object.common
Class ImageManager

java.lang.Object
  object.common.ImageManager

All Implemented Interfaces:

java.io.Serializable

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

Description
ImageManager Object is used to access data from quantification file and
display it at the screen in the Microarray data managment web interface
Infos : KLB - IPMC - 08/2003

See Also:

Organism, Oligo, Exon, Cytoband, Oligo_externe, Oligo_adhoc, GoLink, Serialized Form

Field Summary

private java.lang.String	appli External application reference for download file (directory : 'file')
private int	array_1 Int concerning the first microarray for graph visualization (directory : 'graph')
private int	array_2 Int concerning the second microarray for graph visualization (directory : 'graph')
private double	Bvalue
private java.lang.String	directory Type of datas to display at screen, could be : - 'select' : selection of microarrays - 'imag' : visualization of image of microarray quantification - 'cart' : download of gene datas according to the gene cart - 'file' : download of pre-formatted files for external applications - 'chro' : visuallization of genes cart on a chromosome map - 'graphe' : visualization of graphs concerning microarrays selected - 'image' : modification of quantification image light and contrast
private DisplayParams	displayParams DisplayParams Object contains informations about displaying images (directory : 'file')
private GeneCart	genecart GeneCart Object for this ImageManager Object
private java.util.Hashtable	hashCalcul Hashtable containing values of calcul asked by user
protected static java.util.Hashtable	hashColor
private java.util.Hashtable	hashDatas Hashtable containing Quantification_file Object
private java.util.Hashtable	hashFile Hashtable containing Files path downloadables
private java.util.Hashtable	hashImage Hashtable containing Images path displayed on screen
protected static java.util.Hashtable	hashLegend
private java.util.Hashtable	hashMap Hashtable containing Html Maps for Images displayed on screen
private java.lang.String[]	labRefList String[] containing distinct labeling references among the Project_order Object concerned
private double	logFC
private int	nb_bloc Numero of the bloc to display at the screen
private boolean	onlyCart True if only genes in cart must be displayed on the visualization graph (directory : 'graph')
protected static java.lang.String	pathImages
protected static java.lang.String	pathMicroarray
protected static java.lang.String	pathSpotting
protected static java.lang.String	pathTmp
private Project_order	project_order Project_order Object concerning this ImageManager Object
private Rstat	rstat
private int	size_spot
private java.lang.String	title_graph Title of graph
private java.lang.String	toptable
private boolean	twoarraygraph
private java.lang.String	type_graphe Type of graph for visualization (directory : 'graph')
private int	user_id ID of User owning this ImageManager Object
private java.util.Vector	vectorMicroarrays Vector containing Microarray Objects selected for visualization

Constructor Summary

ImageManager()
Default constructor

ImageManager(int user_id, Project_order project_order)
Constructs an ImageManager object

