Extensions for Diagram Layout

SBML do not defines standard approach to store diagram layout. For this purpose they suggest to use <annotation> element where tools can store all needed information in they particular format. An example of such tool is JDesigner.

We are also reusing functions of biouml.model.util.DiagramXmlWriter and DiagramXmlReader to read/write diagram layout for SBML models. 

Further details:

	compartment layout information
	node layout information
	edge layout information
	implementation notes
	usage example

Element <compartmentInfo> is used to store compartment location, size, shape and color.

<compartmentInfo> is part of <annotation> for <compartment> element.

DTD for compartment layout information:

<!ELEMENT compartmentInfo>
<!-- "shape" attribute possible values are: 
 0-rectangle; 1-round rectangle; 2-oval -->
<!ATTLIST compartmentInfo
  kernel                CDATA #REQUIRED
  x                     CDATA #REQUIRED
  y                     CDATA #REQUIRED
  width                 CDATA #REQUIRED
  height                CDATA #REQUIRED
  title                 CDATA 
  shape                 CDATA "0"
  color                 CDATA "255, 255, 255"
>

Element <nodeInfo> is used to store node title and location. <image> element is reserved to store description of image that can be used as node view, this feature is under construction and will be completed in BioUML v. 0.7.2.

<nodeInfo> is part of <annotation> for <specie> and <reaction> SBML elements that are mapped into BioUML nodes.

DTD for node layout information:

<!ELEMENT nodeInfo (image?)>
<!ATTLIST nodeInfo
  title                 CDATA 
  x                     CDATA
  y                     CDATA
>

<!ELEMENT image>
<!ATTLIST image 
  src                   CDATA		#REQUIRED 
  width                 CDATA	
  height                CDATA
  hideTitle             CDATA		"false"
>	 

Element <specieInfo> is used to store specie type and allows SbmlDiagramViewBuilder to generate corresponding node view.

Possible specie type values are: molecule-substance, molecule-gene, molecule-RNA or molecule-protein.

DTD for additional specie information:

<!ELEMENT specieInfo>
<!ATTLIST specieInfo
  type                  CDATA 
>

Currently element <edgeInfo> is used to store edge title, edge start and end points. Currently this feature is under construction and will be completed in BioUML v. 0.7.2 that will allow application to store complex line path for graph edge.

<edgeInfo> is part of <annotation> for <specieReference> SBML elements that is mapped into BioUML edge diagram element.

DTD for edge layout information:

<!ELEMENT edgeInfo>
<!ATTLIST edgeInfo
  title                 CDATA  
  inPort                CDATA
  outPort               CDATA
>

Constants for elements and namespaces to diagram layout information are declared at biouml.plugins.sbml.SbmlConstants:

    public static final String BIOUML_XMLNS_ATTR                = "xmlns:biouml";
    public static final String BIOUML_XMLNS_VALUE               = "http://www.biouml.org/ns";
    public static final String BIOUML_COMPARTMENT_INFO_ELEMENT  = "biouml:compartmentInfo";
    public static final String BIOUML_NODE_INFO_ELEMENT         = "biouml:nodeInfo";
    public static final String BIOUML_EDGE_INFO_ELEMENT         = "biouml:edgeInfo";

SbmlDiagramWriter uses methods provided by biouml.model.util.DiagramXmlWriter to write diagram layout information:

• writeCompartmentInfo - writes compartment location, size, shape and color.

• writeNodeInfo -  writes node title and location.

• isEdgeInfoInformative - indicates whether information about edge is informative and should be written.

• writeEdgeInfo - writes edge title, edge start and end points.

SbmlDiagramReader uses methods provided by biouml.model.util.DiagramXmlReader to read diagram layout information:

• readCompartmentInfo - reads compartment location, size, shape and color.
• readNodeInfo -  reads node title and location.
• readEdgeInfo - reads edge title, edge start and end points.

...