コード例 #1
0
ファイル: example9.cs プロジェクト: jonasfoe/COPASI
    static void Main()
    {
        // initialize the backend library
           // since we are not interested in the arguments
           // that are passed to main, we pass 0 and NULL to
           // init
           Debug.Assert(CCopasiRootContainer.getRoot() != null);
           // create a new datamodel
           CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel();
           Debug.Assert((dataModel != null));
           Debug.Assert((CCopasiRootContainer.getDatamodelList().size() == 1));
           // next we import a simple SBML model from a string

           // clear the message queue so that we only have error messages from the import in the queue
           CCopasiMessage.clearDeque();
           bool result=true;
           try
           {
         result = dataModel.importSBMLFromString(MODEL_STRING);
           }
           catch
           {
          System.Console.Error.WriteLine("An exception has occured during the import of the SBML model");
          System.Environment.Exit(1);
           }
           // check if the import was successful
           int mostSevere = CCopasiMessage.getHighestSeverity();
           // if it was a filtered error, we convert it to an unfiltered type
           // the filtered error messages have the same value as the unfiltered, but they
           // have the 7th bit set which basically adds 128 to the value
           mostSevere = mostSevere & 127;

           // we assume that the import succeeded if the return value is true and
           // the most severe error message is not an error or an exception
           if (result != true &&  mostSevere < CCopasiMessage.ERROR)
           {
           System.Console.Error.WriteLine("Sorry. Model could not be imported.");
           System.Environment.Exit(1);
           }

           // get the trajectory task object
           CSteadyStateTask task = (CSteadyStateTask)dataModel.getTask("Steady-State");

           CCopasiMessage.clearDeque();

           try
           {
           // now we run the actual trajectory
           task.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES);
           }
           catch
           {
           System.Console.Error.WriteLine("Error. Running the scan failed.");

                String lastErrors =  task.getProcessError();
          // check if there are additional error messages
          if (!string.IsNullOrEmpty(lastErrors))
          {
              // print the messages in chronological order
              System.Console.Error.WriteLine(lastErrors);
          }

           System.Environment.Exit(1);
           }

           // now we can get the result of the steady state calculation, e.g. the jacobian
           // matrix of the model at the steady state
           // here we can either get the jacobian as we did in example 8 as a matrix with
           // getJacobian, or we can use getJacobianAnnotated to get an annotated matrix
           // Corresponding methods for the reduced jacobian are getJacobianX and getJacobianXAnnotated
           CArrayAnnotation aj = task.getJacobianAnnotated();
           Debug.Assert((aj != null));

           if (aj != null)
           {
           // we do the output, but as in contrast to the jacobian in example 8,
           // we now have all the information for the output in one place

           // first the array annotation can tell us how many dimensions it has.
           // Since the matrix is a 2D array, it should have 2 dimensions
           Debug.Assert((aj.dimensionality() == 2));
           // since the matrix has a dimensionality of 2, the inde for the underlaying abstract array
           // object is a vector with two unsigned int elements
           // First element is the index for the outer dimension and the second element is the index
           // for the inner dimension
           SizeTStdVector index=new SizeTStdVector();
           // The constructor does not seem to interpret an integer argument
           // as the size
           // I though that in C# we might be able to achieve this using the Capacity property
           // but that didn't work. Maybe I was using it incorrectly since I don't really know C#
           // So for now, we just add two elements to the vector which seems to do the trick.
           index.Add(0);
           index.Add(0);
           // since the rows and columns have the same annotation for the jacobian, it doesn't matter
           // for which dimension we get the annotations
           StringStdVector annotations = aj.getAnnotationsString(1);
           System.Console.Out.NewLine = "";
           System.Console.WriteLine(System.String.Format("Jacobian Matrix:{0}{0}", System.Environment.NewLine));
           System.Console.Out.WriteLine(System.String.Format("{0,7}"," "));

           for (int i = 0; i < annotations.Count; ++i)
           {
           Console.Out.WriteLine(System.String.Format("{0,7}",annotations[i]));
           }

           Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));

           for (int i = 0; i < annotations.Count; ++i)
           {
           System.Console.Out.WriteLine(System.String.Format("{0,7} ", annotations[i]));
           index[0]=(uint)i;

           for (int j = 0; j < annotations.Count; ++j)
           {
               index[1]=(uint)j;
               System.Console.Out.WriteLine(System.String.Format("{0,7:G2} ",aj.array().get(index)));
           }
           System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
           }
           }
           System.Environment.Exit(0);
    }
コード例 #2
0
ファイル: example9.cs プロジェクト: tlming16/COPASI
    static void Main()
    {
        // initialize the backend library
        // since we are not interested in the arguments
        // that are passed to main, we pass 0 and NULL to
        // init
        Debug.Assert(CCopasiRootContainer.getRoot() != null);
        // create a new datamodel
        CCopasiDataModel dataModel = CCopasiRootContainer.addDatamodel();