Method Summary

void	addToCart()
void	addToCart(int i)
java.lang.String[]	bubbleSearch(java.lang.String[] symbol) This function proceed to a bubble sort on a String[]
void	createApplicationFile(java.util.Hashtable hashParams) This function proceed to the creation of the External Application files.
void	createDatasFile(java.util.Hashtable hashParams) This function proceed to the creation of the Datas files.
void	createGeneAnovaFile(java.util.Vector vectorMicroarray) This function proceed to the creation of GeneAnova analysis.
void	createGEOFile(java.util.Vector vectorMicroarray) This function proceed to the creation of GEO submission file.
void	createGEOMatrix(java.util.Vector vectorMicroarray) This function proceed to the creation of GEO matrix submission file.
void	createIngenuityFile(Toptable toptable) This function proceed to the creation of Ingenuity file.
void	createLimmaFile(java.util.Vector vectorMicroarray) This function proceed to the creation of the Limma Application file.
void	createMageFile(java.util.Vector vectorMicroarray) This function proceed to the creation of the ArrayExpress submission files.
void	createMEVFile(java.util.Vector vectorMicroarray) This function proceed to the creation of .
java.lang.String	getAppli() External application reference for download file (directory : 'file')
int	getArray_1() Int concerning the first microarray for graph visualization (directory : 'graph')
int	getArray_2() Int concerning the second microarray for graph visualization (directory : 'graph')
double	getBvalue() Bvalue for features filtration
java.lang.String	getDirectory() Type of datas to display at screen, could be : - 'select' : selection of microarrays - 'imag' : visualization of image of microarray quantification - 'cart' : download of gene datas according to the gene cart - 'file' : download of pre-formatted files for external applications - 'chro' : visuallization of genes cart on a chromosome map - 'graphe' : visualization of graphs concerning microarrays selected - 'image' : modification of quantification image light and contrast
DisplayParams	getDisplayParams() DisplayParams Object contains informations about displaying images (directory : 'file')
GeneCart	getGenecart() GeneCart Object for this ImageManager Object
java.lang.String	getGroupe(java.lang.String oligo_id, java.lang.String name, double b, double logFC)
java.util.Hashtable	getHashCalcul() Hashtable containing values of calcul asked by user
java.util.Hashtable	getHashColor() Hashtable containing values of color mapping
java.util.Hashtable	getHashCourbes()
java.util.Hashtable	getHashDatas() Hashtable containing Quantification_file Object
java.util.Hashtable	getHashFile() Hashtable containing Files path downloadables
java.util.Hashtable	getHashImage() Hashtable containing Images path displayed on screen
java.util.Hashtable	getHashMap() Hashtable containing Html Maps for Images displayed on screen
java.util.Hashtable	getHashPoints() This function proceed to the creation of the Hashtable needed for the makeImage function of ImageManager.
java.util.Hashtable	getHashPointsToptable() This function proceed to the creation of the Hashtable needed for the makeImage function of ImageManager.
java.lang.String[]	getLabRefList() String[] containing distinct labeling references among the Project_order Object concerned
double	getLogFC() logFC for features filtration
int	getNb_bloc() Numero of the bloc to display at the screen
boolean	getOnlyCart() True if only genes in cart must be displayed on the visualization graph (directory : 'graph')
double	getPearson(java.util.Hashtable hashPoints)
Project_order	getProject_order() Project_order Object concerning this ImageManager Object
Rstat	getRstat() Rstat
int	getSize_spot() Size of spot for features illustration
java.lang.String	getToptable() Toptable for features filtration
java.lang.String	getType_graphe() Type of graph for visualization (directory : 'graph')
int	getUser_id() ID of User owning this ImageManager Object
java.util.Vector	getVectorMicroarrays() Vector containing Microarray Objects selected for visualization
void	loadHashColor() This function load Graph Colors for User.
void	loadLabRefList(int project_order_id) This function load attribute labRefList with distinct labbeling reference among the Project_order Object
void	makeBgDistribGraph()
void	makeChromoImage() This function proceed to the creation of the image of chromosomes according to the Gene Object stored in the cart parameter.
void	makeGraphs(java.util.Hashtable hashPoints, boolean as_line) This function proceed to the generation of graphe image.
void	proceed() This function proceed to Image creation in the visualization directory 'imag'.
void	proceedCalcul(java.lang.String type) This function proceed to the calcul of Quality Control defined in the type parameter received.
void	proceedGraphs()
void	proceedPlate384(int index) This function proceed to the creation of an image reformatting the Plate384 Object from the image of the Microarray hybridization.
void	proceedPlate96(int index) This function proceed to the creation of an image reformatting the Plate96 Object from the image of the Microarray hybridization.
void	resetCart()
void	resetImages() This function reset images Path from the hastable this.hashImage
void	saveCart(java.lang.String desciption)
void	saveHashColor(int user_id) This function save or update Graph Colors for User.
void	setAppli(java.lang.String appli)
void	setArray_1(int array_1)
void	setArray_2(int array_2)
void	setBvalue(double Bvalue)
void	setDirectory(java.lang.String directory)
void	setDisplayParams(DisplayParams displayParams)
void	setGenecart(GeneCart genecart)
void	setHashCalcul(java.util.Hashtable hashCalcul)
void	setHashColor(java.util.Hashtable hashColor)
void	setHashDatas(java.util.Hashtable hashDatas)
void	setHashFile(java.util.Hashtable hashFile)
void	setHashImage(java.util.Hashtable hashImage)
void	setHashMap(java.util.Hashtable hashMap)
void	setLabRefList(java.lang.String[] labRefList)
void	setLogFC(double logFC)
void	setNb_bloc(int nb_bloc)
void	setOnlyCart(boolean onlyCart)
void	setProject_order(Project_order project_order)
void	setRstat(Rstat rstat)
void	setSize_spot(int size_spot)
void	setStaticParams(java.util.Hashtable configFields) Initialize static parameters from the configuration file - pathMicroarray - pathSpotting - pathImages - pathTmp
void	setToptable(java.lang.String toptable)
void	setType_graphe(java.lang.String type_graphe)
void	setUser_id(int user_id)
void	setVectorMicroarrays(java.util.Vector vectorMicroarrays)
void	update(java.lang.String slide_code) This function update the list of Microarrays in the attribute this.vectorMicroarrays

