src/jalview/hmmer/HMMERCommands.java

   1 package jalview.hmmer;
   2
   3 import jalview.datamodel.Alignment;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.HiddenMarkovModel;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignFrame;
   8 import jalview.io.HMMFile;
   9 import jalview.io.StockholmFile;
  10
  11 import java.io.BufferedReader;
  12 import java.io.File;
  13 import java.io.IOException;
  14 import java.io.InputStreamReader;
  15 import java.io.PrintWriter;
  16 import java.util.List;
  17
  18 public class HMMERCommands
  19 {
  20   // Path of hmmer binaries directory
  21   String HMMERFOLDER = "/Documents/";
  22
  23   public String JALVIEWDIRECTORY = System.getProperty("user.dir")
  24           + "/";
  25
  26   public String HMMALIGN = "/hmmalign ";
  27
  28   public String HMMBUILD = "/hmmbuild ";
  29
  30   public String HMMSEARCH = "/hmmsearch ";
  31
  32   public String HMMBUFFER;
  33
  34   public String ALIGNMENTBUFFER;
  35
  36   public String ALIGNMENTINPUT;
  37
  38   public String OUTPUTALIGNMENT;
  39
  40   public String NAME = "-n ";
  41
  42   public String SPACE = " ";
  43
  44   public String ALLCOL = "--allcol ";
  45
  46   public String TRIM = "--trim ";
  47
  48
  49   /**
  50    * Runs a command in the terminal.
  51    *
  52    * @param command
  53    * @throws IOException
  54    * @throws InterruptedException
  55    */
  56   public void runCommand(String command)
  57           throws IOException, InterruptedException
  58   {
  59     final Process p = Runtime.getRuntime().exec(command);
  60
  61     new Thread(new Runnable()
  62     {
  63       @Override
  64       public void run()
  65       {
  66         BufferedReader input = new BufferedReader(
  67                 new InputStreamReader(p.getInputStream()));
  68         String line = null;
  69
  70         try
  71         {
  72           while ((line = input.readLine()) != null)
  73           {
  74             System.out.println(line);
  75           }
  76         } catch (IOException e)
  77         {
  78           e.printStackTrace();
  79         }
  80       }
  81     }).start();
  82
  83     p.waitFor();
  84   }
  85
  86   /**
  87    * Exports an alignment to the buffer location in Jalview.
  88    *
  89    * @param alignment
  90    * @throws IOException
  91    */
  92   public void exportData(AlignmentI alignment,
  93           File stoLocation, HiddenMarkovModel hmm, File hmmLocation)
  94           throws IOException
  95   {
  96     if (alignment != null)
  97     {
  98       if (!alignment.isAligned())
  99       {
 100         alignment.padGaps();
 101       }
 102       List<SequenceI> list = alignment.getSequences();
 103       SequenceI[] array = new SequenceI[list.size()];
 104       list.toArray(array);
 105       StockholmFile file = new StockholmFile(new Alignment(array));
 106       file.setSeqs(array);
 107       String output = file.print();
 108       PrintWriter writer = new PrintWriter(stoLocation);
 109       writer.println(output);
 110       writer.close();
 111     }
 112
 113     if (hmm != null)
 114     {
 115       HMMFile file = new HMMFile(hmm);
 116       file.exportFile(hmmLocation);
 117     }
 118   }
 119
 120   public void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
 121           Integer position)
 122   {
 123     seq.getHMM().initHMMSequence(af, position);
 124     AlignmentI al = af.getViewport().getAlignment();
 125     af.getViewport().setAlignment(al);
 126     af.alignPanel.adjustAnnotationHeight();
 127     af.getViewport().updateSequenceIdColours();
 128     af.buildSortByAnnotationScoresMenu();
 129   }
 130
 131
 132 }