Intact Core Documentation (Version 0.8)

Packages

uk.ac.ebi.html
uk.ac.ebi.intact.application.commons.business
uk.ac.ebi.intact.application.commons.exception
uk.ac.ebi.intact.application.commons.search
uk.ac.ebi.intact.application.commons.struts.taglibs
uk.ac.ebi.intact.application.commons.util
uk.ac.ebi.intact.application.dataConversion
uk.ac.ebi.intact.application.editor.business	The classes implementing the business logic of the CvEdit application are in this package.
uk.ac.ebi.intact.application.editor.exception	This package includes exception classes for the CvEdit application.
uk.ac.ebi.intact.application.editor.exception.validation
uk.ac.ebi.intact.application.editor.struts.action	This package contains classes related to the Controller component of the MVC framework.
uk.ac.ebi.intact.application.editor.struts.action.biosrc
uk.ac.ebi.intact.application.editor.struts.action.experiment
uk.ac.ebi.intact.application.editor.struts.action.interaction
uk.ac.ebi.intact.application.editor.struts.action.util
uk.ac.ebi.intact.application.editor.struts.framework	This package contains common classes required for the MVC framework.
uk.ac.ebi.intact.application.editor.struts.framework.util	This package contains utility methods common for the struts framework.
uk.ac.ebi.intact.application.editor.struts.security	The classes required for the security of the application are in this package.
uk.ac.ebi.intact.application.editor.struts.view	This package contains classes belonging to the View component of the MVC framework.
uk.ac.ebi.intact.application.editor.struts.view.biosrc
uk.ac.ebi.intact.application.editor.struts.view.cv
uk.ac.ebi.intact.application.editor.struts.view.experiment
uk.ac.ebi.intact.application.editor.struts.view.interaction
uk.ac.ebi.intact.application.editor.util
uk.ac.ebi.intact.application.goDensity.business.binaryInteractions
uk.ac.ebi.intact.application.goDensity.business.dag
uk.ac.ebi.intact.application.goDensity.business.data
uk.ac.ebi.intact.application.goDensity.business.image
uk.ac.ebi.intact.application.goDensity.exception
uk.ac.ebi.intact.application.goDensity.setupGoDensity
uk.ac.ebi.intact.application.goDensity.struts.business
uk.ac.ebi.intact.application.goDensity.struts.controller
uk.ac.ebi.intact.application.goDensity.struts.view
uk.ac.ebi.intact.application.graph2MIF	The classes of the Graph2MIF application are in this package.
uk.ac.ebi.intact.application.graph2MIF.client	This package contains the example clients of graph2MIF. You should easiely be able to copy the important lines for creating imports methods to you local application.
uk.ac.ebi.intact.application.graph2MIF.conversion
uk.ac.ebi.intact.application.graph2MIF.exception
uk.ac.ebi.intact.application.hierarchView.business	Some utility classes and packages.
uk.ac.ebi.intact.application.hierarchView.business.graph	Contains classes to specialize the generic Graph class, and so give a specific behaviour like TLP export.
uk.ac.ebi.intact.application.hierarchView.business.image	Image producing framework.
uk.ac.ebi.intact.application.hierarchView.business.servlet	Some Servlets used to : - display the produced picture on the browser.
uk.ac.ebi.intact.application.hierarchView.business.tulip	Client and Server side of the Tulip web service.
uk.ac.ebi.intact.application.hierarchView.business.tulip.client	Make the task to access the web service easier for the client.
uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated
uk.ac.ebi.intact.application.hierarchView.business.tulip.webService	Server side of the web service, Interface and implementation of the web service tasks.
uk.ac.ebi.intact.application.hierarchView.exception
uk.ac.ebi.intact.application.hierarchView.highlightment	Generic framework to highlight part of an interaction network.
uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour	What modification do we apply to the interaction network.
uk.ac.ebi.intact.application.hierarchView.highlightment.source	From what do we select the proteins to highlight.
uk.ac.ebi.intact.application.hierarchView.struts	This package provides struts related classes.
uk.ac.ebi.intact.application.hierarchView.struts.controller
uk.ac.ebi.intact.application.hierarchView.struts.framework
uk.ac.ebi.intact.application.hierarchView.struts.taglibs
uk.ac.ebi.intact.application.hierarchView.struts.view
uk.ac.ebi.intact.application.hierarchView.struts.view.utils
uk.ac.ebi.intact.application.intSeq.business	The classes implementing the business logic of the IntSeq application are in this package.
uk.ac.ebi.intact.application.intSeq.exception	This package includes exception classes for the IntSeq application.
uk.ac.ebi.intact.application.intSeq.struts.controller	This package contains classes related to the Controller component of the MVC framework.
uk.ac.ebi.intact.application.intSeq.struts.framework	This package contains common classes required for the MVC framework.
uk.ac.ebi.intact.application.intSeq.struts.view	This package contains classes belonging to the View component of the MVC framework.
uk.ac.ebi.intact.application.intSeq.struts.view.utils	This package contains classes indirectly belonging to the View component of the MVC framework. It contains beans classes which make results objects for each line of the display table. It contains also Decorator classes which imply to include the Design Pattern technology.
uk.ac.ebi.intact.application.predict.business
uk.ac.ebi.intact.application.predict.struts.action
uk.ac.ebi.intact.application.predict.struts.framework
uk.ac.ebi.intact.application.predict.struts.view
uk.ac.ebi.intact.application.predict.util
uk.ac.ebi.intact.application.search2.business
uk.ac.ebi.intact.application.search2.struts.controller
uk.ac.ebi.intact.application.search2.struts.framework
uk.ac.ebi.intact.application.search2.struts.framework.util
uk.ac.ebi.intact.application.search2.struts.view
uk.ac.ebi.intact.application.search2.struts.view.details
uk.ac.ebi.intact.application.search2.struts.view.html
uk.ac.ebi.intact.application.search2.struts.view.single
uk.ac.ebi.intact.application.search2.struts.view.single.chunked
uk.ac.ebi.intact.application.statisticView.business	Classes which implement the business logic of the StatisticView application are in this package.
uk.ac.ebi.intact.application.statisticView.business.data	Contains the classes holding the statistics data.
uk.ac.ebi.intact.application.statisticView.business.graphic	Chart drawing package.
uk.ac.ebi.intact.application.statisticView.struts.controller
uk.ac.ebi.intact.application.statisticView.struts.view
uk.ac.ebi.intact.application.synchron	This package provides a capability for different IntAct servers (nodes) to exchange data entries.
uk.ac.ebi.intact.business	This package contains the helper class which allows clients to access the business tier for intact.
uk.ac.ebi.intact.model	This package is the implementation of the IntAct data model.
uk.ac.ebi.intact.model.proxy
uk.ac.ebi.intact.persistence	This package provides a persistence capability for intact.
uk.ac.ebi.intact.simpleGraph	A simple graph package for temporary processing, for example to prepare output for graph analysis packages.
uk.ac.ebi.intact.util	Various utilities and auxiliary scripts.
uk.ac.ebi.intact.util.fileParsing
uk.ac.ebi.intact.util.fileParsing.beans
uk.ac.ebi.intact.util.logging	Contains IntAct dedicated Appender for log4J.