Methods inherited from class java.lang.Object

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

Field Detail

project_order

private Project_order project_order

Project_order Object concerning this ImageManager Object

vectorMicroarrays

private java.util.Vector vectorMicroarrays

Vector containing Microarray Objects selected for visualization

genecart

private GeneCart genecart

GeneCart Object for this ImageManager Object

user_id

private int user_id

ID of User owning this ImageManager Object

nb_bloc

private int nb_bloc

Numero of the bloc to display at the screen

directory

private java.lang.String directory

Type of datas to display at screen, could be :
- 'select' : selection of microarrays
- 'imag' : visualization of image of microarray quantification
- 'cart' : download of gene datas according to the gene cart
- 'file' : download of pre-formatted files for external applications
- 'chro' : visuallization of genes cart on a chromosome map
- 'graphe' : visualization of graphs concerning microarrays selected
- 'image' : modification of quantification image light and contrast

appli

private java.lang.String appli

External application reference for download file (directory : 'file')

hashMap

private java.util.Hashtable hashMap

Hashtable containing Html Maps for Images displayed on screen

hashImage

private java.util.Hashtable hashImage

Hashtable containing Images path displayed on screen

hashFile

private java.util.Hashtable hashFile

Hashtable containing Files path downloadables

hashCalcul

private java.util.Hashtable hashCalcul

Hashtable containing values of calcul asked by user

hashDatas

private java.util.Hashtable hashDatas

Hashtable containing Quantification_file Object

labRefList

private java.lang.String[] labRefList

String[] containing distinct labeling references among the Project_order Object concerned

displayParams

private DisplayParams displayParams

DisplayParams Object contains informations about displaying images (directory : 'file')

array_1

private int array_1

Int concerning the first microarray for graph visualization (directory : 'graph')

array_2

private int array_2

Int concerning the second microarray for graph visualization (directory : 'graph')

type_graphe

private java.lang.String type_graphe

Type of graph for visualization (directory : 'graph')

title_graph

private java.lang.String title_graph

Title of graph

onlyCart

private boolean onlyCart

True if only genes in cart must be displayed on the visualization graph (directory : 'graph')

toptable

private java.lang.String toptable

Bvalue

private double Bvalue

logFC

private double logFC

size_spot

private int size_spot

twoarraygraph

private boolean twoarraygraph

rstat

private Rstat rstat

pathMicroarray

protected static java.lang.String pathMicroarray

pathSpotting

protected static java.lang.String pathSpotting

pathImages

protected static java.lang.String pathImages

pathTmp

protected static java.lang.String pathTmp

hashColor

protected static java.util.Hashtable hashColor

hashLegend

protected static java.util.Hashtable hashLegend

Constructor Detail

ImageManager

public ImageManager()

