uk.ac.ebi.intact.application.hierarchView.business
Interface IntactUserI

All Superinterfaces:

java.util.EventListener, javax.servlet.http.HttpSessionBindingListener, IntactUserI, java.io.Serializable

All Known Implementing Classes:

IntactUser

public interface IntactUserI

extends java.io.Serializable, javax.servlet.http.HttpSessionBindingListener, IntactUserI

This interface stores information about an Intact Web user session. Instead of binding multiple objects, only an object of this class is bound to a session, thus serving a single access point for multiple information.

This class implements the HttpSessionBindingListener interface for it can be notified of session time outs.

Version:

$Id: IntactUserI.java,v 1.15 2003/11/13 14:15:21 skerrien Exp $

Author:

Samuel Kerrien (skerrien@ebi.ac.uk)

Field Summary

static java.util.Properties	GRAPH_PROPERTIES
static java.util.Properties	GRAPH2MIF_PROPERTIES
static java.util.Properties	HIGHLIGHTING_PROPERTIES
static java.util.Properties	SEARCH_PROPERTIES
static java.util.Properties	WEB_SERVICE_PROPERTIES

Method Summary

void	addHighlightOption(java.lang.String name, java.lang.Object value) Add a new option in the option set. That new option is referenced by its name
boolean	clickBehaviourIsAdd()
boolean	clickBehaviourIsCenter()
void	desacreaseDepth()
java.lang.String	getApplicationPath()
java.lang.String	getBehaviour()
int	getCurrentDepth()
IntactHelper	getHelper()
java.lang.Object	getHighlightOption(java.lang.String name) Get the value associated to the option name.
ImageBean	getImageBean()
InteractionNetwork	getInteractionNetwork()
java.util.Collection	getKeys()
java.lang.String	getMethodClass()
java.lang.String	getMethodLabel()
java.lang.String	getQueryString()
java.lang.String	getSearchUrl()
java.lang.String	getSearchUrl(java.lang.String query, boolean addFullContext)
java.lang.String	getSelectedKey()
java.lang.String	getSourceURL()
boolean	hasSourceUrlToDisplay()
void	increaseDepth()
void	init() Set the default value of user's data
boolean	InteractionNetworkReadyToBeDisplayed()
boolean	InteractionNetworkReadyToBeHighlighted()
boolean	maximalDepthReached()
boolean	minimalDepthReached()
void	resetHighlightOptions() Clear all highlight options.
void	resetSourceURL()
void	setBehaviour(java.lang.String behaviour)
void	setClickBehaviour(ClickBehaviourForm form)
void	setCurrentDepth(int i)
void	setDepthToDefault()
void	setImageBean(ImageBean imageBean)
void	setInteractionNetwork(InteractionNetwork in)
void	setKeys(java.util.Collection keys)
void	setMethodClass(java.lang.String methodClass)
void	setMethodLabel(java.lang.String methodLabel)
void	setQueryString(java.lang.String aQueryString)
void	setSelectedKey(java.lang.String key)
void	setSourceURL(java.lang.String url)
InteractionNetwork	subGraph(InteractionNetwork in, int graphDepth, java.util.Collection experiments, int complexExpansion) Returns a subgraph centered on startNode.

Methods inherited from interface javax.servlet.http.HttpSessionBindingListener

valueBound, valueUnbound

Methods inherited from interface uk.ac.ebi.intact.application.commons.business.IntactUserI

getDatabaseName, getUserName, search

Field Detail

GRAPH_PROPERTIES

public static final java.util.Properties GRAPH_PROPERTIES

SEARCH_PROPERTIES

public static final java.util.Properties SEARCH_PROPERTIES

WEB_SERVICE_PROPERTIES

public static final java.util.Properties WEB_SERVICE_PROPERTIES

HIGHLIGHTING_PROPERTIES

public static final java.util.Properties HIGHLIGHTING_PROPERTIES

GRAPH2MIF_PROPERTIES

public static final java.util.Properties GRAPH2MIF_PROPERTIES

Method Detail

getQueryString

public java.lang.String getQueryString()

