idare.sbmlannotator.internal

Class SBMLAnnotaterTask

java.lang.Object

org.cytoscape.work.AbstractTask

idare.sbmlannotator.internal.SBMLAnnotaterTask

All Implemented Interfaces:

org.cytoscape.work.Task

public class SBMLAnnotaterTask
extends org.cytoscape.work.AbstractTask

Field Summary

Fields inherited from class org.cytoscape.work.AbstractTask

cancelled

Constructor Summary

Constructors

Constructor and Description

SBMLAnnotaterTask(org.cytoscape.application.CyApplicationManager cymanager, SBMLDocument SBMLDoc, boolean GenerateGeneNodes, org.cytoscape.event.CyEventHelper eventHelper, String GeneAnnotDB, String ProtAnnotDB, Map<String,Set<CVTerm>> ProtAnnot, String sbmlTypeCol, String sbmlIDCol, String sbmlCompCol, String SBMLInteractionCol, IDAREImageNodeApp app) A Task reading in an SBML File and parsing its Notes fields adding the information to the Nodes of the current network.

Method Summary

Modifier and Type	Method and Description
double	GetYPosition(int number, int count, double y, double width) Get the Y Position for the number-th of code Nodes
void	run(org.cytoscape.work.TaskMonitor TaskMonitor)

Methods inherited from class org.cytoscape.work.AbstractTask

cancel, insertTasksAfterCurrentTask, insertTasksAfterCurrentTask, setTaskIterator

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLAnnotaterTask

public SBMLAnnotaterTask(org.cytoscape.application.CyApplicationManager cymanager,
                         SBMLDocument SBMLDoc,
                         boolean GenerateGeneNodes,
                         org.cytoscape.event.CyEventHelper eventHelper,
                         String GeneAnnotDB,
                         String ProtAnnotDB,
                         Map<String,Set<CVTerm>> ProtAnnot,
                         String sbmlTypeCol,
                         String sbmlIDCol,
                         String sbmlCompCol,
                         String SBMLInteractionCol,
                         IDAREImageNodeApp app)

A Task reading in an SBML File and parsing its Notes fields adding the information to the Nodes of the current network.

Parameters:

cymanager - The CyApplicationManager used to obtain the currently choosen network for this Task.

SBMLDoc - The SBMLDocument to obtain the annotation from

GenerateGeneNodes - whether to generate gene (and potentially protein) nodes

eventHelper - The CyEventHelper used to update the views.

GeneAnnotDB - The identifier used for protein name annotation ,

ProtAnnotDB - The name of the protein annotation database to be used.

ProtAnnot - a Map associating the protein names with their CVTerms,

sbmlTypeCol - The column of the in which the SBML Types are stored

sbmlIDCol - The nodeTable column in which the SBML IDs are stored

sbmlCompCol - The Column in which the SBML compartment is stored

SBMLInteractionCol - The Column to obtain the sbml interaction type from

app - The IDAREImageNodeApp used to keep the current network up to date.

Method Detail

run

public void run(org.cytoscape.work.TaskMonitor TaskMonitor)
         throws Exception

Specified by:

run in interface org.cytoscape.work.Task

Specified by:

run in class org.cytoscape.work.AbstractTask

Throws:

Exception

GetYPosition

public double GetYPosition(int number,
                           int count,
                           double y,
                           double width)

Get the Y Position for the number-th of code Nodes

Parameters:

number - - the position of the node (should be between 1 and count)

count - - the total count of nodes (this corresponds to the sections a circle is split into)

y - - the y position of the center of the circle

width - - the width of the circle.

Returns:

The Y position on the circle for the number-th of count nodes