Simulate SBML-derived ODEs

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Script

list = new LinkedList();
list.add("time");
list.add(str);

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list = Arrays.asList(new String[]{str});

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renamed = dataXml.replaceAll("(]*name=)\""+oldName+"\"", "$1\""+newName+"\"");
if (!renamed.equals(dataXml)) {
    renamed = renamed.replaceFirst("]*)>", "");
}

Script

filteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
    String item = (String) i.next();
    if (item.matches(regex)) {
        filteredlist.add(item);
    }
}

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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();

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Script

List split = new ArrayList();
if (!string.equals("")) {
    String regexString = ",";
    if (regex != void) {
        regexString = regex;
    }
    String[] result = string.split(regexString);
    for (int i = 0; i < result.length; i++) {
        split.add(result[i]);
    }
}

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