idare.sbmlannotator.internal.Tasks

Class SBMLAnnotatorTask

java.lang.Object

org.cytoscape.work.AbstractTask

idare.sbmlannotator.internal.Tasks.SBMLAnnotatorTask

All Implemented Interfaces:

org.cytoscape.work.swing.RequestsUIHelper, org.cytoscape.work.Task

Direct Known Subclasses:

SBMLAnnotatorTaskFBC

public class SBMLAnnotatorTask
extends org.cytoscape.work.AbstractTask
implements org.cytoscape.work.swing.RequestsUIHelper

A Task that annotates an network with data from an SBML file that is gene and protein specific. There are three expected ways how GPRS can be annotated: 1. By FBC GeneProductAssociations and the respective GeneProduct fields 2. by COBRA notes fields. 3. By ModifierSpecies annotated to reactions. We expect these methods to be mutually exclusive and not used simultaneously in one SBML! Furthermore, we expect, that GeneProducts or Species EITHER represent Genes OR Represent Proteins. Thus the protein/gene annotation will likely fail if a mixed annotation is done. If annotation is done via FBC, then COBRA Fields Are ignored for any reaction that is annotated by FBC GeneProductAssociations. Any formerly loaded fbc AND or OR nodes (e.g. by cy3sbml) will eb removed and a new logic will be calculated. GeneProduct Nodes will be retained but will get their sbml-type adjusted to the type they represent (either Gene or Protein). The same applies for modifierspecies, which will also be reannotated as gene or protein, if their annotation fields contain the information. FBC GeneProducts without annotation wil be considered as Genes.

Author:

Thomas Pfau

Field Summary

Fields

Modifier and Type	Field and Description
SBMLDocument	doc
org.cytoscape.work.util.ListSingleSelection<String>	geneAnnotationDataBase
boolean	generateGeneNodes
org.cytoscape.work.util.ListSingleSelection<String>	proteinAnnotationDataBase
boolean	removeFBCNodes
org.cytoscape.work.util.ListSingleSelection<String>	sbmlidcolsel
org.cytoscape.work.util.ListSingleSelection<String>	sbmltypecolsel

Fields inherited from class org.cytoscape.work.AbstractTask

cancelled

Constructor Summary

Constructors

Constructor and Description
SBMLAnnotatorTask(SBMLManagerHolder holder, org.cytoscape.model.CyNetwork network, org.cytoscape.view.model.CyNetworkView networkView, IDARESettingsManager ism, org.cytoscape.service.util.CyServiceRegistrar reg, SBMLDocument doc)

Method Summary

Modifier and Type	Method and Description
void	addCobraInformationAnnotation()
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)
void	setUIHelper(org.cytoscape.work.swing.TunableUIHelper arg0)
void	setupSBMLObjectIDs()

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

Field Detail

generateGeneNodes

public boolean generateGeneNodes

removeFBCNodes

public boolean removeFBCNodes

proteinAnnotationDataBase

public org.cytoscape.work.util.ListSingleSelection<String> proteinAnnotationDataBase

geneAnnotationDataBase

public org.cytoscape.work.util.ListSingleSelection<String> geneAnnotationDataBase

sbmltypecolsel

public org.cytoscape.work.util.ListSingleSelection<String> sbmltypecolsel

sbmlidcolsel

public org.cytoscape.work.util.ListSingleSelection<String> sbmlidcolsel

doc

public SBMLDocument doc

Constructor Detail

SBMLAnnotatorTask

public SBMLAnnotatorTask(SBMLManagerHolder holder,
                         org.cytoscape.model.CyNetwork network,
                         org.cytoscape.view.model.CyNetworkView networkView,
                         IDARESettingsManager ism,
                         org.cytoscape.service.util.CyServiceRegistrar reg,
                         SBMLDocument doc)

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

setupSBMLObjectIDs

public void setupSBMLObjectIDs()

addCobraInformationAnnotation

public void addCobraInformationAnnotation()

setUIHelper

public void setUIHelper(org.cytoscape.work.swing.TunableUIHelper arg0)

Specified by:

setUIHelper in interface org.cytoscape.work.swing.RequestsUIHelper

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