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     Map<Integer, SequenceI> seqs = alignment.getHMMConsensusSequences(true);
  64     exportAlignment(alignment);
  65     final String command = HMMBUILD + NAME + af.getName() + SPACE
  66             + JALVIEWDIRECTORY + HMMBUFFER
  67             + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
  68
  69     runCommand(command);
  70
  71     af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE,
  72             FileFormat.HMMER3, null);
  73     for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
  74     {
  75       SequenceI seq = entry.getValue();
  76       Integer pos = entry.getKey();
  77       addHMMConsensusSequence(af, seq, pos);
  78     }
  79     af.alignPanel.alignmentChanged();
  80   }
  81
  82   public static void hmmAlign(AlignFrame af, boolean createNewFrame,
  83           HiddenMarkovModel hmm)
  84           throws IOException, InterruptedException
  85   {
  86
  87     PrintWriter clearer = new PrintWriter(ALIGNMENTINPUT);
  88     clearer.print("");
  89     clearer.close();
  90
  91     AlignmentI al = af.getViewport().getAlignment();
  92     Map<Integer, SequenceI> seqs = al.getHMMConsensusSequences(true);
  93     int index = 0;
  94     if (hmm == null)
  95     {
  96       JOptionPane.showMessageDialog(af,
  97               MessageManager.getString("warn.null_hmm"));
  98       return;
  99     }
 100     exportAlignment(al);
 101
 102     HMMFile file = new HMMFile(hmm);
 103     file.exportFile(HMMBUFFER);
 104
 105     String command = HMMALIGN;
 106     if (!hmm.getFileHeader().contains("HMMER3/f"))
 107     {
 108       command += ALLCOL;
 109     }
 110     command += TRIM + OUTPUTALIGNMENT + JALVIEWDIRECTORY + HMMBUFFER
 111             + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
 112
 113     runCommand(command);
 114
 115     if (createNewFrame)
 116     {
 117       FileLoader loader = new FileLoader();
 118       AlignFrame newFrame = loader.LoadFileWaitTillLoaded(ALIGNMENTINPUT,
 119             DataSourceType.FILE);
 120       for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
 121       {
 122         SequenceI seq = entry.getValue();
 123         Integer pos = entry.getKey();
 124         addHMMConsensusSequence(newFrame, seq, pos);
 125       }
 126       newFrame.alignPanel.alignmentChanged();
 127     }
 128     else
 129     {
 130       af.getViewport().getAlignment().getSequences().clear();
 131       af.loadJalviewDataFile(ALIGNMENTBUFFER, DataSourceType.FILE,
 132               FileFormat.Stockholm, null);
 133       for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
 134       {
 135         SequenceI seq = entry.getValue();
 136         Integer pos = entry.getKey();
 137         addHMMConsensusSequence(af, seq, pos);
 138       }
 139
 140     }
 141
 142
 143   }
 144
 145
 146   /**
 147    * Runs a command in the terminal.
 148    *
 149    * @param command
 150    * @throws IOException
 151    * @throws InterruptedException
 152    */
 153   private static void runCommand(String command)
 154           throws IOException, InterruptedException
 155   {
 156     final Process p = Runtime.getRuntime().exec(command);
 157
 158     new Thread(new Runnable()
 159     {
 160       @Override
 161       public void run()
 162       {
 163         BufferedReader input = new BufferedReader(
 164                 new InputStreamReader(p.getInputStream()));
 165         String line = null;
 166
 167         try
 168         {
 169           while ((line = input.readLine()) != null)
 170           {
 171             System.out.println(line);
 172           }
 173         } catch (IOException e)
 174         {
 175           e.printStackTrace();
 176         }
 177       }
 178     }).start();
 179
 180     p.waitFor();
 181   }
 182
 183   /**
 184    * Exports an alignment to the buffer location in Jalview.
 185    *
 186    * @param alignment
 187    * @throws FileNotFoundException
 188    */
 189   private static void exportAlignment(AlignmentI alignment)
 190           throws FileNotFoundException
 191   {
 192     List<SequenceI> list = alignment.getSequences();
 193     SequenceI[] array = new SequenceI[list.size()];
 194     list.toArray(array);
 195
 196     StockholmFile file = new StockholmFile(new Alignment(array));
 197     file.setSeqs(array);
 198     String output = file.print();
 199     PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER);
 200     writer.println(output);
 201     writer.close();
 202   }
 203
 204   private static void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
 205           Integer position)
 206   {
 207     seq.getHMM().initHMMSequence(af, position);
 208     AlignmentI al = af.getViewport().getAlignment();
 209     af.getViewport().setAlignment(al);
 210     af.alignPanel.adjustAnnotationHeight();
 211     af.getViewport().updateSequenceIdColours();
 212     af.buildSortByAnnotationScoresMenu();
 213   }
 214
 215
 216 }