: Document

void gov::lbl::genome::common::CommUnit::setCodeBaseURL (  String  cb  )  [inline]

set CodeBase URL Parameters: cb  String

void gov::lbl::genome::common::CommUnit::setServletURL (  String  s  )  [inline]

set Servlet URL Parameters: s  String

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

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

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