JAL-2629 implement hmmbuild

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index f05f7bc..97f8c8d 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1315,6 +1315,6 @@ label.warning_hidden = Warning: {0} {1} is currently hidden
 label.change_hmmer_directory = Change HMMER suite location
 label.auto_align_seqs = Automatically Align New Sequences
 label.hmmalign = Align Sequences to HMM
-label.hmmbuild = Build HMM From Alignment
+label.hmmbuild = Build HMM from Alignment
 label.hmmsearch = Search for Related Sequences
 

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index 96a5a6f..727ffc7 100644 (file)
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -469,14 +469,33 @@ public class HiddenMarkovModel
    */
   public char getConsensusAtAlignColumn(int columnIndex)
   {
-    char value;
+    char mostLikely = '-';
+    if (consensusResidueIsActive())
+    {
+
     Integer index = findNodeIndex(columnIndex);
     if (index == null)
     {
       return '-';
     }
-    value = getNodes().get(index).getConsensusResidue();
-    return value;
+      mostLikely = getNodes().get(index).getConsensusResidue();
+      return mostLikely;
+    }
+    else
+    {
+      double highestProb = 0;
+      for (char character : symbols)
+      {
+        Double prob = getMatchEmissionProbability(columnIndex, character);
+        if (prob > highestProb)
+        {
+          highestProb = prob;
+          mostLikely = character;
+        }
+      }
+      return mostLikely;
+    }
+
   }
 
   /**
@@ -933,7 +952,9 @@ public class HiddenMarkovModel
       }
 
       Character cons;
+
       cons = getConsensusAtAlignColumn(alignPos);
+
       cons = Character.toUpperCase(cons);
 
       String description = String.format("%.3f", content);
@@ -948,6 +969,7 @@ public class HiddenMarkovModel
             "The information content of each column, measured in bits",
             annotations,
             0f, max, AlignmentAnnotation.BAR_GRAPH);
+    annotation.setHMM(this);
     return annotation;
   }
 
@@ -1008,14 +1030,9 @@ public class HiddenMarkovModel
     for (int index = 0; index < length; index++)
     {
       Character character;
-      if (consensusResidueIsActive())
-      {
+
         character = getConsensusAtAlignColumn(index);
-      }
-      else
-      {
-        character = findConsensusCharacter(index);
-      }
+
       if (character == null || character == '-')
       {
         sequence[index] = '-';
@@ -1031,29 +1048,6 @@ public class HiddenMarkovModel
     return seq;
   }
 
-  /**
-   * Finds the most probable character at a column in an alignment based on the
-   * HMM.
-   * 
-   * @param nodeIndex
-   *          The index of the node.
-   * @return
-   */
-  Character findConsensusCharacter(int column)
-  {
-    Character mostLikely = null;
-    double highestProb = 0;
-    for (char character : symbols)
-    {
-      Double prob = getMatchEmissionProbability(column, character);
-      if (prob > highestProb)
-      {
-        highestProb = prob;
-        mostLikely = character;
-      }
-    }
-    return mostLikely;
-  }
 
   /**
    * Maps the nodes of the hidden Markov model to the reference annotation.
@@ -1089,5 +1083,17 @@ public class HiddenMarkovModel
 