        Debug.Assert((dataModel != null));
        Debug.Assert((CCopasiRootContainer.getDatamodelList().size() == 1));
        // next we import a simple SBML model from a string

        // clear the message queue so that we only have error messages from the import in the queue
        CCopasiMessage.clearDeque();
        bool result = true;

        try
        {
            result = dataModel.importSBMLFromString(MODEL_STRING);
        }
        catch
        {
            System.Console.Error.WriteLine("An exception has occured during the import of the SBML model");
            System.Environment.Exit(1);
        }
        // check if the import was successful
        int mostSevere = CCopasiMessage.getHighestSeverity();

        // if it was a filtered error, we convert it to an unfiltered type
        // the filtered error messages have the same value as the unfiltered, but they
        // have the 7th bit set which basically adds 128 to the value
        mostSevere = mostSevere & 127;

        // we assume that the import succeeded if the return value is true and
        // the most severe error message is not an error or an exception
        if (result != true && mostSevere < CCopasiMessage.ERROR)
        {
            System.Console.Error.WriteLine("Sorry. Model could not be imported.");
            System.Environment.Exit(1);
        }

        // get the trajectory task object
        CSteadyStateTask task = (CSteadyStateTask)dataModel.getTask("Steady-State");

        CCopasiMessage.clearDeque();

        try
        {
            // now we run the actual trajectory
            task.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES);
        }
        catch
        {
            System.Console.Error.WriteLine("Error. Running the scan failed.");

            String lastErrors = task.getProcessError();
            // check if there are additional error messages
            if (!string.IsNullOrEmpty(lastErrors))
            {
                // print the messages in chronological order
                System.Console.Error.WriteLine(lastErrors);
            }

            System.Environment.Exit(1);
        }

        // now we can get the result of the steady state calculation, e.g. the jacobian
        // matrix of the model at the steady state
        // here we can either get the jacobian as we did in example 8 as a matrix with
        // getJacobian, or we can use getJacobianAnnotated to get an annotated matrix
        // Corresponding methods for the reduced jacobian are getJacobianX and getJacobianXAnnotated
        CArrayAnnotation aj = task.getJacobianAnnotated();

        Debug.Assert((aj != null));

        if (aj != null)
        {
            // we do the output, but as in contrast to the jacobian in example 8,
            // we now have all the information for the output in one place

            // first the array annotation can tell us how many dimensions it has.
            // Since the matrix is a 2D array, it should have 2 dimensions
            Debug.Assert((aj.dimensionality() == 2));
            // since the matrix has a dimensionality of 2, the inde for the underlaying abstract array
            // object is a vector with two unsigned int elements
            // First element is the index for the outer dimension and the second element is the index
            // for the inner dimension
            SizeTStdVector index = new SizeTStdVector();
            // The constructor does not seem to interpret an integer argument
            // as the size
            // I though that in C# we might be able to achieve this using the Capacity property
            // but that didn't work. Maybe I was using it incorrectly since I don't really know C#
            // So for now, we just add two elements to the vector which seems to do the trick.
            index.Add(0);
            index.Add(0);
            // since the rows and columns have the same annotation for the jacobian, it doesn't matter
            // for which dimension we get the annotations
            StringStdVector annotations = aj.getAnnotationsString(1);
            System.Console.Out.NewLine = "";
            System.Console.WriteLine(System.String.Format("Jacobian Matrix:{0}{0}", System.Environment.NewLine));
            System.Console.Out.WriteLine(System.String.Format("{0,7}", " "));

            for (int i = 0; i < annotations.Count; ++i)
            {
                Console.Out.WriteLine(System.String.Format("{0,7}", annotations[i]));
            }

            Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));

            for (int i = 0; i < annotations.Count; ++i)
            {
                System.Console.Out.WriteLine(System.String.Format("{0,7} ", annotations[i]));
                index[0] = (uint)i;

                for (int j = 0; j < annotations.Count; ++j)
                {
                    index[1] = (uint)j;
                    System.Console.Out.WriteLine(System.String.Format("{0,7:G2} ", aj.array().get(index)));
                }
                System.Console.WriteLine(System.String.Format("{0}", System.Environment.NewLine));
            }
        }
        System.Environment.Exit(0);
    }