Default constructor

ImageManager

public ImageManager(int user_id,
                    Project_order project_order)

Constructs an ImageManager object

Parameters:

user_id - ID of existing User Object

project_order - Project_order Object to visualize

See Also:

Project_order, DisplayParams

Method Detail

setStaticParams

public void setStaticParams(java.util.Hashtable configFields)

Initialize static parameters from the configuration file
- pathMicroarray
- pathSpotting
- pathImages
- pathTmp

getUser_id

public int getUser_id()

ID of User owning this ImageManager Object

setUser_id

public void setUser_id(int user_id)

getNb_bloc

public int getNb_bloc()

Numero of the bloc to display at the screen

setNb_bloc

public void setNb_bloc(int nb_bloc)

getDirectory

public java.lang.String getDirectory()

Type of datas to display at screen, could be :
- 'select' : selection of microarrays
- 'imag' : visualization of image of microarray quantification
- 'cart' : download of gene datas according to the gene cart
- 'file' : download of pre-formatted files for external applications
- 'chro' : visuallization of genes cart on a chromosome map
- 'graphe' : visualization of graphs concerning microarrays selected
- 'image' : modification of quantification image light and contrast

setDirectory

public void setDirectory(java.lang.String directory)

getAppli

public java.lang.String getAppli()

External application reference for download file (directory : 'file')

setAppli

public void setAppli(java.lang.String appli)

getGenecart

public GeneCart getGenecart()

GeneCart Object for this ImageManager Object

setGenecart

public void setGenecart(GeneCart genecart)

getHashMap

public java.util.Hashtable getHashMap()

Hashtable containing Html Maps for Images displayed on screen

setHashMap

public void setHashMap(java.util.Hashtable hashMap)

getHashImage

public java.util.Hashtable getHashImage()

Hashtable containing Images path displayed on screen

setHashImage

public void setHashImage(java.util.Hashtable hashImage)

getHashFile

public java.util.Hashtable getHashFile()

Hashtable containing Files path downloadables

setHashFile

public void setHashFile(java.util.Hashtable hashFile)

getHashCalcul

public java.util.Hashtable getHashCalcul()

Hashtable containing values of calcul asked by user

setHashCalcul

public void setHashCalcul(java.util.Hashtable hashCalcul)

getHashColor

public java.util.Hashtable getHashColor()

Hashtable containing values of color mapping

setHashColor

public void setHashColor(java.util.Hashtable hashColor)

getProject_order

public Project_order getProject_order()

Project_order Object concerning this ImageManager Object

setProject_order

public void setProject_order(Project_order project_order)

getVectorMicroarrays

public java.util.Vector getVectorMicroarrays()

Vector containing Microarray Objects selected for visualization

setVectorMicroarrays

public void setVectorMicroarrays(java.util.Vector vectorMicroarrays)

getDisplayParams

public DisplayParams getDisplayParams()

DisplayParams Object contains informations about displaying images (directory : 'file')

setDisplayParams

public void setDisplayParams(DisplayParams displayParams)

getArray_1

public int getArray_1()

Int concerning the first microarray for graph visualization (directory : 'graph')

setArray_1

public void setArray_1(int array_1)

getArray_2

public int getArray_2()

Int concerning the second microarray for graph visualization (directory : 'graph')

setArray_2

public void setArray_2(int array_2)

getType_graphe

public java.lang.String getType_graphe()

Type of graph for visualization (directory : 'graph')

setType_graphe

public void setType_graphe(java.lang.String type_graphe)

getOnlyCart

public boolean getOnlyCart()

True if only genes in cart must be displayed on the visualization graph (directory : 'graph')

setOnlyCart

public void setOnlyCart(boolean onlyCart)

getLabRefList

public java.lang.String[] getLabRefList()

