object.hts
Class Hts_RManager

java.lang.Object
  object.hts.Hts_RManager

All Implemented Interfaces:

java.io.Serializable

public class Hts_RManager
extends java.lang.Object
implements java.io.Serializable

Description
A Hts_RManager object allow to perform R queies for Hts Objects
Infos : KLB - IPMC - 10/2008

See Also:

Serialized Form

Field Summary

private java.util.Hashtable	hashFiles Hashtable containing Listing of available files for this Hts_RManager query
private java.util.Hashtable	hashGroupLabel Hashtable containing Hts_sample group labels
private Hts_analysis	hts_analysis
private Hts_type	hts_type
static java.lang.String	MAIL_FROM Mail From for sending mail (mediante@ipmc.cnrs.fr)
static java.lang.String	MAIL_HOST Mail Host for sending mail (gelas.ipmc.cnrs.fr)
private java.lang.String	message
protected static java.lang.String	pathTmp path to temporary directory
private Project_order	project_order
private int	user_id ID of Users performing R queries
private java.util.Vector	vectorCMD Vector containing Command to R
private java.util.Vector	vectorHts_order Vector containing Hts_order Objects
private java.util.Vector	vectorHts_sample Vector containing Hts_sample Objects
private java.lang.String	workingDIR

Constructor Summary

Hts_RManager(int user_id)
Default constructor

Method Summary

boolean	checkHts_order(Hts_order hts_order)
boolean	checkHts_sample(Hts_sample hts_sample)
boolean	checkIsValidObject(Hts_type hts_t)
boolean	checkReplicates()
void	doAbundHisto()
void	doHeatMap()
void	doLimma()
void	doMatchingPeak()
void	doMergeCount()
void	doNcrnaHisto()
void	doPdfRepport()
void	doSageFiles()
void	doVolcanoPlot()
java.util.Hashtable	getHashFiles() Hashtable containing Listing of available files for this Hts_RManager query
java.util.Hashtable	getHashGroupLabel() Hashtable containing Hts_sample group labels
Hts_analysis	getHts_analysis() Hts_analysis to performs
Hts_type	getHts_type() Hts_type to performs
java.lang.String	getMessage() Message information
Project_order	getProject_order() project_order
int	getUser_id() user_id
java.util.Vector	getVectorCMD() Vector containing Command to R
java.util.Vector	getVectorHts_order() Vector containing Hts_order Objects
java.util.Vector	getVectorHts_sample() Vector containing Hts_sample Objects
java.lang.String	getWorkingDIR() workingDIR
void	initWorkingDIR()
void	launchRQuery()
void	loadParams(java.util.Hashtable hashParams) This function loadParams from HTML form.
void	perform()
void	serieToFile()
void	setHashFiles(java.util.Hashtable hashFiles)
void	setHashGroupLabel(java.util.Hashtable hashGroupLabel)
void	setHts_analysis(Hts_analysis hts_analysis)
void	setHts_type(Hts_type hts_type)
void	setMessage(java.lang.String message)
void	setProject_order(Project_order project_order)
void	setStaticParams(java.util.Hashtable hashMailConfiguration, java.util.Hashtable configFields) Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM
void	setUser_id(int user_id)
void	setVectorCMD(java.util.Vector vectorCMD)
void	setVectorHts_order(java.util.Vector vectorHts_order)
void	setVectorHts_sample(java.util.Vector vectorHts_sample)
void	setWorkingDIR(java.lang.String workingDIR)

