biouml.plugins.sbml
Class SbmlSemanticController

biouml.model.DefaultSemanticController
  |
  +--biouml.standard.diagram.PathwaySemanticController
        |
        +--biouml.standard.diagram.PathwaySimulationSemanticController
              |
              +--biouml.plugins.sbml.SbmlSemanticController

public class SbmlSemanticController

extends PathwaySimulationSemanticController

Methods inherited from class biouml.model.DefaultSemanticController

canAccept, canAccept, isResizable, move, moveEdges, moveNode

Field Detail

RESERVED_KEY_WORDS

public final static String[] RESERVED_KEY_WORDS

Array of reserves key words.

public DiagramElement createInstance(Compartment parent, Class type, 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.

Parameters:

parent - compartment where new diagram element should be located

type - kernel type

point - diagram element location

viewEditor - diagram view editor.

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

Generates unique reaction name for the specified diagram.

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

public static boolean isReservedKeyWord(String str)

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

public static Object resolveName(Diagram diagram, 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.

pending process rules and units

public static String validateSName(String name)

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

Returns: valid SBML SName.

Association Links

to Class java.lang.String

Array of reserves key words.