String[] containing distinct labeling references among the Project_order Object concerned

setLabRefList

public void setLabRefList(java.lang.String[] labRefList)

getHashDatas

public java.util.Hashtable getHashDatas()

Hashtable containing Quantification_file Object

setHashDatas

public void setHashDatas(java.util.Hashtable hashDatas)

getToptable

public java.lang.String getToptable()

Toptable for features filtration

setToptable

public void setToptable(java.lang.String toptable)

getBvalue

public double getBvalue()

Bvalue for features filtration

setBvalue

public void setBvalue(double Bvalue)

getLogFC

public double getLogFC()

logFC for features filtration

setLogFC

public void setLogFC(double logFC)

getSize_spot

public int getSize_spot()

Size of spot for features illustration

setSize_spot

public void setSize_spot(int size_spot)

getRstat

public Rstat getRstat()

Rstat

setRstat

public void setRstat(Rstat rstat)

resetCart

public void resetCart()

addToCart

public void addToCart()

addToCart

public void addToCart(int i)

saveCart

public void saveCart(java.lang.String desciption)

loadLabRefList

public void loadLabRefList(int project_order_id)

This function load attribute labRefList with distinct labbeling reference among the Project_order Object

Parameters:

project_order_id - ID of Project_order concerning this ImageManager Object

resetImages

public void resetImages()

This function reset images Path from the hastable this.hashImage

update

public void update(java.lang.String slide_code)

This function update the list of Microarrays in the attribute this.vectorMicroarrays

Parameters:

slide_code - slide_code of the microarray concerned

See Also:

Microarray, Microarray.Microarray(String)

proceed

public void proceed()
             throws java.lang.Exception

This function proceed to Image creation in the visualization directory 'imag'.
Two case of Image creation :
- by blocs
- by spots
Initialization of hashMap and hashImage with the key "V"

Throws:

java.lang.Exception

See Also:

bubbleSearch(String[]), Feature, Microarray, Microarray.Microarray(int), Spotting, Spotting.Spotting(int), Scan

bubbleSearch

public java.lang.String[] bubbleSearch(java.lang.String[] symbol)

This function proceed to a bubble sort on a String[]

Parameters:

symbol - String[] which this function make a bubble sort

Returns:

retour String[] sorted

createDatasFile

public void createDatasFile(java.util.Hashtable hashParams)

This function proceed to the creation of the Datas files.

Parameters:

hashParams - Hastable containing all informations for creating the datas file, .xls format

createApplicationFile

public void createApplicationFile(java.util.Hashtable hashParams)

This function proceed to the creation of the External Application files.

Parameters:

hashParams - Hastable containing all informations for creating the External Application file, .tar.gz format

createGEOFile

public void createGEOFile(java.util.Vector vectorMicroarray)

This function proceed to the creation of GEO submission file.

Parameters:

vectorMicroarray - Vector of microarray Object for which we have to create a .gz archive for GEO submission

createGeneAnovaFile

public void createGeneAnovaFile(java.util.Vector vectorMicroarray)

This function proceed to the creation of GeneAnova analysis.

Parameters:

vectorMicroarray - Vector of microarray Object for which we have to create a .gz archive for GeneAnova analysis

createMEVFile

public void createMEVFile(java.util.Vector vectorMicroarray)

This function proceed to the creation of .

Parameters:

vectorMicroarray - Vector of microarray Object for which we have to create a .gz archive for MEV application

createLimmaFile

public void createLimmaFile(java.util.Vector vectorMicroarray)

This function proceed to the creation of the Limma Application file.

Parameters:

vectorMicroarray - Vector of microarray Object for which we have to create a .gz archive for Limma Application

createMageFile

public void createMageFile(java.util.Vector vectorMicroarray)

This function proceed to the creation of the ArrayExpress submission files.

