JAL-2629 current hmmer commands are now executed in threads

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index ce9cb62..5291493 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1144,6 +1144,9 @@ status.loading_cached_pdb_entries = Loading Cached PDB Entries
 status.searching_for_pdb_structures = Searching for PDB Structures
 status.opening_file_for = opening file for
 status.colouring_chimera = Colouring Chimera
+status.running_hmmbuild = "Building hidden Markov model"
+status.running_hmmalign = "Creating alignment with hidden Markov model"
+status.running_hmmsearch = "Searching for matching sequences"
 label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
 label.font_too_small = Font size is too small
 label.error_loading_file_params = Error loading file {0}

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 954bb34..76f9958 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,9 +20,6 @@
  */
 package jalview.bin;
 
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -66,6 +63,9 @@ import java.util.Vector;
 
 import javax.swing.UIManager;
 
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
 /**
  * Main class for Jalview Application <br>
  * <br>
@@ -175,8 +175,11 @@ public class Jalview
    * 
    * @param args
    *          open <em>filename</em>
+   * @throws InterruptedException
+   * @throws IOException
    */
   public static void main(String[] args)
+          throws IOException, InterruptedException
   {
     instance = new Jalview();
     instance.doMain(args);
@@ -184,8 +187,10 @@ public class Jalview
 
   /**
    * @param args
+   * @throws InterruptedException
+   * @throws IOException
    */
-  void doMain(String[] args)
+  void doMain(String[] args) throws IOException, InterruptedException
   {
     System.setSecurityManager(null);
     System.out.println("Java version: "
@@ -968,7 +973,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<String, Object>();
+      Map<String, Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {
@@ -1035,7 +1040,7 @@ public class Jalview
                         + nickname + "|" + url);
         if (source == null)
         {
-          source = new Vector<String>();
+          source = new Vector<>();
         }
         source.addElement(nickname);
       }
@@ -1053,7 +1058,7 @@ public class Jalview
       System.out.println("adding source '" + data + "'");
       if (source == null)
       {
-        source = new Vector<String>();
+        source = new Vector<>();
       }
       source.addElement(data);
     }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 05b1e33..dba6717 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,7 +63,8 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.hmmer.HMMERCommands;
+import jalview.hmmer.HMMAlignThread;
+import jalview.hmmer.HMMBuildThread;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
@@ -92,7 +93,6 @@ import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
-import jalview.workers.InformationThread;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.jws1.Discoverer;
@@ -1044,8 +1044,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hmmBuild_actionPerformed(ActionEvent e)
           throws IOException, InterruptedException
   {
-
-    HMMERCommands.hmmBuild(this);
+    new Thread(new HMMBuildThread(this)).start();
     alignPanel.repaint();
 
   }
@@ -1056,7 +1055,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     SequenceI seq = getViewport().getAlignment()
             .getHMMConsensusSequences(false).get(0);
-    HMMERCommands.hmmAlign(this, true, seq.getHMM());
+    new Thread(new HMMAlignThread(this, true)).start();
     alignPanel.repaint();
   }
 
@@ -4727,20 +4726,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else if (FileFormat.HMMER3.equals(format))
           {
-            HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO
-                                                                            // need
-                                                                            // to
-                                                                            // follow
-                                                                            // standard
-                                                                            // pipeline
-            hmmFile.parse();
+            HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType));
             HiddenMarkovModel hmm = hmmFile.getHMM();
             SequenceI hmmSeq = hmm.initHMMSequence(this, 0);
             getViewport().initInformation(hmmSeq);
-            new Thread(new InformationThread(getViewport(),
-                    getViewport().getAlignPanel())
-            {
-            }).start();
+            getViewport().updateInformation(alignPanel);
 
             isAnnotation = true;
 
@@ -4803,7 +4793,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       recurring = true;
       HiddenMarkovModel hmm = getViewport().getAlignment()
               .getHMMConsensusSequences(false).get(0).getHMM();
-      HMMERCommands.hmmAlign(this, false, hmm);
+      new Thread(new HMMAlignThread(this, false)).start();
     }
     recurring = false;
   }
@@ -5761,4 +5751,5 @@ class PrintThread extends Thread
       }
     }
   }
+
 }

diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java
new file mode 100644 (file)
index 0000000..8cd4270
--- /dev/null
+++ b/src/jalview/hmmer/HMMAlignThread.java
@@ -0,0 +1,128 @@
+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.FileLoader;
+import jalview.util.MessageManager;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Map;
+
+public class HMMAlignThread implements Runnable
+{
+
+  AlignFrame af;
+
+  AlignmentI alignment;
+
+  HiddenMarkovModel hmm;
+
+  boolean newFrame;
+
+  long barID;
+
+  Map<Integer, SequenceI> hmmSeqs;
+
+  public HMMAlignThread(AlignFrame af, boolean createNewFrame)
+  {
+    this.af = af;
+    alignment = af.getViewport().getAlignment();
+    hmm = alignment.getSequenceAt(0).getHMM();
+    newFrame = createNewFrame;
+  }
+
+  @Override
+  public void run()
+  {
+    barID = System.currentTimeMillis();
+    af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+            barID);
+
+    try
+    {
+      try
+      {
+        hmmSeqs = alignment.getHMMConsensusSequences(true);
+        HMMERCommands.exportData(alignment, true, true, hmm);
+      } catch (FileNotFoundException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+
+      }
+      try
+      {
+        runCommand();
+      } catch (IOException | InterruptedException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
+      try
+      {
+        importData();
+      } catch (IOException | InterruptedException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
+    } catch (Exception e)
+    {
+
+    } finally
+    {
+      af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+              barID);
+    }
+  }
+
+  private void runCommand() throws IOException, InterruptedException
+  {
+    String command = HMMERCommands.HMMALIGN;
+    if (!hmm.getFileHeader().contains("HMMER3/f"))
+    {
+      command += HMMERCommands.ALLCOL;
+    }
+    command += HMMERCommands.TRIM + HMMERCommands.OUTPUTALIGNMENT
+            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
+            + HMMERCommands.JALVIEWDIRECTORY
+            + HMMERCommands.ALIGNMENTBUFFER;
+    HMMERCommands.runCommand(command);
+  }
+
+  private void importData() throws IOException, InterruptedException
+  {
+    if (newFrame)
+    {
+      FileLoader loader = new FileLoader();
+      AlignFrame newAFrame = loader.LoadFileWaitTillLoaded(
+              HMMERCommands.ALIGNMENTINPUT, DataSourceType.FILE);
+      addSeqs(newAFrame);
+    }
+    else
+    {
+      af.getViewport().getAlignment().getSequences().clear();
+      af.loadJalviewDataFile(HMMERCommands.ALIGNMENTBUFFER,
+              DataSourceType.FILE, FileFormat.Stockholm, null);
+      addSeqs(af);
+    }
+  }
+
+  private void addSeqs(AlignFrame alignFrame)
+  {
+    for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
+    {
+      SequenceI seq = entry.getValue();
+      Integer pos = entry.getKey();
+      HMMERCommands.addHMMConsensusSequence(alignFrame, seq, pos);
+    }
+  }
+
+  }
+
+

