Simulate SBML-derived ODEs

Script

source(new URL("http://bioputer.mimuw.edu.pl/tav4sb/workflows/projectCoordinates.bsh"));

Script

outList = new LinkedList();
for (extList: inExtListOfLists) {
    list = new LinkedList(inBaseList);
    list.addAll(extList);
    outList.add(list);
}

Value

Script

//From a proposal by Mikolaj Rybinski
import javax.xml.transform.Source;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;

param(paramstr) {
    nameAndValue = paramstr.split("=");
    if (nameAndValue.length != 2) {
        throw new RuntimeException("Wrong parameter format: \"" + paramstr + "\".");
    }
    name = nameAndValue[0].trim();
    value = nameAndValue[1].trim();
    return this;
}

if ((sourceString == void) || (sourceString == null)) {
        throw new RuntimeException("sourceString must be specified");
}

if ((xsltString == void) || (xsltString == null)) {
        throw new RuntimeException("xsltString must be specified");
}

Source inSource = new StreamSource(new StringReader(sourceString));
Source xslSource = new StreamSource(new StringReader(xsltString));

// the factory pattern supports different XSLT processors
// e.g. set the "javax.xml.transform.TransformerFactory" system property
TransformerFactory tnfFact = TransformerFactory.newInstance();
Transformer tnf = tnfFact.newTransformer(xslSource);

if (paramList != void) {
  for (String paramstr : paramList) {
    p = param(paramstr);
    tnf.setParameter(p.name, p.value);
  }
}

Writer outputWriter = new StringWriter();
tnf.transform(inSource, new StreamResult(outputWriter));
outputString = outputWriter.toString();

Script

BufferedReader getReader (String fileUrl, String encoding) throws IOException {
        InputStreamReader reader;
        try {
            if (encoding == null) {
                reader = new FileReader(fileUrl);
            } else {
                reader = new InputStreamReader(new FileInputStream(fileUrl),encoding);
            }
        }
        catch (FileNotFoundException e) {
            // try a real URL instead
            URL url = new URL(fileUrl);
            if (encoding == null) {
                reader = new InputStreamReader (url.openStream());
            } else {
                reader = new InputStreamReader (url.openStream(), encoding);
            }
        }
        return new BufferedReader(reader);
    }



StringBuffer sb = new StringBuffer(4000);

if (encoding == void) {
    encoding = null;
}

BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
    sb.append(str);
    sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();

Value