Parameters:

vectorMicroarray - Vector of microarray Object for which we have to create a .gz archive for ArrayExpress submission

createIngenuityFile

public void createIngenuityFile(Toptable toptable)

This function proceed to the creation of Ingenuity file.

Parameters:

toptable - toptable Object for which we need an Ingenuity file.

makeChromoImage

public void makeChromoImage()
                     throws java.lang.Exception

This function proceed to the creation of the image of chromosomes according to the Gene Object stored in the cart parameter.

Throws:

java.lang.Exception

proceedPlate384

public void proceedPlate384(int index)
                     throws java.lang.Exception

This function proceed to the creation of an image reformatting the Plate384 Object from the image of the Microarray hybridization.

Parameters:

index - Number of the Plate384 in the .BCR file of the Spotting Object from which we begin to reformt the Plate384 OBject and the next 8 Plate384.

Throws:

java.lang.Exception

See Also:

Microarray, Spotting, Plate, Plate384, Scan

proceedPlate96

public void proceedPlate96(int index)
                    throws java.lang.Exception

This function proceed to the creation of an image reformatting the Plate96 Object from the image of the Microarray hybridization.

Parameters:

index - Number of the Plate96 in the .BCR file of the Spotting Object from which we begin to reformt the Plate96 OBject and the next 8 Plate96.

Throws:

java.lang.Exception

See Also:

Microarray, Spotting, Plate, Plate96, Scan

proceedGraphs

public void proceedGraphs()

makeGraphs

public void makeGraphs(java.util.Hashtable hashPoints,
                       boolean as_line)
                throws java.lang.Exception

This function proceed to the generation of graphe image.

Parameters:

hashPoints - Hashtable of Point Object concerned by this graph.

as_line - boolean true if we need Point object to be link with line onto the graph image produced.

Throws:

java.lang.Exception

See Also:

Point

getHashPoints

public java.util.Hashtable getHashPoints()
                                  throws java.lang.Exception

This function proceed to the creation of the Hashtable needed for the makeImage function of ImageManager.

Returns:

hashPoint Hashtable of Point Object concerned by the graph to be created by the makeImage function of ImageManager.

Throws:

java.lang.Exception

See Also:

Microarray, Microarray.Microarray(int), Microarray_project_type, Microarray_project_type.getShortRef(), Scan, Point

getHashPointsToptable

public java.util.Hashtable getHashPointsToptable()
                                          throws java.lang.Exception

This function proceed to the creation of the Hashtable needed for the makeImage function of ImageManager.

Returns:

hashPoint Hashtable of Point Object concerned by the graph to be created by the makeImage function of ImageManager.

Throws:

java.lang.Exception

See Also:

Microarray, Microarray.Microarray(int), Microarray_project_type, Microarray_project_type.getShortRef(), Scan, Point

makeBgDistribGraph

public void makeBgDistribGraph()
                        throws java.lang.Exception

Throws:

java.lang.Exception

getGroupe

public java.lang.String getGroupe(java.lang.String oligo_id,
                                  java.lang.String name,
                                  double b,
                                  double logFC)

getHashCourbes

public java.util.Hashtable getHashCourbes()
                                   throws java.lang.Exception

Throws:

java.lang.Exception

proceedCalcul

public void proceedCalcul(java.lang.String type)
                   throws java.lang.Exception

This function proceed to the calcul of Quality Control defined in the type parameter received.

Parameters:

type - Type of calcul to be performed.

Throws:

java.lang.Exception

See Also:

Microarray

getPearson

public double getPearson(java.util.Hashtable hashPoints)

loadHashColor

public void loadHashColor()

This function load Graph Colors for User.

saveHashColor

public void saveHashColor(int user_id)

This function save or update Graph Colors for User.

createGEOMatrix

public void createGEOMatrix(java.util.Vector vectorMicroarray)

This function proceed to the creation of GEO matrix submission file.

Parameters:

vectorMicroarray - Vector of Microarray Object for creating GEO matrix submission file, .tar.gz format