Methods inherited from class java.lang.Object

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

Field Detail

user_id

private int user_id

ID of Users performing R queries

project_order

private Project_order project_order

vectorHts_sample

private java.util.Vector vectorHts_sample

Vector containing Hts_sample Objects

vectorHts_order

private java.util.Vector vectorHts_order

Vector containing Hts_order Objects

hashGroupLabel

private java.util.Hashtable hashGroupLabel

Hashtable containing Hts_sample group labels

vectorCMD

private java.util.Vector vectorCMD

Vector containing Command to R

hashFiles

private java.util.Hashtable hashFiles

Hashtable containing Listing of available files for this Hts_RManager query

hts_type

private Hts_type hts_type

hts_analysis

private Hts_analysis hts_analysis

workingDIR

private java.lang.String workingDIR

message

private java.lang.String message

MAIL_HOST

public static java.lang.String MAIL_HOST

Mail Host for sending mail (gelas.ipmc.cnrs.fr)

MAIL_FROM

public static java.lang.String MAIL_FROM

Mail From for sending mail (mediante@ipmc.cnrs.fr)

pathTmp

protected static java.lang.String pathTmp

path to temporary directory

Constructor Detail

Hts_RManager

public Hts_RManager(int user_id)

Default constructor

Method Detail

setStaticParams

public void setStaticParams(java.util.Hashtable hashMailConfiguration,
                            java.util.Hashtable configFields)

Initialize static parameters from the configuration file - MAIL_HOST - MAIL_FROM

getUser_id

public int getUser_id()

user_id

setUser_id

public void setUser_id(int user_id)

getProject_order

public Project_order getProject_order()

project_order

setProject_order

public void setProject_order(Project_order project_order)

getVectorHts_sample

public java.util.Vector getVectorHts_sample()

Vector containing Hts_sample Objects

setVectorHts_sample

public void setVectorHts_sample(java.util.Vector vectorHts_sample)

getHashGroupLabel

public java.util.Hashtable getHashGroupLabel()

Hashtable containing Hts_sample group labels

setHashGroupLabel

public void setHashGroupLabel(java.util.Hashtable hashGroupLabel)

getVectorHts_order

public java.util.Vector getVectorHts_order()

Vector containing Hts_order Objects

setVectorHts_order

public void setVectorHts_order(java.util.Vector vectorHts_order)

getVectorCMD

public java.util.Vector getVectorCMD()

Vector containing Command to R

setVectorCMD

public void setVectorCMD(java.util.Vector vectorCMD)

getHashFiles

public java.util.Hashtable getHashFiles()

Hashtable containing Listing of available files for this Hts_RManager query

setHashFiles

public void setHashFiles(java.util.Hashtable hashFiles)

getWorkingDIR

public java.lang.String getWorkingDIR()

workingDIR

setWorkingDIR

public void setWorkingDIR(java.lang.String workingDIR)

getMessage

public java.lang.String getMessage()

Message information

setMessage

public void setMessage(java.lang.String message)

getHts_type

public Hts_type getHts_type()

Hts_type to performs

setHts_type

public void setHts_type(Hts_type hts_type)

getHts_analysis

public Hts_analysis getHts_analysis()

Hts_analysis to performs

setHts_analysis

public void setHts_analysis(Hts_analysis hts_analysis)

loadParams

public void loadParams(java.util.Hashtable hashParams)

This function loadParams from HTML form.

Parameters:

hashParams - Hashtable containing parameters

checkHts_sample

public boolean checkHts_sample(Hts_sample hts_sample)

checkHts_order

public boolean checkHts_order(Hts_order hts_order)

checkIsValidObject

public boolean checkIsValidObject(Hts_type hts_t)

checkReplicates

public boolean checkReplicates()

perform

public void perform()

doMergeCount

public void doMergeCount()

doPdfRepport

public void doPdfRepport()

doAbundHisto

public void doAbundHisto()

doLimma

public void doLimma()

doVolcanoPlot

public void doVolcanoPlot()

serieToFile

public void serieToFile()

doNcrnaHisto

public void doNcrnaHisto()

doHeatMap

public void doHeatMap()

doSageFiles

public void doSageFiles()

doMatchingPeak

public void doMatchingPeak()

launchRQuery

public void launchRQuery()

initWorkingDIR

public void initWorkingDIR()