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