gov.lbl.genome.common
Class CommUnit

java.lang.Object
  gov.lbl.genome.common.CommUnit

public class CommUnit
extends java.lang.Object

Title: CommUnit

Description: Communication Unit

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

Company: LBNL

Field Summary

protected static java.lang.String	CHROM_INFO
protected java.lang.String	codeBaseURL
boolean	debug
protected static java.lang.String	GET_ANNO
protected static java.lang.String	GET_AVAIL_CURVES
protected static java.lang.String	GET_CURVE
protected static java.lang.String	GET_GENES
protected static java.lang.String	GET_INIT
protected static int	RETRIES
protected java.lang.String	servletURL
protected static java.lang.String	UP2DATE
protected static java.lang.String	VERSION

Constructor Summary

CommUnit()
CommUnit

CommUnit(java.lang.String s, java.lang.String cb)
CommUnit

CommUnit(java.lang.String s, java.lang.String cb, boolean dbg)
CommUnit

Method Summary

java.util.Vector	checkCurves(java.util.Vector curves, java.lang.String pos) check Curves for visibility in the specified position
java.util.Vector	getAnno(java.lang.String base, java.lang.String src, java.lang.String pos, java.lang.String genes, java.lang.String curveId) 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
java.lang.String[][]	getAvailCurves() getCurves Returns a list of curves available as an array [id] [name]
java.lang.String[][]	getAvailCurves(java.lang.String url) getCurves returns a list of curves available at a given url as an array [id][name]
ChromInfo	getChromInfo(java.lang.String base, java.lang.String name) get ChromInfo
CurveModel	getCurve(CurveInfo curve, java.lang.String pos, CurveModel cmodel, VistaApp va) get Curve
Gene[]	getGenes(java.lang.String gene, java.lang.String base, java.lang.String curveid, java.lang.String genes) getGenes returns an array of Genes whose names contain the given string
java.util.HashMap	getInitInfo() getInitInfo returns a hashmap genome id -> GenomeInfo
java.util.HashMap	getInitInfo(java.lang.String runs, java.lang.String pos, java.lang.String show, java.lang.String bg) get Init Info
java.util.HashMap	getUp2Date(java.lang.String runs) update init information
java.lang.String	getVersion() getVersion returns current version
Document	sendRequest(java.lang.String src) send Request
void	setCodeBaseURL(java.lang.String cb) set CodeBase URL
void	setServletURL(java.lang.String s) set Servlet URL

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

GET_CURVE

protected static final java.lang.String GET_CURVE

See Also:

Constant Field Values

GET_AVAIL_CURVES

protected static final java.lang.String GET_AVAIL_CURVES

See Also:

Constant Field Values

GET_ANNO

protected static final java.lang.String GET_ANNO

See Also:

Constant Field Values

GET_INIT

protected static final java.lang.String GET_INIT

See Also:

Constant Field Values

GET_GENES

protected static final java.lang.String GET_GENES

See Also:

Constant Field Values

UP2DATE

protected static final java.lang.String UP2DATE

See Also:

Constant Field Values

CHROM_INFO

protected static final java.lang.String CHROM_INFO

See Also:

Constant Field Values

VERSION

protected static final java.lang.String VERSION

See Also:

Constant Field Values

RETRIES

protected static final int RETRIES

See Also:

Constant Field Values

servletURL

protected java.lang.String servletURL

codeBaseURL

protected java.lang.String codeBaseURL

debug

public boolean debug

Constructor Detail

CommUnit

public CommUnit()

CommUnit

CommUnit

public CommUnit(java.lang.String s,
                java.lang.String cb)

CommUnit

Parameters:

s - String

cb - String

CommUnit

public CommUnit(java.lang.String s,
                java.lang.String cb,
                boolean dbg)

CommUnit

Parameters:

s - String

cb - String

dbg - boolean

Method Detail

setServletURL

public void setServletURL(java.lang.String s)

set Servlet URL

Parameters:

s - String

setCodeBaseURL

public void setCodeBaseURL(java.lang.String cb)

set CodeBase URL

Parameters:

cb - String

getInitInfo

public java.util.HashMap getInitInfo()

getInitInfo returns a hashmap genome id -> GenomeInfo

getInitInfo

public java.util.HashMap getInitInfo(java.lang.String runs,
                                     java.lang.String pos,
                                     java.lang.String show,
                                     java.lang.String bg)

get Init Info

Parameters:

runs - String

pos - String

show - String

bg - String

Returns:

HashMap

getUp2Date

public java.util.HashMap getUp2Date(java.lang.String runs)

update init information

Parameters:

runs - String

Returns:

HashMap

getGenes

public Gene[] getGenes(java.lang.String gene,
                       java.lang.String base,
                       java.lang.String curveid,
                       java.lang.String genes)
                throws GeneNotFoundException

getGenes returns an array of Genes whose names contain the given string

Parameters:

gene - String

base - String

curveid - String

genes - String

Returns:

Gene[]

Throws:

GeneNotFoundException

getVersion

public java.lang.String getVersion()

getVersion returns current version

getAvailCurves

public java.lang.String[][] getAvailCurves()

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

getAvailCurves

public java.lang.String[][] getAvailCurves(java.lang.String url)

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

Parameters:

url - String

Returns:

String[][]

getAnno

public java.util.Vector getAnno(java.lang.String base,
                                java.lang.String src,
                                java.lang.String pos,
                                java.lang.String genes,
                                java.lang.String curveId)

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

getChromInfo

public ChromInfo getChromInfo(java.lang.String base,
                              java.lang.String name)
                       throws VGBException

get ChromInfo

Parameters:

base - String

name - String

Returns:

ChromInfo

Throws:

VGBException

getCurve

public CurveModel getCurve(CurveInfo curve,
                           java.lang.String pos,
                           CurveModel cmodel,
                           VistaApp va)

get Curve

Parameters:

curve - CurveInfo

pos - String

cmodel - CurveModel

va - VistaApp

Returns:

CurveModel

checkCurves

public java.util.Vector checkCurves(java.util.Vector curves,
                                    java.lang.String pos)

check Curves for visibility in the specified position

Parameters:

curves - Vector

pos - String

Returns:

Vector

sendRequest

public Document sendRequest(java.lang.String src)

send Request

Parameters:

src - String

Returns:

Document