gov.lbl.genome.common
Class GenomeInfo

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

public class GenomeInfo
extends java.lang.Object

Title: GenomeInfo

Description: Contains information about genome

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

Company: LBNL

Constructor Summary

GenomeInfo(int genomeId, java.lang.String id, java.lang.String adb, java.lang.String name, java.util.Vector curves, GenesInfo[] genes, java.lang.String defPos, boolean isDefault, java.lang.String dataUrl, java.util.Vector browsers, int type)
GenomeInfo

GenomeInfo(java.lang.String id, java.lang.String adb, java.lang.String name, java.util.Vector curves, GenesInfo[] genes)
GenomeInfo

GenomeInfo(java.lang.String id, java.lang.String adb, java.util.Vector curves, boolean deleted)
GenomeInfo

Method Summary

void	addCurve(CurveInfo curve) add Curve
java.lang.String	getAdb() get Annotation db
java.util.Vector	getBrowsers() return all available Browsers
java.util.Vector	getCheckedCurves() return list of Checked Curves
ChromInfo	getContig(java.lang.String name) get Contig (Chromosome)
java.lang.String	getCurrentPos() get Current Position
CurveInfo	getCurve(int index) get Curve Info
CurveInfo	getCurve(java.lang.String ID)
java.util.Vector	getCurves() get Curves
java.lang.String	getDataUrl() get Data Url string
java.lang.String	getDefPos() ge tDefault Position
GenesInfo[]	getGenesInfos() return GenesInfos
int	getGenomeId() get Genome Id
java.lang.String	getId() get Id
java.lang.String	getName() get Name
int	getNumberOfCurves() get Number Of Curves
int	getType() get Type
boolean	isDefault() return true if Default
boolean	isDeleted() return true if deleted
void	setCheckedCurves(java.util.Vector curves) set list of Checked Curves
void	setContig(java.lang.String name, ChromInfo contig) setContig (Chromosome)
void	setCurrentPos(java.lang.String pos) set Current Position
void	setDeleted(boolean deleted) set genome as Deleted
java.lang.String	toString() return XML formatted summary string

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomeInfo

public GenomeInfo(java.lang.String id,
                  java.lang.String adb,
                  java.util.Vector curves,
                  boolean deleted)

GenomeInfo

Parameters:

id - String

adb - String

curves - Vector

deleted - boolean

GenomeInfo

public GenomeInfo(java.lang.String id,
                  java.lang.String adb,
                  java.lang.String name,
                  java.util.Vector curves,
                  GenesInfo[] genes)

GenomeInfo

Parameters:

id - String

adb - String

name - String

curves - Vector

genes - GenesInfo[]

GenomeInfo

public GenomeInfo(int genomeId,
                  java.lang.String id,
                  java.lang.String adb,
                  java.lang.String name,
                  java.util.Vector curves,
                  GenesInfo[] genes,
                  java.lang.String defPos,
                  boolean isDefault,
                  java.lang.String dataUrl,
                  java.util.Vector browsers,
                  int type)

GenomeInfo

Parameters:

genomeId - int

id - String

adb - String

name - String

curves - Vector

genes - GenesInfo[]

defPos - String

isDefault - boolean

dataUrl - String

browsers - Vector

type - int

Method Detail

getGenomeId

public int getGenomeId()

get Genome Id

Returns:

int

getId

public java.lang.String getId()

get Id

Returns:

String

getAdb

public java.lang.String getAdb()

get Annotation db

Returns:

String

getName

public java.lang.String getName()

get Name

Returns:

String

getCurves

public java.util.Vector getCurves()

get Curves

Returns:

Vector

getCurve

public CurveInfo getCurve(int index)

get Curve Info

Parameters:

index - int

Returns:

CurveInfo

getCurve

public CurveInfo getCurve(java.lang.String ID)

setCheckedCurves

public void setCheckedCurves(java.util.Vector curves)

set list of Checked Curves

Parameters:

curves - Vector

getCheckedCurves

public java.util.Vector getCheckedCurves()

return list of Checked Curves

Returns:

Vector

getDefPos

public java.lang.String getDefPos()

ge tDefault Position

Returns:

String

getCurrentPos

public java.lang.String getCurrentPos()

get Current Position

Returns:

String

setCurrentPos

public void setCurrentPos(java.lang.String pos)

set Current Position

Parameters:

pos - String

isDefault

public boolean isDefault()

return true if Default

Returns:

boolean

getGenesInfos

public GenesInfo[] getGenesInfos()

return GenesInfos

Returns:

GenesInfo[]

See Also:

GenesInfo

isDeleted

public boolean isDeleted()

return true if deleted

Returns:

boolean

getDataUrl

public java.lang.String getDataUrl()

get Data Url string

Returns:

String

getBrowsers

public java.util.Vector getBrowsers()

return all available Browsers

Returns:

Vector

getType

public int getType()

get Type

Returns:

int

setDeleted

public void setDeleted(boolean deleted)

set genome as Deleted

Parameters:

deleted - boolean

addCurve

public void addCurve(CurveInfo curve)

add Curve

Parameters:

curve - CurveInfo

getNumberOfCurves

public int getNumberOfCurves()

get Number Of Curves

Returns:

int

toString

public java.lang.String toString()

return XML formatted summary string

Overrides:

toString in class java.lang.Object

Returns:

String

getContig

public ChromInfo getContig(java.lang.String name)

get Contig (Chromosome)

Parameters:

name - String

Returns:

ChromInfo

setContig

public void setContig(java.lang.String name,
                      ChromInfo contig)

setContig (Chromosome)

Parameters:

contig - ChromInfo