src/jalview/util/ProbabilityAnalyserKickstarter.java

   1 package jalview.util;
   2
   3 import java.io.IOException;
   4 import java.util.Scanner;
   5
   6 /**
   7  * This class contains the brain of the analyser program, and contains a number
   8  * of commands for the processing of data.
   9  *
  10  * @author TZVanaalten
  11  *
  12  */
  13
  14 public class ProbabilityAnalyserKickstarter
  15 {
  16
  17   public static void main(String[] args)
  18           throws IOException, InterruptedException
  19   {
  20
  21     // this does all of the processing
  22     HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
  23
  24     boolean running = true;
  25     System.out.println("ACTIVATED");
  26     while (running)
  27     {
  28       Scanner keyboard = new Scanner(System.in);
  29       String command = keyboard.nextLine();
  30
  31       Scanner inputScanner = new Scanner(command);
  32       // prints family to console. Syntax is printFam <index>
  33       if (command.indexOf("printFam") > -1)
  34       {
  35         try
  36         {
  37           inputScanner.next();
  38           int index = inputScanner.nextInt();
  39           analyser.printFam(index);
  40           continue;
  41         } catch (Exception e)
  42         {
  43           System.out.println("Command failed");
  44         }
  45
  46       }
  47       // prints HMM to console. Syntax is printHMM <index>
  48       if (command.indexOf("printHMM") > -1)
  49       {
  50         try
  51         {
  52         inputScanner.next();
  53         int index = inputScanner.nextInt();
  54         analyser.printHMM(index);
  55         continue;
  56         } catch (Exception e)
  57         {
  58           System.out.println("Command failed");
  59         }
  60       }
  61       // prints family to file in current folder. Syntax is exportFam <index>.
  62       if (command.indexOf("exportFam") > -1)
  63       {
  64         try
  65         {
  66         inputScanner.next();
  67         int index = inputScanner.nextInt();
  68           String location = inputScanner.next();
  69           analyser.exportFam(index, location);
  70         continue;
  71         } catch (Exception e)
  72         {
  73           System.out.println("Command failed");
  74         }
  75       }
  76       // prints HMM to file in current folder. Syntax is exportHMM <index>.
  77       if (command.indexOf("exportHMM") > -1)
  78       {
  79         try
  80         {
  81         inputScanner.next();
  82         int index = inputScanner.nextInt();
  83           String location = inputScanner.next();
  84           analyser.exportHMM(index, location);
  85         continue;
  86         } catch (Exception e)
  87         {
  88           System.out.println("Command failed");
  89         }
  90       }
  91       // Processes data. Syntax is run <number of loops> <increments>. The
  92       // number loops specifies the number of increments the program will run.
  93       // After each increment, the data stored currently in the program is
  94       // exported and re-read back into the program. This is to ensure that the
  95       // program can be terminated without losing a large quantity of data. The
  96       // increment is the number of families read per 'save'.
  97       if (command.indexOf("run") > -1 && !(command.indexOf("ToEnd") > -1))
  98       {
  99         try
 100         {
 101
 102         inputScanner.next();
 103
 104         int loops = inputScanner.nextInt();
 105         int increments = inputScanner.nextInt();
 106         boolean keepRaw = inputScanner.nextBoolean();
 107
 108         for (int i = 0; i < loops; i++)
 109         {
 110           analyser.run(increments, keepRaw);
 111           System.out.println("Saved");
 112         }
 113         System.out.println("Task completed");
 114         continue;
 115         } catch (Exception e)
 116         {
 117           System.out.println("Command failed");
 118         }
 119         continue;
 120       }
 121       if ((command.indexOf("runToEnd") > -1))
 122       {
 123         try
 124         {
 125
 126           inputScanner.next();
 127           int minCount = inputScanner.nextInt();
 128           int maxCount = inputScanner.nextInt();
 129           boolean keepRaw = inputScanner.nextBoolean();
 130           boolean forClans = inputScanner.nextBoolean();
 131           analyser.runToEnd(minCount, maxCount, keepRaw, forClans);
 132           System.out.println("Task completed");
 133         } catch (Exception e)
 134         {
 135           System.out.println("Command failed");
 136         }
 137         continue;
 138       }
 139       // terminates program. Syntax is terminate.
 140       if (command.indexOf("terminate") > -1)
 141       {
 142         running = false;
 143         continue;
 144       }
 145       // clears files in current directory (Only a specific set of files).
 146       // Syntax is clear.
 147       if (command.indexOf("clear") > -1)
 148       {
 149         analyser.clear();
 150         continue;
 151       }
 152       // changes current directory. Syntax is cd <directory>
 153       if (command.indexOf("cd") > -1)
 154       {
 155         try
 156         {
 157         inputScanner.next();
 158         analyser.setFolder(inputScanner.next());
 159         } catch (Exception e)
 160         {
 161           System.out.println("Command failed");
 162
 163         }
 164         continue;
 165       }
 166
 167       if (command.indexOf("getFamName") > -1)
 168       {
 169         try
 170         {
 171         inputScanner.next();
 172         System.out.println(analyser.getFamilyName(inputScanner.nextInt()));
 173
 174         } catch (Exception e)
 175         {
 176           System.out.println("Command failed");
 177         }
 178         continue;
 179       }
 180       if (command.indexOf("sortIntoClans") > -1)
 181       {
 182         inputScanner.next();
 183         analyser.sortIntoClans(inputScanner.next());
 184           continue;
 185
 186       }
 187       if (command.indexOf("setFamilies") > -1)
 188       {
 189         inputScanner.next();
 190         analyser.setFamilies(inputScanner.next());
 191         continue;
 192
 193       }
 194
 195       if (command.indexOf("setHMMs") > -1)
 196       {
 197         inputScanner.next();
 198         analyser.setHmms(inputScanner.next());
 199         continue;
 200
 201       }
 202
 203       if (command.indexOf("alignWithinClans") > -1)
 204       {
 205         inputScanner.next();
 206         String export = inputScanner.next();
 207         String clans = inputScanner.next();
 208         analyser.alignWithinClan(export, clans);
 209         continue;
 210
 211       }
 212
 213       System.out.println("Unrecognised command");
 214     }
 215
 216
 217
 218
 219   }
 220
 221 }