src/jalview/util/ProbabilityAnalyserKickstarter.java

   1 package jalview.util;
   2
   3 import java.io.IOException;
   4 import java.util.Scanner;
   5
   6 public class ProbabilityAnalyserKickstarter
   7 {
   8
   9   public static void main(String[] args)
  10           throws IOException, InterruptedException
  11   {
  12
  13     HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
  14
  15     boolean running = true;
  16     System.out.println("ACTIVATED");
  17     while (running)
  18     {
  19       Scanner keyboard = new Scanner(System.in);
  20       String command = keyboard.nextLine();
  21
  22       Scanner inputScanner = new Scanner(command);
  23       if (command.indexOf("printFam") > -1)
  24       {
  25         inputScanner.next();
  26         int index = inputScanner.nextInt();
  27         analyser.printFam(index);
  28         continue;
  29       }
  30
  31       if (command.indexOf("printHMM") > -1)
  32       {
  33
  34         inputScanner.next();
  35         int index = inputScanner.nextInt();
  36         analyser.printHMM(index);
  37         continue;
  38       }
  39
  40       if (command.indexOf("exportFam") > -1)
  41       {
  42
  43         inputScanner.next();
  44         int index = inputScanner.nextInt();
  45         String location = inputScanner.next();
  46         analyser.printFamToFile(index);
  47         continue;
  48       }
  49
  50       if (command.indexOf("exportHMM") > -1)
  51       {
  52
  53         inputScanner.next();
  54         int index = inputScanner.nextInt();
  55         String location = inputScanner.next();
  56         analyser.printHMMToFile(index);
  57         continue;
  58       }
  59
  60       if (command.indexOf("run") > -1)
  61       {
  62         inputScanner.next();
  63
  64         int loops = inputScanner.nextInt();
  65         int increments = inputScanner.nextInt();
  66
  67         for (int i = 0; i < loops; i++)
  68         {
  69           analyser.run(increments);
  70         }
  71         continue;
  72       }
  73
  74       if (command.indexOf("terminate") > -1)
  75       {
  76         running = false;
  77         continue;
  78       }
  79
  80       if (command.indexOf("clear") > -1)
  81       {
  82         analyser.clear();
  83         continue;
  84       }
  85
  86       if (command.indexOf("cd") > -1)
  87       {
  88         inputScanner.next();
  89         analyser.setFolder(inputScanner.next());
  90       }
  91       inputScanner.close();
  92       continue;
  93     }
  94
  95
  96
  97
  98   }
  99
 100 }