     }
   }
+
+  public AlignmentI initPlaceholder(AlignmentI alignment)
+  {
+    int length = alignment.getWidth();
+    Sequence consensus = getConsensusSequence(length);
+    consensus.setHMM(this);
+    SequenceI[] consensusArr = new Sequence[] { consensus };
+    AlignmentI newAlignment = new Alignment(consensusArr);
+    newAlignment.append(alignment);
+    return newAlignment;
+  }
+
 }
 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0c951fa..8ac7c8a 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,6 +63,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMERCommands;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
@@ -125,6 +126,7 @@ import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.io.FileWriter;
+import java.io.IOException;
 import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
@@ -1033,6 +1035,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  public void hmmBuild_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
+  {
+
+    HMMERCommands.hmmBuild(this);
+    alignPanel.repaint();
+  }
+
+  @Override
+  public void hmmAlign_actionPerformed(ActionEvent e)
+  {
+
+    alignPanel.repaint();
+  }
+
+  @Override
+  public void hmmSearch_actionPerformed(ActionEvent e)
+  {
+
+    alignPanel.repaint();
+  }
+
+  @Override
   public void reload_actionPerformed(ActionEvent e)
   {
     if (fileName != null)
@@ -4703,13 +4728,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             AlignmentAnnotation annotation = hmm.createAnnotation(
                     getViewport().getAlignment().getWidth());
             getViewport().getAlignment().addAnnotation(annotation);
-            int length = getViewport().getAlignment().getWidth();
-            Sequence consensus = hmm.getConsensusSequence(length);
-            consensus.setHMM(hmm);
-            annotation.setHMM(hmm);
-            SequenceI[] consensusArr = new Sequence[] { consensus };
-            AlignmentI newAlignment = new Alignment(consensusArr);
-            newAlignment.append(getViewport().getAlignment());
+            AlignmentI newAlignment = hmm
+                    .initPlaceholder(getViewport().getAlignment());
             getViewport().setAlignment(newAlignment);
             isAnnotation = true;
             alignPanel.repaint();

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
new file mode 100644 (file)
index 0000000..ac96c2a
--- /dev/null
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -0,0 +1,91 @@
+package jalview.hmmer;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.StockholmFile;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.List;
+
+public class HMMERCommands
+{
+  // Path of hmmer binaries directory
+  private static final String HMMERFOLDER = "H:/Documents/";
+
+  private static final String HMMALIGN = HMMERFOLDER + "hmmalign";
+
+  private static final String HMMBUILD = HMMERFOLDER + "hmmbuild";
+
+  private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch";
+
+  private static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/";
+
+  private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm";
+
+  private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto";
+
+  private static final String OUTPUTALIGNMENT = "-o " + ALIGNMENTBUFFER;
+
+  private static final String SPACE = " ";
+
+  public static void hmmBuild(AlignFrame af)
+          throws IOException, InterruptedException
+  {
+    HiddenMarkovModel hmm = null;
+    AlignmentI alignment = af.getViewport().getAlignment();
+    List<SequenceI> list = alignment.getSequences();
+    SequenceI[] array = new SequenceI[list.size()];
+    list.toArray(array);
+    StockholmFile file = new StockholmFile(alignment);
+    file.setSeqs(array);
+    String output = file.print();
+    PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER);
+    writer.println(output);
+    writer.close();
+    final String command = HMMBUILD + SPACE + JALVIEWDIRECTORY + HMMBUFFER
+            + SPACE
+            + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
+
+    runCommand(command);
+
+    af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE,
+            FileFormat.HMMER3, null);
+  }
+
+  private static void runCommand(String command)
+          throws IOException, InterruptedException
+  {
+    final Process p = Runtime.getRuntime().exec(command);
+
+    new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        BufferedReader input = new BufferedReader(
+                new InputStreamReader(p.getInputStream()));
+        String line = null;
+
+        try
+        {
+          while ((line = input.readLine()) != null)
+          {
+            System.out.println(line);
+          }
+        } catch (IOException e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }).start();
+
+    p.waitFor();
+  }
+}

diff --git a/src/jalview/hmmer/alignment_buffer.sto b/src/jalview/hmmer/alignment_buffer.sto
new file mode 100644 (file)
index 0000000..d0ad541
--- /dev/null
+++ b/src/jalview/hmmer/alignment_buffer.sto
@@ -0,0 +1,19 @@
+# STOCKHOLM 1.0
+FER_CAPAA            -----------------------------------------------------------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+FER_CAPAN            MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
+FER1_SOLLC           MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA-
+Q93XJ9_SOLTU         MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA-
+FER1_PEA             MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA-
+Q7XA98_TRIPR         MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA-
+FER1_MESCR           MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA-
+FER1_SPIOL           MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA-
+FER3_RAPSA           -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV--
+FER2_ARATH           MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV--
+FER_BRANA            -----------------------------------------------------------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV--
+FER1_ARATH           MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM--
+Q93Z60_ARATH         MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------------------
+FER1_MAIZE           MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA
+O80429_MAIZE         MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL--
+//
+
+

