Serialized Form

Package org.cy3sbml

Exception org.cy3sbml.SBMLReaderError

class SBMLReaderError extends RuntimeException implements Serializable

serialVersionUID:

1L

Package org.cy3sbml.actions

Class org.cy3sbml.actions.BiomodelsAction

class BiomodelsAction extends org.cytoscape.application.swing.AbstractCyAction implements Serializable

serialVersionUID:

1L

Serialized Fields

biomodelsDialog

BiomodelsDialog biomodelsDialog

Class org.cy3sbml.actions.ChangeStateAction

class ChangeStateAction extends org.cytoscape.application.swing.AbstractCyAction implements Serializable

serialVersionUID:

1L

Serialized Fields

webViewPanel

WebViewPanel webViewPanel

Class org.cy3sbml.actions.ExamplesAction

class ExamplesAction extends org.cytoscape.application.swing.AbstractCyAction implements Serializable

serialVersionUID:

1L

Serialized Fields

webViewPanel

WebViewPanel webViewPanel

Class org.cy3sbml.actions.HelpAction

class HelpAction extends org.cytoscape.application.swing.AbstractCyAction implements Serializable

serialVersionUID:

1L

Serialized Fields

webViewPanel

WebViewPanel webViewPanel

Class org.cy3sbml.actions.ImportAction

class ImportAction extends org.cytoscape.application.swing.AbstractCyAction implements Serializable

serialVersionUID:

1L

Serialized Fields

adapter

ServiceAdapter adapter

Class org.cy3sbml.actions.LoadLayoutAction

class LoadLayoutAction extends org.cytoscape.application.swing.AbstractCyAction implements Serializable

serialVersionUID:

1L

Serialized Fields

adapter

ServiceAdapter adapter

Class org.cy3sbml.actions.MergeCofactorsAction

class MergeCofactorsAction extends org.cy3sbml.actions.AbstractCofactorAction implements Serializable

serialVersionUID:

1L

Class org.cy3sbml.actions.SaveLayoutAction

class SaveLayoutAction extends org.cytoscape.application.swing.AbstractCyAction implements Serializable

serialVersionUID:

1L

Serialized Fields

adapter

ServiceAdapter adapter

Class org.cy3sbml.actions.SplitCofactorsAction

class SplitCofactorsAction extends org.cy3sbml.actions.AbstractCofactorAction implements Serializable

serialVersionUID:

1L

Package org.cy3sbml.archive

Exception org.cy3sbml.archive.CombineArchiveException

class CombineArchiveException extends Exception implements Serializable

Package org.cy3sbml.biomodel

Class org.cy3sbml.biomodel.BiomodelsDialog

class BiomodelsDialog extends JDialog implements Serializable

Serialized Fields

biomodelsList

JList biomodelsList

busyWorker

SwingWorker<?,?> busyWorker

The running search, null if none.

chckbxAND

JCheckBox chckbxAND

chckbxOR

JCheckBox chckbxOR

details

Map<String,Biomodel> details

The details of the models of the current search result looked up so far, by id.

idTextArea

JTextArea idTextArea

infoPane

JEditorPane infoPane

infoScrollPane

JScrollPane infoScrollPane

loadIdsButton

JButton loadIdsButton

loading

Set<String> loading

The ids of the models of the current search result whose details are being looked up.

loadModels

Consumer<List<String>> loadModels

loadSelectedButton

JButton loadSelectedButton

modelOffsets

Map<String,Integer> modelOffsets

The position of every model in the information, by id.

nameField

JTextField nameField

parseIdsButton

JButton parseIdsButton

resetButton

JButton resetButton

searchBioModel

SearchBioModel searchBioModel

searchButton

JButton searchButton

searchResult

SearchBioModel.Result searchResult

The current search result, null if none.

Package org.cy3sbml.cofactors

Class org.cy3sbml.cofactors.Network2CofactorMapper

class Network2CofactorMapper extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

clone2cofactor

Map<Long,One2ManyMapping<Long,Long>> clone2cofactor

cloneEdge2edge

Map<Long,Map<Long,Long>> cloneEdge2edge

cofactor2clone

Map<Long,One2ManyMapping<Long,Long>> cofactor2clone

positions

Map<Long,Map<Long,double[]>> positions

Package org.cy3sbml.gui

Class org.cy3sbml.gui.WebViewPanel

class WebViewPanel extends javafx.embed.swing.JFXPanel implements Serializable

serialVersionUID:

1L

Serialized Fields

adapter

ServiceAdapter adapter

biomodelsDialog

BiomodelsDialog biomodelsDialog

cofactorManager

CofactorManager cofactorManager

cytoPanelEast

org.cytoscape.application.swing.CytoPanel cytoPanelEast

html

String html

htmlFactory

SBaseHTMLFactory htmlFactory

pages

org.cy3sbml.gui.PageLoader pages

renderExecutor

LatestTaskExecutor renderExecutor

sbmlManager

SBMLManager sbmlManager

Package org.cy3sbml.mapping

Class org.cy3sbml.mapping.Network2SBMLMapper

class Network2SBMLMapper extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

documentMap

Map<Long,org.sbml.jsbml.SBMLDocument> documentMap

modelMap

Map<Long,org.sbml.jsbml.Model> modelMap

node2sbaseMappingMap

Map<Long,One2ManyMapping<Long,String>> node2sbaseMappingMap

sbase2nodeMappingMap

Map<Long,One2ManyMapping<String,Long>> sbase2nodeMappingMap

Class org.cy3sbml.mapping.One2ManyMapping

class One2ManyMapping extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

map

HashMap<T1,HashSet<T2>> map