de Bruin et al. Workflow 1

Script

/****************** Input descriptions ****************/
//input port: ArrayList input_files (depth 1)
//input port: String arguments (depth 0)
//input port: String log_file (depth 0)
//output port: String output_file (depth 0)


/****************** Class Declarations ****************/
class InProcStreamReader extends Thread
{
    private StringBuffer sb;
    public  InputStream is;
    
    InProcStreamReader(InputStream is) {
        this.is = is;
    }// InProcStreamReader(InputStream is) 
    
    public void run() {
        try {
            InputStreamReader isr = new InputStreamReader(is);
            sb = new StringBuffer();
            while ((c = isr.read()) != -1)
                sb.append((char) c);
        } catch (IOException ioe)
        {
          ioe.printStackTrace();  
        }/// catch
    }// run

    public String getOutput() { 
      return sb.toString();
    }// getOutput
}// InProcStreamReader


/****************** Global variables ******************/
tppDir = "C:\\Inetpub\\tpp-bin\\";


/****************** Global functions ******************/
// Replaces substrings in a string with a replacement string
String replace(String str, String pattern, String replace) { 
  int s = 0; 
  int e = 0; 
  StringBuffer result = new StringBuffer(); 
  while ((e = str.indexOf(pattern, s)) >= 0) { 
    result.append(str.substring(s, e)); 
    result.append(replace); 
    s = e+pattern.length(); 
  }// while
  result.append(str.substring(s)); 
  return result.toString(); 
}//  String replace(String str, String pattern, String replace) 

// Generates the output file name based on the input file
String genOutputFileName(String inputFile) {
  return replace(inputFile, "pep.xml", "interact.pep.xml");
}// String genOutputFileName(String inputFile)

// Splits argument string into separate array elements
String[] filterArguments(String arguments) {
  String[] retval = arguments.split(" ");
  return retval;
}// String[] filterArguments(String arguments) {


/************** Main matter, input checking ************/
if (input_files == void) {
  throw new RuntimeException("The 'input_files' port cannot be null.");
}// if


/************ Main matter, Running executable **********/
// Setting up the command line 
appArray = new ArrayList();

// Adding the command itself
appArray.add(tppDir + "xinteract.exe");

// Setting the output file
tmpout = genOutputFileName(input_files.get(0));
fin = new File(tmpout);
if (fin.exists())
  fin.delete();
appArray.add("-N"+tmpout);

// Filtering out arguments, or setting defaults
if (arguments == void || arguments.equals("")) {
  arguments = "-p0.05 -l7 -MONO -OigGtus";
}// if
arglist = filterArguments(arguments);
if (!(arglist ==  void || arglist[0].equals(""))) { 
  for (int i = 0; i < arglist.length; i++) {
    appArray.add(arglist[i]);
  }// for
}// if

// Adding the inputs 
for (int i = 0; i < input_files.size(); i++) {
  if (!input_files.get(i).contains("interact")) {
    appArray.add(input_files.get(i));
  }// if
}// for

workdir = new File(tppDir);
launcher = new ProcessBuilder(appArray);
launcher.directory = workdir;
proc = launcher.start();

outputReader = new InProcStreamReader(proc.getInputStream());
outputReader.start();

// any error???
exitVal = proc.waitFor();
outputReader.join();


/************** Main matter, generating log ************/
fstream = new FileWriter(log_file, true);
out = new BufferedWriter(fstream);

if (!(log_file == void || log_file.equals(""))) {
  out.write("=============== PeptideProphet ==============="); 
  out.newLine();
  out.write("Parameters:");
  for (i=0; i