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.DataSourceType;
   9 import jalview.io.FileFormat;
  10 import jalview.io.FileLoader;
  11 import jalview.io.HMMFile;
  12 import jalview.io.StockholmFile;
  13 import jalview.util.MessageManager;
  14
  15 import java.io.BufferedReader;
  16 import java.io.FileNotFoundException;
  17 import java.io.IOException;
  18 import java.io.InputStreamReader;
  19 import java.io.PrintWriter;
  20 import java.util.List;
  21 import java.util.Map;
  22
  23 import javax.swing.JOptionPane;
  24
  25 public class HMMERCommands
  26 {
  27   // Path of hmmer binaries directory
  28   private static final String HMMERFOLDER = "H:/Documents/";
  29
  30   private static final String HMMALIGN = HMMERFOLDER + "hmmalign ";
  31
  32   private static final String HMMBUILD = HMMERFOLDER + "hmmbuild ";
  33
  34   private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch ";
  35
  36   private static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/";
  37
  38   private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm ";
  39
  40   private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto ";
  41
  42   private static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto ";
  43
  44   private static final String OUTPUTALIGNMENT = "-o " + JALVIEWDIRECTORY
  45           + ALIGNMENTINPUT;
  46
  47   private static final String NAME = "-n ";
  48
  49   private static final String SPACE = " ";
  50
  51   private static final String ALLCOL = "--allcol ";
  52
  53   private static final String TRIM = "--trim ";
  54
  55   public static void hmmBuild(AlignFrame af)
  56           throws IOException, InterruptedException
  57   {
  58
  59     PrintWriter clearer = new PrintWriter(HMMBUFFER);
  60     clearer.print("");
  61     clearer.close();
  62     AlignmentI alignment = af.getViewport().getAlignment();
  63     if (!alignment.isAligned())
  64     {
  65       alignment.padGaps();
  66     }
  67     Map<Integer, SequenceI> seqs = alignment.getHMMConsensusSequences(true);
  68     exportAlignment(alignment);
  69     final String command = HMMBUILD + NAME + af.getName() + SPACE
  70             + JALVIEWDIRECTORY + HMMBUFFER
  71             + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
  72
  73     runCommand(command);
  74
  75     af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE,
  76             FileFormat.HMMER3, null);
  77     for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
  78     {
  79       SequenceI seq = entry.getValue();
  80       Integer pos = entry.getKey();
  81       addHMMConsensusSequence(af, seq, pos);
  82     }
  83     af.alignPanel.alignmentChanged();
  84   }
  85
  86   public static void hmmAlign(AlignFrame af, boolean createNewFrame,
  87           HiddenMarkovModel hmm)
  88           throws IOException, InterruptedException
  89   {
  90
  91     PrintWriter clearer = new PrintWriter(ALIGNMENTINPUT);
  92     clearer.print("");
  93     clearer.close();
  94     AlignmentI al = af.getViewport().getAlignment();
  95     if (!al.isAligned())
  96     {
  97       al.padGaps();
  98     }
  99     Map<Integer, SequenceI> seqs = al.getHMMConsensusSequences(true);
 100     int index = 0;
 101     if (hmm == null)
 102     {
 103       JOptionPane.showMessageDialog(af,
 104               MessageManager.getString("warn.null_hmm"));
 105       return;
 106     }
 107     exportAlignment(al);
 108
 109     HMMFile file = new HMMFile(hmm);
 110     file.exportFile(HMMBUFFER);
 111
 112     String command = HMMALIGN;
 113     if (!hmm.getFileHeader().contains("HMMER3/f"))
 114     {
 115       command += ALLCOL;
 116     }
 117     command += TRIM + OUTPUTALIGNMENT + JALVIEWDIRECTORY + HMMBUFFER
 118             + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
 119
 120     runCommand(command);
 121
 122     if (createNewFrame)
 123     {
 124       FileLoader loader = new FileLoader();
 125       AlignFrame newFrame = loader.LoadFileWaitTillLoaded(ALIGNMENTINPUT,
 126             DataSourceType.FILE);
 127       for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
 128       {
 129         SequenceI seq = entry.getValue();
 130         Integer pos = entry.getKey();
 131         addHMMConsensusSequence(newFrame, seq, pos);
 132       }
 133       newFrame.alignPanel.alignmentChanged();
 134     }
 135     else
 136     {
 137       af.getViewport().getAlignment().getSequences().clear();
 138       af.loadJalviewDataFile(ALIGNMENTBUFFER, DataSourceType.FILE,
 139               FileFormat.Stockholm, null);
 140       for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
 141       {
 142         SequenceI seq = entry.getValue();
 143         Integer pos = entry.getKey();
 144         addHMMConsensusSequence(af, seq, pos);
 145       }
 146
 147     }
 148
 149
 150   }
 151
 152
 153   /**
 154    * Runs a command in the terminal.
 155    *
 156    * @param command
 157    * @throws IOException
 158    * @throws InterruptedException
 159    */
 160   private static void runCommand(String command)
 161           throws IOException, InterruptedException
 162   {
 163     final Process p = Runtime.getRuntime().exec(command);
 164
 165     new Thread(new Runnable()
 166     {
 167       @Override
 168       public void run()
 169       {
 170         BufferedReader input = new BufferedReader(
 171                 new InputStreamReader(p.getInputStream()));
 172         String line = null;
 173
 174         try
 175         {
 176           while ((line = input.readLine()) != null)
 177           {
 178             System.out.println(line);
 179           }
 180         } catch (IOException e)
 181         {
 182           e.printStackTrace();
 183         }
 184       }
 185     }).start();
 186
 187     p.waitFor();
 188   }
 189
 190   /**
 191    * Exports an alignment to the buffer location in Jalview.
 192    *
 193    * @param alignment
 194    * @throws FileNotFoundException
 195    */
 196   private static void exportAlignment(AlignmentI alignment)
 197           throws FileNotFoundException
 198   {
 199     List<SequenceI> list = alignment.getSequences();
 200     SequenceI[] array = new SequenceI[list.size()];
 201     list.toArray(array);
 202
 203     StockholmFile file = new StockholmFile(new Alignment(array));
 204     file.setSeqs(array);
 205     String output = file.print();
 206     PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER);
 207     writer.println(output);
 208     writer.close();
 209   }
 210
 211   private static void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
 212           Integer position)
 213   {
 214     seq.getHMM().initHMMSequence(af, position);
 215     AlignmentI al = af.getViewport().getAlignment();
 216     af.getViewport().setAlignment(al);
 217     af.alignPanel.adjustAnnotationHeight();
 218     af.getViewport().updateSequenceIdColours();
 219     af.buildSortByAnnotationScoresMenu();
 220   }
 221
 222
 223 }