Package miscellaneous

Examples of miscellaneous.CSVList

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    // {
    // Logs.log("Install Cairo Package for R to enable plotting (best package for plotting using server version of R).",
    // 0, "R");
    // return false;
    // }
    CSVList args = new CSVList();
    args.add(R.quotedPath(file.getAbsolutePath()));
    args.add("height=" + height_inches);
    args.add("width=" + width_inches);
    if(!extension.equals("svg") && !extension.equals("pdf"))
    {
      args.add("res=" + res_ppi);
      args.add("units='in'");
      args.add("type='cairo'");
    }
    args.add("pointsize=" + fontsize_pts);
    if(optionalFont != null)
    {
      if(extension.equals("pdf"))
      {
        if(R.isPostScriptFont(optionalFont))
        {
          args.add("family=" + R.sQuote(optionalFont));
        }
        else
        {
          args.add("family=" + R.sQuote(FONT_HELVETICA));
        }
      }
     
    }
    if(extension.equals("tif") && optionalTifCompression != null)
    {
      args.add("compression=" + R.sQuote(optionalTifCompression));
    }
    String command = commandStart + "(" + args.toString() + ")";
    if(R.eval(command) == null)
    {
      Logs.log("Couldn't start the " + extension + " plot in R", 0, "R");
      return false;
    }
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  public DimensionMap(String csvDimStr)
  {
    super();
   
    CSVList csv = new CSVList(csvDimStr);
    for (String s : csv)
    {
      String[] dimNameValue = s.split("=");
      if(dimNameValue.length < 2)
      {
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  }
 
  @Override
  public String toString()
  {
    CSVList l = new CSVList();
    for (Entry<String,String> e : this.entrySet())
    {
      l.add(e.getKey() + "=" + e.getValue());
    }
    return l.toString();
  }
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    this.updateDimValueSet();
  }
 
  public Dim(String csvString)
  {
    CSVList csv = new CSVList(csvString);
    this.dimName = csv.get(0);
    this.dimValues = new Vector<String>();
    this.dimValues.addAll(csv.subList(1, csv.size()));
    this.updateDimValueSet();
  }
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  }
 
  public Dim(String dimName, String csvValues)
  {
    this.dimName = dimName;
    this.dimValues = new CSVList(csvValues);
    this.updateDimValueSet();
  }
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    }
   
    // reactantString=reactantString.substring(0,
    // reactantString.length()-1);
    reactantString += " --> ";
    CSVList repeatedProduct = new CSVList();
    String repeatedProductString = new String();
    for (Product product : this.products)
    {
      // if we have not added the product, add it normally
      if(product.isRepeated)
      {
        repeatedProduct.add(product.toStringRepeated());
        repeatedProductString = product.name + "(" + product.pool.name + ")";
      }
      else
      {
        productString += product.toString() + " +";
      }
    }
    if(!repeatedProduct.isEmpty())
    {
      repeatedProductString = "[" + repeatedProduct.toString() + "]*" + repeatedProductString;
    }
    if(productString.length() < 1)
    {
      productString = "0";
    }
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   * @return comma separated list of item strings?
   */
  @Override
  public String toString()
  {
    CSVList ret = new CSVList();
    for (String str : this.descendingKeySet())
    {
      Item i = this.get(str);
      ret.add(i.toString());
    }
    return ret.toString();
  }
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  // Also, write a file that contains the paths of where we intend to write all the results
  public boolean startSims()
  {
   
    // Gather parameters
    CSVList k_TRANSCRIPTION = new CSVList(this.parameters.getValueOfParameter(Statics.k_TRANSCRIPTION));
    CSVList ratio_TRANSCRIPTION_2_REPLICATION = new CSVList(this.parameters.getValueOfParameter(Statics.ratio_TRANSCRIPTION_2_REPLICATION));
    CSVList ratio_GENOME_2_ANTIGENOME = new CSVList(this.parameters.getValueOfParameter(Statics.ratio_GENOME_2_ANTIGENOME));
    CSVList stoich_ERROR = new CSVList(this.parameters.getValueOfParameter(Statics.stoich_ERROR));
    CSVList k_POL_FORMATION = new CSVList(this.parameters.getValueOfParameter(Statics.k_POL_FORMATION));
    CSVList k_CONDENSATION = new CSVList(this.parameters.getValueOfParameter(Statics.k_CONDENSATION));
    CSVList k_DETECTION = new CSVList(this.parameters.getValueOfParameter(Statics.k_DETECTION));
    CSVList pol_SPEED = new CSVList(this.parameters.getValueOfParameter(Statics.pol_SPEED));
    CSVList pol_SPACING = new CSVList(this.parameters.getValueOfParameter(Statics.pol_SPACING));
    CSVList rib_SPEED = new CSVList(this.parameters.getValueOfParameter(Statics.rib_SPEED));
    CSVList rib_SPACING = new CSVList(this.parameters.getValueOfParameter(Statics.rib_SPACING));
   
    this.paramTable = new DimTable();
    this.paramTable.add(new Dim(Statics.k_TRANSCRIPTION, k_TRANSCRIPTION));
    this.paramTable.add(new Dim(Statics.ratio_TRANSCRIPTION_2_REPLICATION, ratio_TRANSCRIPTION_2_REPLICATION));
    this.paramTable.add(new Dim(Statics.ratio_GENOME_2_ANTIGENOME, ratio_GENOME_2_ANTIGENOME));
View Full Code Here
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Related Classes of miscellaneous.CSVList

  • reaction.Reaction
  • reaction.SimplePool
  • rtools.R
  • simulation.MultiSim
  • tables.Dim
  • tables.DimensionMap
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