biouml.plugins.sbml
Class SbmlSemanticController

java.lang.Object
  biouml.model.DefaultSemanticController
      biouml.standard.diagram.PathwaySemanticController
          biouml.standard.diagram.PathwaySimulationSemanticController
              biouml.plugins.sbml.SbmlSemanticController

All Implemented Interfaces:

SemanticController

public class SbmlSemanticController

extends PathwaySimulationSemanticController

Field Summary

static java.lang.String[]

RESERVED_KEY_WORDS Array of reserves key words.

Fields inherited from class biouml.standard.diagram.PathwaySemanticController

log

Fields inherited from interface biouml.model.SemanticController

ERROR_CAN_NOT_CLONE_NODE, ERROR_NODE_IS_DUPLICATED

Constructor Summary

SbmlSemanticController()

Method Summary

DiagramElement	createInstance(Compartment parent, java.lang.Class type, java.awt.Point point, ViewEditorPane viewEditor) Creates diagram element for the specified kernel type, parent compartment and location.
protected static void	fillNameMap(Compartment compartment, java.util.HashMap map)
java.lang.String	generateReactionName(Diagram diagram) Generates unique reaction name for the specified diagram.
static boolean	isReservedKeyWord(java.lang.String str) Returns true if the specified string is reserved SBML key word.
static java.lang.Object	resolveName(Diagram diagram, java.lang.String sname) Search SBML model element with the specified name.
static java.lang.String	validateSName(java.lang.String name) Checks whether the name is valid SBML SName and replaces all invalid chaacters by '_'.

Methods inherited from class biouml.standard.diagram.PathwaySimulationSemanticController

createRule

Methods inherited from class biouml.standard.diagram.PathwaySemanticController

createDiagramElement, getNode, remove

Methods inherited from class biouml.model.DefaultSemanticController

canAccept, canAccept, findNewNode, isResizable, move, moveEdge, moveEdges, moveEdges, moveNode, remapEdge

Methods inherited from class java.lang.Object

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

Field Detail

RESERVED_KEY_WORDS

public static final java.lang.String[] RESERVED_KEY_WORDS

Array of reserves key words.

Constructor Detail

SbmlSemanticController

public SbmlSemanticController()

Method Detail

isReservedKeyWord

public static boolean isReservedKeyWord(java.lang.String str)

Returns true if the specified string is reserved SBML key word.

resolveName

public static java.lang.Object resolveName(Diagram diagram,
                                           java.lang.String sname)

Search SBML model element with the specified name. Generally this method is used to check whether sname is unique. Note: this the rather slow method while it parse all model and put the elements into hash map: sname - object.

Returns:

Object with the specified name or null of no object was found.

Pendung:

process rules and units

fillNameMap

protected static void fillNameMap(Compartment compartment,
                                  java.util.HashMap map)

validateSName

public static java.lang.String validateSName(java.lang.String name)

Checks whether the name is valid SBML SName and replaces all invalid chaacters by '_'.

Returns:

valid SBML SName.

generateReactionName

public java.lang.String generateReactionName(Diagram diagram)
                                      throws java.lang.Exception

Generates unique reaction name for the specified diagram.

Overrides:

generateReactionName in class PathwaySemanticController

Throws:

java.lang.Exception

Pendung:

verify that nhere is no parameter, rule or unit with the same name.

createInstance

public DiagramElement createInstance(Compartment parent,
                                     java.lang.Class type,
                                     java.awt.Point point,
                                     ViewEditorPane viewEditor)

Creates diagram element for the specified kernel type, parent compartment and location. The created diagram element can be compartment, specie node or reaction node.

Specified by:

createInstance in interface SemanticController

Overrides:

createInstance in class PathwaySimulationSemanticController

Parameters:

parent - compartment where new diagram element should be located

type - kernel type

point - diagram element location

viewEditor - diagram view editor.