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
new file mode 100644 (file)
index 0000000..868404b
--- /dev/null
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -0,0 +1,112 @@
+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.util.MessageManager;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Map;
+
+public class HMMBuildThread implements Runnable
+{
+
+  AlignFrame af;
+  AlignmentI alignment;
+
+  long barID;
+
+  Map<Integer, SequenceI> hmmSeqs;
+  
+  public HMMBuildThread(AlignFrame af)
+  {
+    this.af = af;
+    alignment = af.getViewport().getAlignment();
+  }
+
+  @Override
+  public void run()
+  {
+    barID = System.currentTimeMillis();
+    af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+            barID);
+
+    try
+    {
+    try
+    {
+      exportAlignment();
+    } catch (FileNotFoundException e)
+    {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+
+    }
+    try
+    {
+      runCommand();
+    } catch (IOException | InterruptedException e)
+    {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+    }
+    try
+    {
+      importData();
+    } catch (IOException | InterruptedException e)
+    {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+    }
+    } catch (Exception e)
+    {
+
+    } finally
+    {
+      af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+              barID);
+    }
+  }
+
+  
+  private void exportAlignment() throws IOException
+  {
+    hmmSeqs = alignment.getHMMConsensusSequences(true);
+    if (!alignment.isAligned())
+    {
+      alignment.padGaps();
+    }
+    HMMERCommands.exportData(alignment, true, false,
+            new HiddenMarkovModel());
+  }
+  
+  private void runCommand() throws IOException, InterruptedException
+  {
+    final String command = HMMERCommands.HMMBUILD + HMMERCommands.NAME
+            + af.getName() + HMMERCommands.SPACE
+            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
+            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;
+    HMMERCommands.runCommand(command);
+  }
+  
+  private void importData() throws IOException, InterruptedException
+  {
+    af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE,
+            FileFormat.HMMER3, null);
+    for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
+    {
+      SequenceI seq = entry.getValue();
+      Integer pos = entry.getKey();
+      HMMERCommands.addHMMConsensusSequence(af, seq, pos);
+    }
+    af.alignPanel.alignmentChanged();
+  }
+  
+  
+  
+ 
+}

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index c8d26e4..5a84989 100644 (file)
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -5,149 +5,44 @@ 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.FileLoader;
 import jalview.io.HMMFile;
 import jalview.io.StockholmFile;
-import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
 import java.util.List;
-import java.util.Map;
-
-import javax.swing.JOptionPane;
 
 public class HMMERCommands
 {
   // Path of hmmer binaries directory
-  private static final String HMMERFOLDER = "H:/Documents/";
+  static final String HMMERFOLDER = "H:/Documents/";
 
-  private static final String HMMALIGN = HMMERFOLDER + "hmmalign ";
+  static final String HMMALIGN = HMMERFOLDER + "hmmalign ";
 
-  private static final String HMMBUILD = HMMERFOLDER + "hmmbuild ";
+  static final String HMMBUILD = HMMERFOLDER + "hmmbuild ";
 
-  private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch ";
+  static final String HMMSEARCH = HMMERFOLDER + "hmmsearch ";
 
-  private static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/";
+  static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/";
 
-  private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm ";
+  static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm ";
 
-  private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto ";
+  static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto ";
 
-  private static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto ";
+  static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto ";
 
-  private static final String OUTPUTALIGNMENT = "-o " + JALVIEWDIRECTORY
+  static final String OUTPUTALIGNMENT = "-o " + JALVIEWDIRECTORY
           + ALIGNMENTINPUT;
 
-  private static final String NAME = "-n ";
-
-  private static final String SPACE = " ";
-
-  private static final String ALLCOL = "--allcol ";
+  static final String NAME = "-n ";
 
-  private static final String TRIM = "--trim ";
-
-  public static void hmmBuild(AlignFrame af)
-          throws IOException, InterruptedException
-  {
+  static final String SPACE = " ";
 
-    PrintWriter clearer = new PrintWriter(HMMBUFFER);
-    clearer.print("");
-    clearer.close();
-    AlignmentI alignment = af.getViewport().getAlignment();
-    if (!alignment.isAligned())
-    {
-      alignment.padGaps();
-    }
-    Map<Integer, SequenceI> seqs = alignment.getHMMConsensusSequences(true);
-    exportAlignment(alignment);
-    final String command = HMMBUILD + NAME + af.getName() + SPACE
-            + JALVIEWDIRECTORY + HMMBUFFER
-            + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
+  static final String ALLCOL = "--allcol ";
 
-    runCommand(command);
-
-    af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE,
-            FileFormat.HMMER3, null);
-    for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
-    {
-      SequenceI seq = entry.getValue();
-      Integer pos = entry.getKey();
-      addHMMConsensusSequence(af, seq, pos);
-    }
-    af.alignPanel.alignmentChanged();
-  }
-
-  public static void hmmAlign(AlignFrame af, boolean createNewFrame,
-          HiddenMarkovModel hmm)
-          throws IOException, InterruptedException
-  {
-
-    PrintWriter clearer = new PrintWriter(ALIGNMENTINPUT);
-    clearer.print("");
-    clearer.close();
-    AlignmentI al = af.getViewport().getAlignment();
-    if (!al.isAligned())
-    {
-      al.padGaps();
-    }
-    Map<Integer, SequenceI> seqs = al.getHMMConsensusSequences(true);
-    int index = 0;
-    if (hmm == null)
-    {
-      JOptionPane.showMessageDialog(af,
-              MessageManager.getString("warn.null_hmm"));
-      return;
-    }
-    exportAlignment(al);
-
-    HMMFile file = new HMMFile(hmm);
-    file.exportFile(HMMBUFFER);
-
-    String command = HMMALIGN;
-    if (!hmm.getFileHeader().contains("HMMER3/f"))
-    {
-      command += ALLCOL;
-    }
-    command += TRIM + OUTPUTALIGNMENT + JALVIEWDIRECTORY + HMMBUFFER
-            + JALVIEWDIRECTORY + ALIGNMENTBUFFER;
-
-    runCommand(command);
-
-    if (createNewFrame)
-    {
-      FileLoader loader = new FileLoader();
-      AlignFrame newFrame = loader.LoadFileWaitTillLoaded(ALIGNMENTINPUT,
-            DataSourceType.FILE);
-      for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
-      {
-        SequenceI seq = entry.getValue();
-        Integer pos = entry.getKey();
-        addHMMConsensusSequence(newFrame, seq, pos);
-      }
-      newFrame.alignPanel.alignmentChanged();
-    }
-    else
-    {
-      af.getViewport().getAlignment().getSequences().clear();
-      af.loadJalviewDataFile(ALIGNMENTBUFFER, DataSourceType.FILE,
-              FileFormat.Stockholm, null);
-      for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
-      {
-        SequenceI seq = entry.getValue();
-        Integer pos = entry.getKey();
-        addHMMConsensusSequence(af, seq, pos);
-      }
-
-    }
-
-
-  }
+  static final String TRIM = "--trim ";
 