diff --git a/src/jalview/hmmer/hmm_buffer.hmm b/src/jalview/hmmer/hmm_buffer.hmm
new file mode 100644 (file)
index 0000000..9e3cb11
--- /dev/null
+++ b/src/jalview/hmmer/hmm_buffer.hmm
@@ -0,0 +1,464 @@
+HMMER3/b [3.0 | March 2010]
+NAME  alignment_buffer
+LENG  148
+ALPH  amino
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Jul 27 17:11:32 2017
+NSEQ  15
+EFFN  0.648193
+CKSUM 2563184735
+STATS LOCAL MSV      -10.0682  0.70956
+STATS LOCAL VITERBI  -10.7870  0.70956
+STATS LOCAL FORWARD   -4.6837  0.70956
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.40816  3.71583  2.80837  2.63551  3.47092  2.77036  3.85028  2.88279  2.80267  2.53589  3.68425  3.22102  3.34428  3.14560  3.11474  2.53177  2.75990  2.58070  5.00144  3.51101
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.10433  3.97705  2.52157  0.61958  0.77255  0.00000        *
+      1   2.99317  4.53706  4.08224  3.67789  3.22093  3.85692  4.40592  2.39958  3.44433  1.81088  1.32037  3.95163  4.31759  3.82413  3.64608  3.34553  3.29902  2.40928  5.06591  3.83044      1 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+      2   0.97044  4.20710  3.49350  3.28598  4.08269  3.03087  4.30444  3.21278  3.30302  3.09300  4.12129  3.42792  3.77296  3.64134  3.55157  2.55705  2.83652  2.86187  5.50678  4.31039      2 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.11955  3.90315  2.38048  0.61958  0.77255  0.55549  0.85282
+      3   1.74035  4.09199  3.34495  3.00819  4.05288  2.91638  4.05509  3.33461  3.01251  3.11462  3.97728  3.20348  3.62940  3.32849  3.32799  1.99191  1.99086  2.89563  5.42641  4.20726      3 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03323  3.81683  4.53917  0.61958  0.77255  0.62561  0.76558
+      4   2.37663  4.18625  3.55838  3.17855  3.75132  3.18264  4.13666  2.64341  3.07328  2.62344  3.69712  3.39774  3.83139  3.44405  3.35689  2.61052  1.64486  2.15973  5.30034  4.05468      4 - -
+          2.68617  4.42230  2.77525  2.73129  3.46359  2.40511  3.72500  3.29359  2.67746  2.69350  4.24695  2.90352  2.73719  3.18152  2.89806  2.37885  2.77501  2.98524  4.58482  3.61508
+          0.33937  1.47682  2.82312  0.71438  0.67236  0.50642  0.92294
+      5   1.78828  4.31568  3.18846  2.75366  3.97645  3.11838  3.84000  3.34055  2.67250  3.02453  3.87541  3.10729  3.71676  3.06391  2.67828  2.15246  2.50645  2.96422  5.30410  4.05011      9 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03188  3.85742  4.57976  0.61958  0.77255  0.59400  0.80322
+      6   2.60146  4.34120  4.20318  3.64233  3.23200  4.03946  4.38229  1.91078  3.53317  1.46276  2.80385  3.95250  4.35454  3.78680  3.77614  3.34686  3.12310  1.90138  5.05979  3.90282     10 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03188  3.85742  4.57976  0.61958  0.77255  0.59400  0.80322
+      7   2.51618  4.38929  3.20785  2.68482  3.53842  3.39630  3.71025  2.97988  2.63127  2.66315  3.23915  3.11866  3.35060  2.98059  3.01133  2.11689  2.77574  2.72369  4.95633  3.10650     11 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03188  3.85742  4.57976  0.61958  0.77255  0.59400  0.80322
+      8   1.83112  4.12334  3.20156  2.95461  4.23963  1.79514  4.09699  3.64646  3.07597  3.33878  4.16582  3.16397  3.61350  3.35846  3.40724  1.96001  2.64648  3.10558  5.57497  4.34818     12 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.07518  3.85742  2.97012  0.61958  0.77255  0.59400  0.80322
+      9   2.02467  4.19921  3.47207  3.00878  3.03795  3.27081  3.95597  2.70270  2.96218  2.55248  3.54468  3.31239  3.83177  3.27950  3.28895  2.63385  2.09090  2.46488  5.06606  3.80489     13 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03327  3.81551  4.53786  0.61958  0.77255  0.56041  0.84624
+     10   2.25155  4.19461  3.85704  3.29295  2.92371  3.72128  4.04839  2.07964  3.20853  2.08962  2.71310  3.60847  4.09120  3.47607  3.47945  3.00735  2.74040  2.14097  4.86082  3.65928     14 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03170  3.86316  4.58551  0.61958  0.77255  0.53107  0.88667
+     11   2.97746  4.34766  4.53309  3.96552  2.78843  4.21079  4.53997  1.80103  3.85948  1.59494  2.57669  4.20401  4.48099  4.02954  4.02513  3.53069  3.20806  1.63119  5.03312  3.89134     15 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     12   2.01604  4.15364  3.23013  2.99255  4.26101  2.66741  4.12859  3.66796  3.09383  3.37186  4.20680  3.19709  3.64453  3.39377  3.41395  1.27425  2.68165  3.13093  5.59931  4.36607     16 - -
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    138   3.09498  4.49149  4.45102  4.07022  3.43002  4.15408  4.78347  0.98199  3.89992  1.99977  3.35310  4.30411  4.57779  4.24002  4.08717  3.65761  3.39284  1.85079  5.33749  4.08258    146 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    139   3.02382  5.15051  2.52384  0.91441  4.50717  3.32764  3.92196  3.97736  2.81286  3.58149  4.55225  2.98104  3.93620  3.13613  3.22992  2.99812  3.32879  3.65289  5.66334  4.38601    147 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    140   2.45786  4.30296  3.50186  3.25812  4.04222  3.13941  4.26905  3.17937  3.20271  3.03994  4.08552  3.45408  3.84975  3.59352  3.45722  2.66008  1.04037  2.86556  5.47283  4.25897    148 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    141   3.08695  4.88934  3.20791  2.97643  3.34377  3.51816  0.98092  3.80251  2.81733  3.28606  4.33566  3.38232  4.07539  3.34383  3.07797  3.15699  3.39324  3.53609  4.80769  3.29239    149 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    142   2.99214  5.06805  3.26268  2.74531  4.47846  3.57206  3.65342  3.86981  1.12103  3.36156  4.25702  3.16311  3.99796  2.80635  2.11223  3.00404  3.19554  3.55761  5.42835  4.23089    150 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    143   3.02382  5.15051  2.52384  0.91441  4.50717  3.32764  3.92196  3.97736  2.81286  3.58149  4.55225  2.98104  3.93620  3.13613  3.22992  2.99812  3.32879  3.65289  5.66334  4.38601    151 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    144   2.49167  5.21869  2.13891  1.38935  4.54510  3.23855  3.71342  3.98470  2.64038  3.55288  4.39217  2.73628  3.81159  2.87379  3.17028  2.74234  3.08340  3.59770  5.74876  4.31122    152 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    145   2.67924  5.36825  1.81597  1.42545  4.67130  3.22067  3.71949  4.14895  2.68617  3.67868  4.51726  2.69278  3.81366  2.87890  3.25116  2.76699  3.13943  3.73938  5.85528  4.37934    153 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    146   3.24708  4.60677  4.69416  4.13988  3.08947  4.47063  4.76500  1.92492  3.96672  0.95356  2.71915  4.43331  4.67883  4.15873  4.13317  3.81764  3.47493  2.15974  5.15578  4.04247    154 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    147   2.69781  4.29649  3.84369  3.29786  3.44437  3.73086  4.15124  2.24231  3.19336  2.10104  3.11890  3.63278  4.14347  3.51043  3.49251  3.03876  2.03846  1.78833  5.07714  3.86271    155 - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.18495  3.95434  1.89921  0.61958  0.77255  0.50828  0.92013
+    148   1.44115  4.10304  3.22225  2.99375  4.15355  2.08176  4.10711  3.47540  3.09081  3.24183  4.11431  3.18864  3.61518  3.39097  3.39593  2.35434  2.65737  2.99565  5.50492  4.29375    156 - -
+          2.68608  4.42226  2.77520  2.73124  3.46354  2.40513  3.72495  3.29355  2.67741  2.69355  4.24690  2.90347  2.73740  3.18147  2.89801  2.37887  2.77520  2.98519  4.58477  3.61504
+          0.08120  2.55114        *  0.46726  0.98542  0.00000        *
+//

diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java
index 95e2017..18d9e78 100644 (file)
--- a/src/jalview/io/HMMFile.java
+++ b/src/jalview/io/HMMFile.java
@@ -188,23 +188,23 @@ public class HMMFile extends AlignFile
    */
   void parseModel(BufferedReader input) throws IOException
   {
-    for (int i = 0; i < hmm.getLength() + 1; i++)
+    String line = input.readLine();
+    int node = 0;
+    while (!"//".equals(line))
     {
       hmm.getNodes().add(new HMMNode());
       String next;
-      String line;
-      line = input.readLine();
       Scanner matchReader = new Scanner(line);
       next = matchReader.next();
-      if (next.equals(COMPO) || i > 0)
+      if (next.equals(COMPO) || node > 0)
       {
         // stores match emission line in list
         List<Double> matches = new ArrayList<>();
         matches = fillList(matchReader, numberOfSymbols);
-        hmm.getNodes().get(i).setMatchEmissions(matches);
-        if (i > 0)
+        hmm.getNodes().get(node).setMatchEmissions(matches);
+        if (node > 0)
         {
-          parseAnnotations(matchReader, i);
+          parseAnnotations(matchReader, node);
         }
       }
       matchReader.close();
@@ -213,7 +213,7 @@ public class HMMFile extends AlignFile
       Scanner insertReader = new Scanner(line);
       List<Double> inserts = new ArrayList<>();
       inserts = fillList(insertReader, numberOfSymbols);
-      hmm.getNodes().get(i).setInsertEmissions(inserts);
+      hmm.getNodes().get(node).setInsertEmissions(inserts);
       insertReader.close();
 
