Package miscellaneous

Examples of miscellaneous.LSVList


    this.duration = duration;
    this.dt = dt;
    this.dtRecorder = dtRecorder;
   
    // Print the reactions used
    LSVList reactions = new LSVList();
    reactions.add(" ");
    for (Reaction r : this.rxns)
    {
      reactions.add(r.toString());
    }
    Recorder.log(reactions.toString(), this);
  }
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    return reactantString + productString + repeatedProductString + kString;
  }
 
  public String checkReactionBalance()
  {
    LSVList cnsrvdRctnts = new LSVList();
    cnsrvdRctnts.add("Check balance for conserved reactants");
    String outString = new String();
    // Generate a list of conserved reactants/products
    for (Reactant r : this.reactants)
    {
      double rStoich = r.stoich;
      double pStoich = 0.0;
      boolean conserved = false;
      for (Product p : this.products)
      {
        // if the names are the same and the pools are the same they are
        // the same entity and conserved
        if(r.name == p.name && r.pool == p.pool)
        {
          conserved = true;
          // add up all the products (they are different because of
          // delays)
          pStoich += p.stoich;
        }
      }
      if(conserved)
      {
        // add to the list, and display the reactant product stoich
        outString = r.name + ": " + rStoich + " , " + pStoich;
        cnsrvdRctnts.add(outString);
      }
    }
    return cnsrvdRctnts.toString();
  }
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    this.duration = duration;
    this.dt = dt;
    this.dtRecorder = dtRecorder;
   
    // Print the reactions used
    LSVList reactions = new LSVList();
    reactions.add(" ");
    for (Reaction r : model.rxns)
    {
      reactions.add(r.toString());
    }
    Recorder.log(reactions.toString(), this);
  }
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    // Add reactions
    TestPolymeraseRxn transcription = new TestPolymeraseRxn(cell.templates, "Template", cell.proteins, "Pol", kms, transcriptDelay, cell.transcripts);
    TestPolymeraseRxn translation = new TestPolymeraseRxn(cell.transcripts, "Template", cell.proteins, "Rib", ksp, proteinDelay, cell.proteins);
    rxns.add(transcription);
    rxns.add(translation);
    LSVList reactions = new LSVList();
    reactions.add("Reactions");
    for (Reaction r : rxns)
    {
      reactions.add(r.toString());
    }
    Recorder.log(reactions.toString(), "Tester");
   
    double t = 0;
    while (t <= tf)
    {
      // Add matured items to the pool
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    rxns.add(mod.getPOLtRxn());
    rxns.add(mod.getrTemplateRxn());
    rxns.add(mod.getTemplateRxn());
    rxns.add(mod.getTranscriptionRxn());
   
    LSVList reactions = new LSVList();
    reactions.add("Reactions");
    for (Reaction r : rxns)
    {
      reactions.add(r.toString());
    }
    Recorder.log(reactions.toString(), "Tester");
   
    double t = 0;
    double count = -1.0;
    double temp = 0;
    while (t <= tf)
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    this.duration = duration;
    this.dt = dt;
    this.dtRecorder = dtRecorder;
   
    // Print the reactions used
    LSVList reactions = new LSVList();
    reactions.add(" ");
    for (Reaction r : model.rxns)
    {
      reactions.add(r.toString());
    }
   
    Recorder.log(reactions.toString(), this);
  }
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