 
   /**
@@ -157,7 +52,7 @@ public class HMMERCommands
    * @throws IOException
    * @throws InterruptedException
    */
-  private static void runCommand(String command)
+  public static void runCommand(String command)
           throws IOException, InterruptedException
   {
     final Process p = Runtime.getRuntime().exec(command);
@@ -191,24 +86,33 @@ public class HMMERCommands
    * Exports an alignment to the buffer location in Jalview.
    * 
    * @param alignment
-   * @throws FileNotFoundException
+   * @throws IOException
    */
-  private static void exportAlignment(AlignmentI alignment)
-          throws FileNotFoundException
+  public static void exportData(AlignmentI alignment,
+          boolean exportAlignment, boolean exportHMM, HiddenMarkovModel hmm)
+          throws IOException
   {
-    List<SequenceI> list = alignment.getSequences();
-    SequenceI[] array = new SequenceI[list.size()];
-    list.toArray(array);
-
-    StockholmFile file = new StockholmFile(new Alignment(array));
-    file.setSeqs(array);
-    String output = file.print();
-    PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER);
-    writer.println(output);
-    writer.close();
+    if (exportAlignment)
+    {
+      List<SequenceI> list = alignment.getSequences();
+      SequenceI[] array = new SequenceI[list.size()];
+      list.toArray(array);
+      StockholmFile file = new StockholmFile(new Alignment(array));
+      file.setSeqs(array);
+      String output = file.print();
+      PrintWriter writer = new PrintWriter(ALIGNMENTBUFFER);
+      writer.println(output);
+      writer.close();
+    }
+
+    if (exportHMM)
+    {
+      HMMFile file = new HMMFile(hmm);
+      file.exportFile(HMMBUFFER);
+    }
   }
 
-  private static void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
+  public static void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
           Integer position)
   {
     seq.getHMM().initHMMSequence(af, position);

diff --git a/src/jalview/hmmer/alignment_input.sto b/src/jalview/hmmer/alignment_input.sto
index ccfac69..0c2d626 100644 (file)
--- a/src/jalview/hmmer/alignment_input.sto
+++ b/src/jalview/hmmer/alignment_input.sto
@@ -1,11 +1,134 @@
 # STOCKHOLM 1.0
 