getApplicationPath

public java.lang.String getApplicationPath()

getCurrentDepth

public int getCurrentDepth()

minimalDepthReached

public boolean minimalDepthReached()

maximalDepthReached

public boolean maximalDepthReached()

getMethodLabel

public java.lang.String getMethodLabel()

getMethodClass

public java.lang.String getMethodClass()

getBehaviour

public java.lang.String getBehaviour()

getImageBean

public ImageBean getImageBean()

getKeys

public java.util.Collection getKeys()

getSelectedKey

public java.lang.String getSelectedKey()

setClickBehaviour

public void setClickBehaviour(ClickBehaviourForm form)

clickBehaviourIsAdd

public boolean clickBehaviourIsAdd()

clickBehaviourIsCenter

public boolean clickBehaviourIsCenter()

getInteractionNetwork

public InteractionNetwork getInteractionNetwork()

InteractionNetworkReadyToBeDisplayed

public boolean InteractionNetworkReadyToBeDisplayed()

InteractionNetworkReadyToBeHighlighted

public boolean InteractionNetworkReadyToBeHighlighted()

getHelper

public IntactHelper getHelper()

getSourceURL

public java.lang.String getSourceURL()

hasSourceUrlToDisplay

public boolean hasSourceUrlToDisplay()

getSearchUrl

public java.lang.String getSearchUrl(java.lang.String query,
                                     boolean addFullContext)

getSearchUrl

public java.lang.String getSearchUrl()

setQueryString

public void setQueryString(java.lang.String aQueryString)

increaseDepth

public void increaseDepth()

desacreaseDepth

public void desacreaseDepth()

setDepthToDefault

public void setDepthToDefault()

setMethodLabel

public void setMethodLabel(java.lang.String methodLabel)

setMethodClass

public void setMethodClass(java.lang.String methodClass)

setBehaviour

public void setBehaviour(java.lang.String behaviour)

setImageBean

public void setImageBean(ImageBean imageBean)

setKeys

public void setKeys(java.util.Collection keys)

setSelectedKey

public void setSelectedKey(java.lang.String key)

setInteractionNetwork

public void setInteractionNetwork(InteractionNetwork in)

setSourceURL

public void setSourceURL(java.lang.String url)

resetSourceURL

public void resetSourceURL()

init

public void init()

Set the default value of user's data

subGraph

public InteractionNetwork subGraph(InteractionNetwork in,
                                   int graphDepth,
                                   java.util.Collection experiments,
                                   int complexExpansion)
                            throws IntactException

Returns a subgraph centered on startNode. The subgraph will contain all nodes which are up to graphDepth interactions away from startNode. Only Interactions which belong to one of the Experiments in experiments will be taken into account. If experiments is empty, all Interactions are taken into account. Graph depth: This parameter limits the size of the returned interaction graph. All baits are shown with all the interacting preys, even if they would normally be on the "rim" of the graph. Therefore the actual diameter of the graph may be 2*(graphDepth+1). Expansion: If an Interaction has more than two interactors, it has to be defined how pairwise interactions are generated from the complex data. The possible values are defined in the beginning of this file.

Parameters:

in - - the interaction network.

graphDepth - - depth of the graph

experiments - - Experiments which should be taken into account

complexExpansion - - Mode of expansion of complexes into pairwise interactions

Returns:

a InteractionNetwork object.

Throws:

IntactException - - thrown if problems are encountered

resetHighlightOptions

public void resetHighlightOptions()

Clear all highlight options.

addHighlightOption

public void addHighlightOption(java.lang.String name,
                               java.lang.Object value)

Add a new option in the option set.
That new option is referenced by its name

Parameters:

name - name of the option

value - value taken by the option

getHighlightOption

public java.lang.Object getHighlightOption(java.lang.String name)

Get the value associated to the option name.

Parameters:

name - the name of the option we want the value

Returns:

the value associated to the name

setCurrentDepth

public void setCurrentDepth(int i)