Location: Metabolic Component Library @ b9be078f1e21 / CellML-source / CellMLTools / src / annotate / AnnotateVariable.java

Author:

Matthias K?nig <matthias.koenig@charite.de>

Date:

2013-04-18 21:52:42+02:00

Desc:

Wolf Heinrich Example implemented and working !

Permanent Source URI:

https://models.cellml.org/w/matthiaskoenig/MetabolicComponentLibrary/rawfile/b9be078f1e2152d7c1b817af12a7ddcb8db3c0df/CellML-source/CellMLTools/src/annotate/AnnotateVariable.java

package annotate;


import tools.CellMLLoader;
import tools.CellMLReader;
import cellml_api.CellMLComponent;
import cellml_api.CellMLComponentIterator;
import cellml_api.CellMLComponentSet;
import cellml_api.CellMLVariable;
import cellml_api.CellMLVariableIterator;
import cellml_api.CellMLVariableSet;
import cellml_api.Connection;
import cellml_api.ConnectionIterator;
import cellml_api.ConnectionSet;
import cellml_api.MapComponents;
import cellml_api.MapVariables;
import cellml_api.MapVariablesIterator;
import cellml_api.MapVariablesSet;
import cellml_api.Model;

public class AnnotateVariable {  
  CellMLLoader cLoader;
  Model model;
  
  public AnnotateVariable(){
    cLoader = new CellMLLoader();
  }
  
  public AnnotateVariable(String url){
	    cLoader = new CellMLLoader();
	    loadModel(url);
	  }
  
  /** Load model from URL */
  private void loadModel(String url){
	    model = CellMLReader.loadFromURL(cLoader.getCellMLBootstrap(), url);
	    System.out.println("Model Name:" + model.getName() + "\n");  
  }
  
  public Model getModel(){
	  return model;
  }
  

  /** Annotate component */
  private void annotateComponent(CellMLComponent comp, AnnotationInformation info){
	  
	  
  }
  
  
  /** Iterate over the CellML model elements. */
  public void iterateModelElements(){  
	if (model==null){
		System.out.println("No model loaded !");
		return;
	}
	  
    // iterate over the components from model
    CellMLComponentSet componentSet = model.getModelComponents();
    CellMLComponentIterator iter = componentSet.iterateComponents();
    for(int i = 0; i < componentSet.getLength(); i++){
      CellMLComponent comp = iter.nextComponent();
      System.out.println("Component Name:" + comp.getName());
      
      // iterate ove all variables in the component
      CellMLVariableSet variableSet = comp.getVariables();
      CellMLVariableIterator varIter = variableSet.iterateVariables();
      for(int j = 0; j < variableSet.getLength(); j ++){
        CellMLVariable variable = varIter.nextVariable();
        System.out.println("Variable Name:"+variable.getName()+
        						" [" + variable.getUnitsName() + "]");
      }
      System.out.println();
    }
    
    // iterate over the connections of the components
    ConnectionSet connectionSet = model.getConnections();
    ConnectionIterator conIter = connectionSet.iterateConnections();
    for(int i = 0; i < connectionSet.getLength(); i++){
      Connection connection = conIter.nextConnection();
      MapComponents mapComponent = connection.getComponentMapping();
      System.out.println("Connection Component1: "+mapComponent.getFirstComponentName() + 
          "    Component2: " + mapComponent.getSecondComponentName());
      MapVariablesSet variableSet = connection.getVariableMappings();
      MapVariablesIterator varIter = variableSet.iterateMapVariables();
      for(int j =0; j < variableSet.getLength(); j++){
        MapVariables mapVar = varIter.nextMapVariable();
        System.out.println("\t Variable1: "+mapVar.getFirstVariableName() + 
            "    Variable2: " + mapVar.getSecondVariableName());
      }
      System.out.println();
    }
  }
  
  public static void main(String [] args ){
	String url = "http://www.cellml.org/models/hodgkin_huxley_1952_version07/download";
    AnnotateVariable avtest = new AnnotateVariable(url);
    avtest.iterateModelElements();
  }
}