-seq1         TwWWGILK
-#=GR seq1 PP 88*****9
-seq2         T.WW-IIK
-#=GR seq2 PP 9.**.**9
-seq3         -.WWGLLK
-#=GR seq3 PP ..*****9
-#=GC PP_cons 9.*****9
-#=GC RF      x.xxxxxx
+FER_CAPAA            ----..---------------------.--------..-------.----
+#=GR FER_CAPAA    PP ..................................................
+FER_CAPAN            -A--..SVSATMISTSFMPRKPAVTSL.KPIPNVGE..ALFGLKS.A--N
+#=GR FER_CAPAN    PP .4....689******************.********..*******.9..8
+FER1_SOLLC           -A--..SISGTMISTSFLPRKPAVTSL.KAISNVGE..ALFGLKS.G--R
+#=GR FER1_SOLLC   PP .4....789******************.********..*******.*..9
+Q93XJ9_SOLTU         -A--..SISGTMISTSFLPRKPVVTSL.KAISNVGE..ALFGLKS.G--R
+#=GR Q93XJ9_SOLTU PP .4....789******************.********..*******.*..9
+FER1_PEA             MATT.pALYGTAVSTSFLRTQPMPMSV.TTTKAFSN..GFLGLKT.SLKR
+#=GR FER1_PEA     PP 8999.9*********************.********..*******.****
+Q7XA98_TRIPR         MATT.pALYGTAVSTSFMRRQPVPMSV.ATTTTTKAfpSGFGLKSvSTKR
+#=GR Q7XA98_TRIPR PP 8999.9*********************.887777765699****97899*
+FER1_MESCR           MAATtaALSGATMSTAFAPKTP-PMTA.ALPTNVGR..ALFGLKS.SASR
+#=GR FER1_MESCR   PP 56655799***********755.6666.89******..*******.*987
+FER1_SPIOL           MAAT..TTTMMGMATTFVPKPQAPPMMaALPSNTGR..SLFGLKT.GSR-
+#=GR FER1_SPIOL   PP 8888..8888889**********999978999****..*******.954.
+FER3_RAPSA           ----..---------------------.--------..-------.----
+#=GR FER3_RAPSA   PP ..................................................
+FER2_ARATH           MAST..ALSSAIVGTSFIRRSPAPISLrSLPSANTQ..SLFGLKS.GTAR
+#=GR FER2_ARATH   PP 9***..*********************9999*****..*******.****
+FER_BRANA            ----..---------------------.--------..-------.----
+#=GR FER_BRANA    PP ..................................................
+FER1_ARATH           MAST..ALSSAIVSTSFLRRQQTPISLrSLPFANTQ..SLFGLKS.STAR
+#=GR FER1_ARATH   PP 9***..*********************999******..*******.****
+Q93Z60_ARATH         MAST..ALSSAIVSTSFLRRQQTPISLrSLPFANTQ..SLFGLKS.STAR
+#=GR Q93Z60_ARATH PP 9***..*********************999******..*******.****
+FER1_MAIZE           ----..RAPAFFFSSSSLRAAPAPTAV.A-LPAAKV..GIMGRSA.SSRR
+#=GR FER1_MAIZE   PP ......567899***************.5.567899..*******.*988
+O80429_MAIZE         ----..--AATALSMSILRA--PPPCF.SSPLRLRV..AVAKPLA.APMR
+#=GR O80429_MAIZE PP ........57899*****95..34555.89******..*******.****
+#=GC PP_cons         8799..8999*********9*999999.999999**..*******.*999
+#=GC RF              xxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx..xxxxxxx.xxxx
+
+FER_CAPAA            -------ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGS
+#=GR FER_CAPAA    PP .......89*****************************************
+FER_CAPAN            GGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGS
+#=GR FER_CAPAN    PP 9*************************************************
+FER1_SOLLC           NGRITCMASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGS
+#=GR FER1_SOLLC   PP 9*************************************************
+Q93XJ9_SOLTU         NGRITCMASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGS
+#=GR Q93XJ9_SOLTU PP 9*************************************************
+FER1_PEA             GDLAVAMASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGS
+#=GR FER1_PEA     PP **************************************************
+Q7XA98_TRIPR         GDLAVAMATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGS
+#=GR Q7XA98_TRIPR PP **************************************************
+FER1_MESCR           -GRVTAMAAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGS
+#=GR FER1_MESCR   PP .9************************************************
+FER1_SPIOL           -GGRMTMAAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGS
+#=GR FER1_SPIOL   PP .55678********************************************
+FER3_RAPSA           -------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGS
+#=GR FER3_RAPSA   PP .......8******************************************
+FER2_ARATH           GGRVTAMATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGS
+#=GR FER2_ARATH   PP **************************************************
+FER_BRANA            -------ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGS
+#=GR FER_BRANA    PP .......8******************************************
+FER1_ARATH           GGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGS
+#=GR FER1_ARATH   PP **************************************************
+Q93Z60_ARATH         GGRVTAMATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGS
+#=GR Q93Z60_ARATH PP **************************************************
+FER1_MAIZE           --RLRAQATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGS
+#=GR FER1_MAIZE   PP ..9***********************************************
+O80429_MAIZE         RQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGS
+#=GR O80429_MAIZE PP **************************************************
+#=GC PP_cons         *99***********************************************
+#=GC RF              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+FER_CAPAA            CSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEA
+#=GR FER_CAPAA    PP **************************************************
+FER_CAPAN            CSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVTIETHKEA
+#=GR FER_CAPAN    PP **************************************************
+FER1_SOLLC           CSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVTIETHKEE
+#=GR FER1_SOLLC   PP **************************************************
+Q93XJ9_SOLTU         CSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEE
+#=GR Q93XJ9_SOLTU PP **************************************************
+FER1_PEA             CSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVVIETHKEE
+#=GR FER1_PEA     PP **************************************************
+Q7XA98_TRIPR         CSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVTIETHKEE
+#=GR Q7XA98_TRIPR PP **************************************************
+FER1_MESCR           CSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVTIETHKEE
+#=GR FER1_MESCR   PP **************************************************
+FER1_SPIOL           CSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEE
+#=GR FER1_SPIOL   PP **************************************************
+FER3_RAPSA           CSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVTIETHREE
+#=GR FER3_RAPSA   PP **************************************************
+FER2_ARATH           CSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVTIETHKEE
+#=GR FER2_ARATH   PP **************************************************
+FER_BRANA            CSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVTIETHKEE
+#=GR FER_BRANA    PP **************************************************
+FER1_ARATH           CSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVVIETHKEE
+#=GR FER1_ARATH   PP **************************************************
+Q93Z60_ARATH         CSSCAGKVVSGSIDQSDQSFLDD---------------------------
+#=GR Q93Z60_ARATH PP **********************8...........................
+FER1_MAIZE           CSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEE
+#=GR FER1_MAIZE   PP **************************************************
+O80429_MAIZE         CSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKED
+#=GR O80429_MAIZE PP **************************************************
+#=GC PP_cons         **************************************************
+#=GC RF              xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+FER_CAPAA            ELV-
+#=GR FER_CAPAA    PP *98.
+FER_CAPAN            ELV-
+#=GR FER_CAPAN    PP *98.
+FER1_SOLLC           ELTA
+#=GR FER1_SOLLC   PP **96
+Q93XJ9_SOLTU         ELTA
+#=GR Q93XJ9_SOLTU PP **96
+FER1_PEA             DLTA
+#=GR FER1_PEA     PP **96
+Q7XA98_TRIPR         ELTA
+#=GR Q7XA98_TRIPR PP **96
+FER1_MESCR           ELTA
+#=GR FER1_MESCR   PP **96
+FER1_SPIOL           ELTA
+#=GR FER1_SPIOL   PP **96
+FER3_RAPSA           DMV-
+#=GR FER3_RAPSA   PP *96.
+FER2_ARATH           DIV-
+#=GR FER2_ARATH   PP *96.
+FER_BRANA            ELV-
+#=GR FER_BRANA    PP *97.
+FER1_ARATH           AI--
+#=GR FER1_ARATH   PP 87..
+Q93Z60_ARATH         ----
+#=GR Q93Z60_ARATH PP ....
+FER1_MAIZE           ELT-
+#=GR FER1_MAIZE   PP **8.
+O80429_MAIZE         DLL-
+#=GR O80429_MAIZE PP *95.
+#=GC PP_cons         *986
+#=GC RF              xxxx
 //

