src/jalview/hmmer/HMMERCommands.java

   1 package jalview.hmmer;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.HiddenMarkovModel;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.gui.AlignFrame;
   7 import jalview.io.DataSourceType;
   8 import jalview.io.FileFormat;
   9 import jalview.io.StockholmFile;
  10
  11 import java.io.BufferedReader;
  12 import java.io.IOException;
  13 import java.io.InputStreamReader;
  14 import java.io.PrintWriter;
  15 import java.util.List;
  16
  17 public class HMMERCommands
  18 {
  19   // Path of hmmer binaries directory
  20   private static final String HMMERFOLDER = "H:/Documents/";
  21
  22   private static final String HMMALIGN = HMMERFOLDER + "hmmalign";
  23
  24   private static final String HMMBUILD = HMMERFOLDER + "hmmbuild";
  25
  26   private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch";
  27
  28   private static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/";
  29
  30   private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm";
  31
  32   private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto";
  33
  34   private static final String OUTPUTALIGNMENT = "-o " + ALIGNMENTBUFFER;
  35
  36   private static final String SPACE = " ";
  37
  38   public static void hmmBuild(AlignFrame af)
  39           throws IOException, InterruptedException
  40   {
  41     HiddenMarkovModel hmm = null;
  42     AlignmentI alignment = af.getViewport().getAlignment();
  43     List<SequenceI> list = alignment.getSequences();
  44     SequenceI[] array = new SequenceI[list.size()];
  45     list.toArray(array);
  46     StockholmFile file = new StockholmFile(alignment);
  47     file.setSeqs(array);
  48     String output = file.print();
  49     PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER);
  50     writer.println(output);
  51     writer.close();
  52     final String command = HMMBUILD + SPACE + JALVIEWDIRECTORY + HMMBUFFER
  53             + SPACE
  54             + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
  55
  56     runCommand(command);
  57
  58     af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE,
  59             FileFormat.HMMER3, null);
  60   }
  61
  62   private static void runCommand(String command)
  63           throws IOException, InterruptedException
  64   {
  65     final Process p = Runtime.getRuntime().exec(command);
  66
  67     new Thread(new Runnable()
  68     {
  69       @Override
  70       public void run()
  71       {
  72         BufferedReader input = new BufferedReader(
  73                 new InputStreamReader(p.getInputStream()));
  74         String line = null;
  75
  76         try
  77         {
  78           while ((line = input.readLine()) != null)
  79           {
  80             System.out.println(line);
  81           }
  82         } catch (IOException e)
  83         {
  84           e.printStackTrace();
  85         }
  86       }
  87     }).start();
  88
  89     p.waitFor();
  90   }
  91 }