Run MGCAT for Global Sequence Comparison

Script

String command = cmd;StringBuffer sb = new StringBuffer();String result = "";if (command == null || command.equals("")) { throw new RuntimeException("The 'command' port cannot be null.");}Process proc = null;Runtime rt = Runtime.getRuntime();File f = new File("D:/mgcat");try{proc = rt.exec(command,null,f);// Get the input stream and read from itInputStream in = proc.getInputStream();int c;while ((c = in.read()) != -1) { sb.append((char) c);}in.close();} catch(Exception ex) {   System.out.println(ex); }result = sb.toString();

Value

Script

import java.io.*;String path ="D:/mgcat/output/mgcat.log";StringBuffer sb = new StringBuffer();try {  BufferedReader br = new BufferedReader(new FileReader(path));  String line = br.readLine();  while(line != null) {    sb.append(line + "\n");    line = br.readLine();  }  br.close();}catch(Exception ex) {   System.out.println(ex); }content = sb.toString();  

Script

File inPath =  new File("D:/mgcat/mgcat.ini");File outPath = new File("D:/mgcat/mgcatOut.ini");try {  BufferedReader   br = new BufferedReader(new FileReader(inPath));  FileWriter       fw = new FileWriter(outPath);  String line = br.readLine();  while(line != null)   {    if(line.startsWith("file=") )    {       line = "file=" + fileA + "\n";       fw.write( line );     }     else if (line.startsWith("file1="))      {        fw.write("file1=" + fileB + "\n");     }     else      {       line = line + "\n";       fw.write( line );     }     line = br.readLine();  }  br.close();  fw.close();}catch(Exception ex) {   System.out.println(ex); }try {  BufferedReader br = new BufferedReader(new FileReader(outPath));  FileWriter fw     = new FileWriter(inPath);  String line = br.readLine();  while(line != null) {    fw.write(line + "\n");    line = br.readLine();  }  br.close();  fw.close();}catch(Exception ex) {   System.out.println(ex); }