diff --git a/src/jalview/hmmer/hmm_buffer.hmm b/src/jalview/hmmer/hmm_buffer.hmm
index a4007e7..397e822 100644 (file)
--- a/src/jalview/hmmer/hmm_buffer.hmm
+++ b/src/jalview/hmmer/hmm_buffer.hmm
@@ -3,462 +3,464 @@ NAME  null
 LENG  148
 ALPH  amino
 RF    no
+MM    no
+CONS  no
 CS    no
 MAP   yes
-DATE  Fri Aug  4 12:03:17 2017
+DATE  Mon Aug 7 16:18:25 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
+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 - -
+      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   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 - -
+      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 - -
+      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 - -
+      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 - -
+      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 - -
+      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 - -
+      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 - -
+      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 - -
+     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 - -
+     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 - -
+     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 - -
           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
-     13   2.41396  4.26265  3.40226  2.93569  3.72492  3.24366  3.92462  2.93397  2.83929  2.73560  3.16052  3.25846  3.81309  3.20648  3.16819  2.37913  1.73294  2.65776  5.16309  3.91530     17 - -
+     13   2.41396  4.26265  3.40226  2.93569  3.72492  3.24366  3.92462  2.93397  2.83929  2.73560  3.16052  3.25846  3.81309  3.20648  3.16819  2.37913  1.73294  2.65776  5.16309  3.91530 17 - -
           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
-     14   2.06589  4.14828  3.30608  3.02868  4.20053  2.92394  4.12227  3.52677  3.06750  3.27902  4.13704  3.22373  3.65849  3.38850  3.37961  1.31011  2.40891  3.04032  5.55736  4.32788     18 - -
+     14   2.06589  4.14828  3.30608  3.02868  4.20053  2.92394  4.12227  3.52677  3.06750  3.27902  4.13704  3.22373  3.65849  3.38850  3.37961  1.31011  2.40891  3.04032  5.55736  4.32788 18 - -
           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
-     15   2.74009  4.29274  3.92243  3.42912  1.74599  3.72053  3.90473  2.32427  3.32349  2.18956  3.31553  3.65797  4.14118  3.57919  3.55745  2.71376  3.01017  2.38146  4.46330  2.97696     19 - -
+     15   2.74009  4.29274  3.92243  3.42912  1.74599  3.72053  3.90473  2.32427  3.32349  2.18956  3.31553  3.65797  4.14118  3.57919  3.55745  2.71376  3.01017  2.38146  4.46330  2.97696 19 - -
           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
-     16   2.76094  4.39380  4.31945  3.75589  3.18422  4.12530  4.45889  2.01307  3.63847  1.30728  2.59228  4.05575  4.41925  3.86957  3.85970  3.43754  3.19324  1.94550  5.06650  3.93230     20 - -
+     16   2.76094  4.39380  4.31945  3.75589  3.18422  4.12530  4.45889  2.01307  3.63847  1.30728  2.59228  4.05575  4.41925  3.86957  3.85970  3.43754  3.19324  1.94550  5.06650  3.93230 20 - -
           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
-     17   2.70295  4.73637  3.16526  2.68917  4.18427  3.37581  3.71759  3.61851  2.27125  3.18722  4.06871  3.11427  2.39752  2.89725  1.66361  2.77186  2.98335  3.28411  5.34221  4.10051     21 - -
+     17   2.70295  4.73637  3.16526  2.68917  4.18427  3.37581  3.71759  3.61851  2.27125  3.18722  4.06871  3.11427  2.39752  2.89725  1.66361  2.77186  2.98335  3.28411  5.34221  4.10051 21 - -
           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
           0.07762  3.90315  2.90945  0.61958  0.77255  0.55549  0.85282
-     18   2.49055  4.81399  3.14505  2.59164  4.19520  3.44406  3.60132  3.55142  1.92611  3.12799  3.98038  3.04037  3.86298  2.75679  1.83484  2.76119  2.76042  3.23493  5.31169  4.06564     22 - -
+     18   2.49055  4.81399  3.14505  2.59164  4.19520  3.44406  3.60132  3.55142  1.92611  3.12799  3.98038  3.04037  3.86298  2.75679  1.83484  2.76119  2.76042  3.23493  5.31169  4.06564 22 - -
           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
           0.06501  3.85742  3.17445  0.61958  0.77255  0.59400  0.80322
-     19   2.43450  4.81939  2.81703  2.39298  4.15804  3.33308  3.59871  3.56807  2.06609  3.14527  3.97247  2.89702  3.36070  2.29211  2.66793  2.54254  2.87166  3.22778  5.35034  4.03520     23 - -
+     19   2.43450  4.81939  2.81703  2.39298  4.15804  3.33308  3.59871  3.56807  2.06609  3.14527  3.97247  2.89702  3.36070  2.29211  2.66793  2.54254  2.87166  3.22778  5.35034  4.03520 23 - -
           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
           0.03294  3.82535  4.54770  0.61958  0.77255  0.61916  0.77305
-     20   2.61608  4.67386  2.79167  2.51004  4.07010  3.23635  3.73836  3.55025  2.48903  3.13320  4.04098  2.97430  2.02723  2.34075  2.83811  2.68076  2.93097  3.21608  5.34739  4.03735     24 - -
+     20   2.61608  4.67386  2.79167  2.51004  4.07010  3.23635  3.73836  3.55025  2.48903  3.13320  4.04098  2.97430  2.02723  2.34075  2.83811  2.68076  2.93097  3.21608  5.34739  4.03735 24 - -
           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
           0.03294  3.82535  4.54770  0.61958  0.77255  0.51069  0.91649
-     21   1.83080  4.22890  3.60014  3.08598  3.61014  3.38577  4.01761  2.55536  3.00939  2.52819  3.20189  3.39791  3.91288  3.33215  3.33591  2.72706  2.41446  2.12040  5.12303  3.89826     25 - -
+     21   1.83080  4.22890  3.60014  3.08598  3.61014  3.38577  4.01761  2.55536  3.00939  2.52819  3.20189  3.39791  3.91288  3.33215  3.33591  2.72706  2.41446  2.12040  5.12303  3.89826 25 - -
           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
-     22   2.43845  4.29437  3.39983  3.04145  3.80350  3.19872  4.06195  2.96220  2.98493  2.76612  3.80233  3.32666  1.71751  3.35496  3.29387  2.63325  2.83846  2.21304  5.28839  4.02321     26 - -
+     22   2.43845  4.29437  3.39983  3.04145  3.80350  3.19872  4.06195  2.96220  2.98493  2.76612  3.80233  3.32666  1.71751  3.35496  3.29387  2.63325  2.83846  2.21304  5.28839  4.02321 26 - -
           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
-     23   2.55648  4.28453  3.47615  2.92649  3.45346  3.51308  3.86072  2.37030  2.85167  2.40896  2.93550  3.31525  2.97437  3.17776  3.19434  2.79032  2.33896  2.42929  4.94762  3.71651     27 - -
+     23   2.55648  4.28453  3.47615  2.92649  3.45346  3.51308  3.86072  2.37030  2.85167  2.40896  2.93550  3.31525  2.97437  3.17776  3.19434  2.79032  2.33896  2.42929  4.94762  3.71651 27 - -
           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
-     24   2.23005  4.31546  3.25841  2.77512  3.78441  3.22479  3.82985  3.12652  2.73582  2.83244  3.03171  3.14960  3.26067  3.07830  3.10838  1.85715  2.73859  2.81468  5.16957  3.91289     28 - -
+     24   2.23005  4.31546  3.25841  2.77512  3.78441  3.22479  3.82985  3.12652  2.73582  2.83244  3.03171  3.14960  3.26067  3.07830  3.10838  1.85715  2.73859  2.81468  5.16957  3.91289 28 - -
           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
-     25   2.72216  3.51794  4.14734  3.58168  3.26953  3.85722  4.23682  2.10046  3.47012  1.71220  2.91412  3.83361  4.22096  3.71804  3.68973  3.16541  2.79579  1.71693  4.93656  3.75086     29 - -
+     25   2.72216  3.51794  4.14734  3.58168  3.26953  3.85722  4.23682  2.10046  3.47012  1.71220  2.91412  3.83361  4.22096  3.71804  3.68973  3.16541  2.79579  1.71693  4.93656  3.75086 29 - -
           2.68606  4.42227  2.77522  2.73126  3.46337  2.40515  3.72497  3.29356  2.67743  2.69357  4.24692  2.90349  2.73742  3.18149  2.89784  2.37889  2.77522  2.98521  4.58479  3.61506
           0.31572  1.55442  2.82310  0.27619  1.42159  0.55549  0.85282
-     26   2.06718  4.47388  3.00085  2.59301  4.03403  3.18938  3.75234  3.40130  2.21691  3.06406  3.90876  3.01767  3.74194  2.94856  2.91976  2.09488  2.60568  3.04014  5.32541  4.04568     31 - -
+     26   2.06718  4.47388  3.00085  2.59301  4.03403  3.18938  3.75234  3.40130  2.21691  3.06406  3.90876  3.01767  3.74194  2.94856  2.91976  2.09488  2.60568  3.04014  5.32541  4.04568 31 - -
           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
           0.03205  3.85226  4.57460  0.61958  0.77255  0.52495  0.89548
-     27   2.09937  4.25808  3.35967  2.86682  3.65405  3.28224  3.85971  2.93650  2.81278  2.15397  3.59474  3.22143  3.43624  3.14697  3.16235  2.43009  2.43628  2.66078  5.07593  3.83686     32 - -
+     27   2.09937  4.25808  3.35967  2.86682  3.65405  3.28224  3.85971  2.93650  2.81278  2.15397  3.59474  3.22143  3.43624  3.14697  3.16235  2.43009  2.43628  2.66078  5.07593  3.83686 32 - -
           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
-     28   2.56380  4.32380  3.45039  2.92280  3.52453  3.48960  3.88793  2.33272  2.83649  2.29194  3.45598  3.31192  2.56007  3.18425  3.18050  2.78603  2.52825  2.43071  5.02605  3.78340     33 - -
+     28   2.56380  4.32380  3.45039  2.92280  3.52453  3.48960  3.88793  2.33272  2.83649  2.29194  3.45598  3.31192  2.56007  3.18425  3.18050  2.78603  2.52825  2.43071  5.02605  3.78340 33 - -
           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
-     29   2.52137  4.41862  3.18708  2.64701  3.24265  3.41116  3.70401  2.99879  2.50849  2.54033  3.56040  3.09794  3.19241  2.94883  3.00442  2.32271  2.53579  2.73855  5.01724  3.74765     34 - -
+     29   2.52137  4.41862  3.18708  2.64701  3.24265  3.41116  3.70401  2.99879  2.50849  2.54033  3.56040  3.09794  3.19241  2.94883  3.00442  2.32271  2.53579  2.73855  5.01724  3.74765 34 - -
           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
-     30   2.00013  4.58033  2.94855  2.53646  4.07584  3.24271  3.72285  3.46598  2.50253  3.10366  3.94143  2.28591  3.76727  2.90505  2.65085  2.58556  2.61842  3.10852  5.34830  4.05040     35 - -
+     30   2.00013  4.58033  2.94855  2.53646  4.07584  3.24271  3.72285  3.46598  2.50253  3.10366  3.94143  2.28591  3.76727  2.90505  2.65085  2.58556  2.61842  3.10852  5.34830  4.05040 35 - -
           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
-     31   2.38233  4.27978  3.41241  2.86526  3.23400  3.48475  3.81694  2.67786  2.81404  2.37039  3.42629  2.84230  3.90072  3.13098  3.17039  2.75440  2.50322  2.16090  4.92926  3.68461     36 - -
+     31   2.38233  4.27978  3.41241  2.86526  3.23400  3.48475  3.81694  2.67786  2.81404  2.37039  3.42629  2.84230  3.90072  3.13098  3.17039  2.75440  2.50322  2.16090  4.92926  3.68461 36 - -
           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
-     32   2.57741  4.71210  2.95136  2.48036  4.10354  2.51445  3.64563  3.50876  2.11219  3.10615  3.93363  2.96219  3.79067  2.80786  2.54902  2.50592  2.51289  3.16566  5.32824  4.02677     37 - -
+     32   2.57741  4.71210  2.95136  2.48036  4.10354  2.51445  3.64563  3.50876  2.11219  3.10615  3.93363  2.96219  3.79067  2.80786  2.54902  2.50592  2.51289  3.16566  5.32824  4.02677 37 - -
           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
-     33   2.48649  4.79372  2.91636  2.20828  4.05411  3.38774  3.59403  3.46081  2.32653  3.05709  3.87988  2.78811  3.79502  2.48988  2.50461  2.63652  2.83744  2.71303  5.28703  3.96685     38 - -
+     33   2.48649  4.79372  2.91636  2.20828  4.05411  3.38774  3.59403  3.46081  2.32653  3.05709  3.87988  2.78811  3.79502  2.48988  2.50461  2.63652  2.83744  2.71303  5.28703  3.96685 38 - -
           2.68619  4.42226  2.77520  2.73124  3.46338  2.40514  3.72495  3.29355  2.67742  2.69356  4.24691  2.90348  2.73732  3.18147  2.89802  2.37888  2.77520  2.98519  4.58478  3.61504
           0.07101  2.83445  4.62550  0.63888  0.75053  0.55549  0.85282
-     34   1.61247  4.12982  3.30077  3.01153  4.23531  2.30721  4.11812  3.64225  3.09602  3.33089  4.15414  3.20546  3.63382  3.37908  3.42786  1.71494  2.65404  3.10635  5.57312  4.35188     41 - -
+     34   1.61247  4.12982  3.30077  3.01153  4.23531  2.30721  4.11812  3.64225  3.09602  3.33089  4.15414  3.20546  3.63382  3.37908  3.42786  1.71494  2.65404  3.10635  5.57312  4.35188 41 - -
           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
-     35   2.72153  4.23229  3.98871  3.42694  2.97156  3.37228  4.12428  2.11066  3.32720  1.56866  3.14804  3.72158  4.17041  3.58506  3.57523  3.10753  2.96236  2.01957  4.85619  3.63474     42 - -
+     35   2.72153  4.23229  3.98871  3.42694  2.97156  3.37228  4.12428  2.11066  3.32720  1.56866  3.14804  3.72158  4.17041  3.58506  3.57523  3.10753  2.96236  2.01957  4.85619  3.63474 42 - -
           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
-     36   2.59948  4.33296  4.13320  3.58598  1.90470  3.92561  4.14661  2.31847  3.46961  1.74381  2.73954  3.84829  4.26638  3.69996  3.68809  3.23462  3.08833  2.27549  4.71854  3.39100     43 - -
+     36   2.59948  4.33296  4.13320  3.58598  1.90470  3.92561  4.14661  2.31847  3.46961  1.74381  2.73954  3.84829  4.26638  3.69996  3.68809  3.23462  3.08833  2.27549  4.71854  3.39100 43 - -
           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
-     37   2.58931  4.58161  2.85848  2.66250  4.27569  1.35942  3.92193  3.72667  2.37699  3.36968  4.25453  3.08080  3.80217  3.15095  3.05968  2.68693  2.97358  3.32002  5.50315  4.25822     44 - -
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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
           0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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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
           0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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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
           0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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           2.68618  4.42225  2.77520  2.73124  3.46354  2.40513  3.72495  3.29354  2.67741  2.69355  4.24690  2.90347  2.73740  3.18147  2.89801  2.37887  2.77520  2.98508  4.58477  3.61503
           0.07101  2.83445  4.62550  0.49418  0.94179  0.55549  0.85282
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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
           0.11955  3.90315  2.38048  0.61958  0.77255  0.55549  0.85282
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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
           0.03323  3.81683  4.53917  0.61958  0.77255  0.62561  0.76558
-     43   2.34367  4.62113  3.10732  2.54725  3.88271  3.41056  3.61301  3.25335  2.12788  2.89080  3.32993  3.01581  3.81452  2.79680  2.35592  2.55841  2.82420  2.96607  5.15612  3.88260     51 - -
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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
           0.07842  3.81683  2.92953  0.61958  0.77255  0.50642  0.92294
-     44   2.82371  4.84862  3.20218  2.72371  4.21308  3.44211  3.65714  3.71157  2.07944  3.25434  4.14899  2.84303  3.91564  2.83614  1.36807  2.87376  3.07618  3.38687  5.31229  4.06004     52 - -
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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
           0.12129  3.86316  2.37274  0.61958  0.77255  0.58934  0.80899
-     45   2.50307  4.57358  2.77436  2.48515  4.13002  2.10145  3.72113  3.58708  2.48196  3.19739  4.04544  2.56817  3.72971  2.91621  2.54565  2.57756  2.84032  3.19983  5.38083  4.07634     53 - -
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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
           0.03462  3.77648  4.49883  0.61958  0.77255  0.55399  0.85485
-     46   2.68547  4.96255  2.09111  2.21584  4.36925  1.97687  3.70446  3.84410  2.62382  3.41713  4.25934  2.75900  3.76266  2.58919  3.12019  2.66938  2.98839  3.45462  5.60805  4.21173     54 - -
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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
           0.03205  3.85226  4.57460  0.61958  0.77255  0.52495  0.89548
-     47   2.70472  4.70735  3.22145  2.64799  3.96742  3.15410  3.63371  3.33902  2.12091  2.43520  3.82970  3.09240  3.88741  2.81708  1.91192  2.78290  2.92703  3.06076  5.19463  3.94224     55 - -
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           0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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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
           0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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           0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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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
           0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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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
           0.03044  3.90315  4.62550  0.61958  0.77255  0.44450  1.02483
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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
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-     57   2.78989  4.87427  3.10728  2.66228  4.33471  3.44160  3.70636  3.64306  1.30828  3.25641  4.14609  3.10047  3.92071  2.86764  2.46119  2.83588  2.59339  3.32217  5.44317  4.19498     65 - -
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-     58   3.28295  4.64373  4.65267  4.15432  2.12281  4.39226  4.40565  2.30868  4.01063  0.99404  2.96208  4.34589  4.63887  4.13687  4.14117  3.75853  3.51440  2.42033  4.68321  3.26182     66 - -
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-     82   2.02804  4.79412  2.56696  2.04470  4.09359  3.33689  3.67081  3.44631  2.51465  3.10781  3.94410  2.90500  3.80252  2.83547  2.98166  2.64658  2.87169  2.76307  5.37415  4.03168     90 - -
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-     83   2.79923  4.56350  3.49435  3.40744  4.54632  0.58454  4.52062  4.17205  3.60289  3.81287  4.79002  3.65874  3.95796  3.91884  3.82676  2.97427  3.28861  3.68020  5.61312  4.65200     91 - -
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-     85   2.98626  5.46880  1.08491  1.97249  4.77077  3.21550  3.81546  4.28421  2.87189  3.82944  4.72170  2.71026  3.86087  3.00007  3.46540  2.87647  3.29141  3.87860  5.96770  4.48798     93 - -
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
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           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    103   2.33323  4.28075  3.53672  3.04537  3.62455  3.45748  3.98551  2.58410  2.72399  2.59228  3.55231  3.38781  3.95328  3.30102  3.25844  2.79290  2.46624  1.66085  5.10597  3.87716    111 - -
+    103   2.33323  4.28075  3.53672  3.04537  3.62455  3.45748  3.98551  2.58410  2.72399  2.59228  3.55231  3.38781  3.95328  3.30102  3.25844  2.79290  2.46624  1.66085  5.10597  3.87716 111 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    104   2.09904  4.31904  3.13967  2.79512  4.23584  2.43802  3.97520  3.66080  2.88605  3.30435  4.12032  2.79615  3.70254  3.18983  3.27753  1.61859  2.49732  3.17574  5.54095  4.27688    112 - -
+    104   2.09904  4.31904  3.13967  2.79512  4.23584  2.43802  3.97520  3.66080  2.88605  3.30435  4.12032  2.79615  3.70254  3.18983  3.27753  1.61859  2.49732  3.17574  5.54095  4.27688 112 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    105   2.79923  4.56350  3.49435  3.40744  4.54632  0.58454  4.52062  4.17205  3.60289  3.81287  4.79002  3.65874  3.95796  3.91884  3.82676  2.97427  3.28861  3.68020  5.61312  4.65200    113 - -
+    105   2.79923  4.56350  3.49435  3.40744  4.54632  0.58454  4.52062  4.17205  3.60289  3.81287  4.79002  3.65874  3.95796  3.91884  3.82676  2.97427  3.28861  3.68020  5.61312  4.65200 113 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    106   2.34210  4.57052  2.98887  2.43186  3.63497  3.31233  3.71920  3.32573  2.57569  2.97882  3.82112  2.81207  3.79423  2.91349  3.00476  1.86229  2.69145  3.00524  5.25570  3.95436    114 - -