       // stores state transition line in list
@@ -221,8 +221,10 @@ public class HMMFile extends AlignFile
       Scanner transitionReader = new Scanner(line);
       List<Double> transitions = new ArrayList<>();
       transitions = fillList(transitionReader, NUMBER_OF_TRANSITIONS);
-      hmm.getNodes().get(i).setStateTransitions(transitions);
+      hmm.getNodes().get(node).setStateTransitions(transitions);
       transitionReader.close();
+      line = input.readLine();
+      node++;
     }
 
   }

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index c2f3683..dbb33f3 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -195,7 +195,7 @@ public class StockholmFile extends AlignFile
     String version;
     // String id;
     Hashtable seqAnn = new Hashtable(); // Sequence related annotations
-    LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+    LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
     Regex p, r, rend, s, x;
     // Temporary line for processing RNA annotation
     // String RNAannot = "";
@@ -657,7 +657,7 @@ public class StockholmFile extends AlignFile
               strucAnn = new Hashtable();
             }
 
-            Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+            Vector<AlignmentAnnotation> newStruc = new Vector<>();
             parseAnnotationRow(newStruc, type, ns);
             for (AlignmentAnnotation alan : newStruc)
             {
@@ -709,7 +709,7 @@ public class StockholmFile extends AlignFile
   private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
   {
     DBRefEntry dbrf = null;
-    List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> dbrs = new ArrayList<>();
     String seqdb = "Unknown", sdbac = "" + dbr;
     int st = -1, en = -1, p;
     if ((st = sdbac.indexOf("/")) > -1)
@@ -1151,7 +1151,6 @@ public class StockholmFile extends AlignFile
     out.append(newline);
     print(getSeqsAsArray(), false);
 
-    out.append("//");
     out.append(newline);
     return out.toString();
   }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index ea56bbb..3f55752 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -40,6 +40,7 @@ import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -1690,6 +1691,28 @@ public class GAlignFrame extends JInternalFrame
         selectHighlightedColumns_actionPerformed(actionEvent);
       }
     };
+    hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
+    hmmBuild.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          hmmBuild_actionPerformed(e);
+        } catch (IOException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        } catch (InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
+      }
+
+    });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
@@ -2381,6 +2404,7 @@ public class GAlignFrame extends JInternalFrame
   }
 
   protected void hmmBuild_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }