biouml.plugins.cellml
Class CellMLModelReader

java.lang.Object
  biouml.plugins.cellml.CellMLSupport
      biouml.plugins.cellml.CellMLModelReader

All Implemented Interfaces:

CellMLConstants

public class CellMLModelReader

extends CellMLSupport

Pendung:

whwther we should layout the diagram here

Field Summary

protected java.util.HashMap	componentMap
protected java.util.HashMap	connectionMap
protected LinearFormatter	linearFormatter
protected MathMLParser	mathMLParser
protected int	maxVisibleVariableNumber
protected boolean	shouldLayout
protected int	visibleVariableNumber

Fields inherited from class biouml.plugins.cellml.CellMLSupport

diagram, file, log, modelName, module, resources

Fields inherited from interface biouml.plugins.cellml.CellMLConstants

BIOUML_COMPARTMENT_INFO_ELEMENT, BIOUML_EDGE_INFO_ELEMENT, BIOUML_NODE_INFO_ELEMENT, BIOUML_SPECIES_INFO_ELEMENT, BIOUML_SPECIES_TYPE_ATTR, BIOUML_XMLNS_ATTR, BIOUML_XMLNS_VALUE, COMPONENT_1_ATTR, COMPONENT_2_ATTR, COMPONENT_ELEMENT, CONNECTION_ELEMENT, DIRECTION_ATTR, ENVIRONMENT, INITIAL_VALUE_ATTR, MAP_COMPONENTS_ELEMENT, MATH_ELEMENT, MODEL_ELEMENT, NAME_ATTR, PUBLIC_INTERFACE_ATTR, PUBLIC_INTERFACE_NONE, RDF_ELEMENT, REACTION_ELEMENT, REACTION_REVERSIBLE_ATTR, ROLE_ACTIVATOR, ROLE_ATTR, ROLE_CATALYST, ROLE_ELEMENT, ROLE_INHIBITOR, ROLE_MODIFIER, ROLE_PRODUCT, ROLE_RATE, ROLE_REACTANT, STOICHIOMETRY_ATTR, UNITS_ATTR, VARIABLE_ATTR, VARIABLE_ELEMENT, VARIABLE_REF_ELEMENT

Constructor Summary

CellMLModelReader(java.io.File inFile)

Method Summary

protected void	createReaction(biouml.plugins.cellml.CellMLModelReader.ComponentInfo reactionInfo)
protected Node	createSpecies(biouml.plugins.cellml.CellMLModelReader.ComponentInfo speciesInfo) Creates node for species.
protected void	initComponentMap(org.w3c.dom.Element model)
protected void	initConnectionMap(org.w3c.dom.Element model)
Diagram	read(DataCollection origin, Module module)
protected void	readComponents(org.w3c.dom.Element model) Read components.
protected void	readConnections(org.w3c.dom.Element model) Read connections.
protected Diagram	readDiagram(org.w3c.dom.Element element, DataCollection origin)
protected void	readGroups(org.w3c.dom.Element model) Read groups.
protected void	readKineticLaw(biouml.plugins.cellml.CellMLModelReader.ComponentInfo reactionInfo, Node reaction, org.w3c.dom.Element element, java.lang.String varName)
protected AstStart	readMath(biouml.plugins.cellml.CellMLModelReader.ComponentInfo componentInfo, org.w3c.dom.Element element, java.lang.String equationVar)
protected void	readReactions(org.w3c.dom.Element model)
protected void	readRole(Node reactionNode, org.w3c.dom.Element element, java.lang.String speciesName, java.lang.String role)
protected void	readUnits(org.w3c.dom.Element model) Read unit definitions.
protected org.w3c.dom.Element	readVariable(Variable var, biouml.plugins.cellml.CellMLModelReader.ComponentInfo componentInfo, java.lang.String variableName, boolean checkInitialValue) Read variables information.

Methods inherited from class biouml.plugins.cellml.CellMLSupport

error, getElement, warn

Methods inherited from class java.lang.Object

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

Field Detail

shouldLayout

protected boolean shouldLayout

visibleVariableNumber

protected int visibleVariableNumber

maxVisibleVariableNumber

protected int maxVisibleVariableNumber

componentMap

protected java.util.HashMap componentMap

connectionMap

protected java.util.HashMap connectionMap

mathMLParser

protected MathMLParser mathMLParser

linearFormatter

protected LinearFormatter linearFormatter

Constructor Detail

CellMLModelReader

public CellMLModelReader(java.io.File inFile)
                  throws java.lang.Exception

Method Detail

read

public Diagram read(DataCollection origin,
                    Module module)
             throws java.lang.Exception

Throws:

java.lang.Exception

readDiagram

protected Diagram readDiagram(org.w3c.dom.Element element,
                              DataCollection origin)
                       throws java.lang.Exception

Throws:

java.lang.Exception

readUnits

protected void readUnits(org.w3c.dom.Element model)

Read unit definitions.

Pendung:

todo

readComponents

protected void readComponents(org.w3c.dom.Element model)

Read components.

Pendung:

todo

initComponentMap

protected void initComponentMap(org.w3c.dom.Element model)

readGroups

protected void readGroups(org.w3c.dom.Element model)

Read groups. This information is used to form compartments hierarchy and refine component types. The following rule can be used: if relationship is containment and

createSpecies

protected Node createSpecies(biouml.plugins.cellml.CellMLModelReader.ComponentInfo speciesInfo)
                      throws java.lang.Exception

Creates node for species.

Throws:

java.lang.Exception

readReactions

protected void readReactions(org.w3c.dom.Element model)

createReaction

protected void createReaction(biouml.plugins.cellml.CellMLModelReader.ComponentInfo reactionInfo)
                       throws java.lang.Exception

Throws:

java.lang.Exception

readRole

protected void readRole(Node reactionNode,
                        org.w3c.dom.Element element,
                        java.lang.String speciesName,
                        java.lang.String role)
                 throws java.lang.Exception

Throws:

java.lang.Exception

Pendung:

to which modifier action should coreespond CellML ROLE_MODIFIER?, for modifier stoichiometry should be 0. Whether it is correct for CellML modles?, direction is not supported yet.

readKineticLaw

protected void readKineticLaw(biouml.plugins.cellml.CellMLModelReader.ComponentInfo reactionInfo,
                              Node reaction,
                              org.w3c.dom.Element element,
                              java.lang.String varName)

Pendung:

- rate units.

initConnectionMap

protected void initConnectionMap(org.w3c.dom.Element model)

readConnections

protected void readConnections(org.w3c.dom.Element model)

Read connections.

Pendung:

todo

readVariable

protected org.w3c.dom.Element readVariable(Variable var,
                                           biouml.plugins.cellml.CellMLModelReader.ComponentInfo componentInfo,
                                           java.lang.String variableName,
                                           boolean checkInitialValue)

Read variables information.

Returns:

DOM element corresponding to variable declaration.

readMath

protected AstStart readMath(biouml.plugins.cellml.CellMLModelReader.ComponentInfo componentInfo,
                            org.w3c.dom.Element element,
                            java.lang.String equationVar)