+    106   2.34210  4.57052  2.98887  2.43186  3.63497  3.31233  3.71920  3.32573  2.57569  2.97882  3.82112  2.81207  3.79423  2.91349  3.00476  1.86229  2.69145  3.00524  5.25570  3.95436 114 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    107   3.05964  4.41092  4.64145  4.12759  3.48238  4.35054  4.85240  1.66963  3.99735  1.89738  3.31309  4.37857  4.66775  4.27653  4.21363  3.71953  3.32208  1.07763  5.41853  4.20516    115 - -
+    107   3.05964  4.41092  4.64145  4.12759  3.48238  4.35054  4.85240  1.66963  3.99735  1.89738  3.31309  4.37857  4.66775  4.27653  4.21363  3.71953  3.32208  1.07763  5.41853  4.20516 115 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    108   2.91005  5.38045  1.25818  2.12941  4.69830  3.20228  3.78776  4.26304  2.81947  3.79137  4.65619  2.14323  3.83796  2.96707  3.40279  2.81725  3.21882  3.83565  5.91563  4.42054    116 - -
+    108   2.91005  5.38045  1.25818  2.12941  4.69830  3.20228  3.78776  4.26304  2.81947  3.79137  4.65619  2.14323  3.83796  2.96707  3.40279  2.81725  3.21882  3.83565  5.91563  4.42054 116 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    109   2.96665  4.95377  2.97494  2.73211  4.13599  3.43683  3.89106  3.78353  2.54586  3.27542  4.30113  3.19246  3.99230  1.05904  2.82765  3.01035  3.26391  3.50694  5.38986  4.09082    117 - -
+    109   2.96665  4.95377  2.97494  2.73211  4.13599  3.43683  3.89106  3.78353  2.54586  3.27542  4.30113  3.19246  3.99230  1.05904  2.82765  3.01035  3.26391  3.50694  5.38986  4.09082 117 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    110   2.64618  4.90499  2.31134  2.18942  4.30332  3.26131  3.70172  3.73572  2.57300  3.32434  4.14511  2.84177  3.78986  2.86174  3.06104  1.76618  2.63178  3.35922  5.54260  4.16860    118 - -
+    110   2.64618  4.90499  2.31134  2.18942  4.30332  3.26131  3.70172  3.73572  2.57300  3.32434  4.14511  2.84177  3.78986  2.86174  3.06104  1.76618  2.63178  3.35922  5.54260  4.16860 118 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    111   3.10426  5.24570  0.77891  2.40498  4.63731  3.29196  4.02650  4.24977  3.13093  3.83985  4.82107  2.96628  3.95224  3.26642  3.66070  3.05541  3.44536  3.87811  5.78539  4.49402    119 - -
+    111   3.10426  5.24570  0.77891  2.40498  4.63731  3.29196  4.02650  4.24977  3.13093  3.83985  4.82107  2.96628  3.95224  3.26642  3.66070  3.05541  3.44536  3.87811  5.78539  4.49402 119 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    112   2.73269  4.96873  2.61141  2.26957  4.35491  2.17303  3.70728  3.80016  2.46897  3.36392  4.20366  2.88233  3.83451  1.94009  2.87446  2.73151  3.00866  3.43365  5.54626  4.19876    120 - -
+    112   2.73269  4.96873  2.61141  2.26957  4.35491  2.17303  3.70728  3.80016  2.46897  3.36392  4.20366  2.88233  3.83451  1.94009  2.87446  2.73151  3.00866  3.43365  5.54626  4.19876 120 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    113   2.56630  4.67539  2.76483  2.50324  4.25470  3.20379  3.80042  3.71196  2.47872  3.32135  4.15966  2.47516  3.79205  2.98884  3.00841  1.53662  2.90903  3.30833  5.51362  4.18451    121 - -
+    113   2.56630  4.67539  2.76483  2.50324  4.25470  3.20379  3.80042  3.71196  2.47872  3.32135  4.15966  2.47516  3.79205  2.98884  3.00841  1.53662  2.90903  3.30833  5.51362  4.18451 121 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    114   3.45422  4.77029  4.46140  4.11213  1.01250  4.26302  3.55945  3.07075  3.96969  2.40922  3.69615  4.01237  4.59409  4.02617  4.05737  3.63979  3.68916  3.02613  3.73517  1.83750    122 - -
+    114   3.45422  4.77029  4.46140  4.11213  1.01250  4.26302  3.55945  3.07075  3.96969  2.40922  3.69615  4.01237  4.59409  4.02617  4.05737  3.63979  3.68916  3.02613  3.73517  1.83750 122 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    115   3.27378  4.70553  4.35708  3.99825  3.17780  4.11433  4.62122  2.38848  3.76496  0.75643  3.16963  4.26355  4.53226  4.10824  3.92358  3.69863  3.56359  2.45281  5.09417  3.84135    123 - -
+    115   3.27378  4.70553  4.35708  3.99825  3.17780  4.11433  4.62122  2.38848  3.76496  0.75643  3.16963  4.26355  4.53226  4.10824  3.92358  3.69863  3.56359  2.45281  5.09417  3.84135 123 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    116   2.92493  5.35887  1.12201  2.14550  4.68054  3.19834  3.81470  4.26138  2.86788  3.80711  4.68829  2.43062  3.84716  3.00361  3.45124  2.83676  3.24430  3.83759  5.91360  4.42201    124 - -
+    116   2.92493  5.35887  1.12201  2.14550  4.68054  3.19834  3.81470  4.26138  2.86788  3.80711  4.68829  2.43062  3.84716  3.00361  3.45124  2.83676  3.24430  3.83759  5.91360  4.42201 124 - -
           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
           0.02824  3.97705  4.69940  0.61958  0.77255  0.48576  0.95510
-    117   2.99103  5.43832  1.04731  2.03422  4.75036  3.21916  3.83186  4.26509  2.89245  3.82288  4.72422  2.72815  3.86743  3.02108  3.48036  2.88767  3.30065  3.86474  5.95049  4.48470    125 - -
+    117   2.99103  5.43832  1.04731  2.03422  4.75036  3.21916  3.83186  4.26509  2.89245  3.82288  4.72422  2.72815  3.86743  3.02108  3.48036  2.88767  3.30065  3.86474  5.95049  4.48470 125 - -
           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
           0.05161  3.97705  3.45590  0.61958  0.77255  0.48576  0.95510
-    118   2.86997  5.43069  1.57180  1.74614  4.72729  2.80306  3.71453  4.23943  2.69618  3.73332  4.56237  2.43722  3.80910  2.87126  3.27991  2.76596  3.14983  3.81040  5.89719  4.40314    126 - -
+    118   2.86997  5.43069  1.57180  1.74614  4.72729  2.80306  3.71453  4.23943  2.69618  3.73332  4.56237  2.43722  3.80910  2.87126  3.27991  2.76596  3.14983  3.81040  5.89719  4.40314 126 - -
           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
-    119   2.94701  4.93449  2.95833  2.71460  4.11381  3.42085  3.87354  3.75736  2.52981  3.25157  4.27740  3.17495  3.97565  1.09531  2.81227  2.99143  3.24405  3.48203  5.37148  4.07074    127 - -
+    119   2.94701  4.93449  2.95833  2.71460  4.11381  3.42085  3.87354  3.75736  2.52981  3.25157  4.27740  3.17495  3.97565  1.09531  2.81227  2.99143  3.24405  3.48203  5.37148  4.07074 127 - -
           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
-    120   2.77849  4.28259  3.99549  3.02221  3.34513  3.89873  4.21017  1.60238  3.32583  1.96055  3.04166  3.76188  4.24121  3.61775  3.59603  3.18793  3.01465  1.89778  5.01613  3.81900    128 - -
+    120   2.77849  4.28259  3.99549  3.02221  3.34513  3.89873  4.21017  1.60238  3.32583  1.96055  3.04166  3.76188  4.24121  3.61775  3.59603  3.18793  3.01465  1.89778  5.01613  3.81900 128 - -
           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
-    121   2.05663  4.99383  2.42035  1.95337  4.30142  3.11016  3.64379  3.74448  2.38547  3.30891  4.11909  2.80952  3.78509  2.79112  2.97996  2.54099  2.92358  3.37653  5.51637  4.13250    129 - -
+    121   2.05663  4.99383  2.42035  1.95337  4.30142  3.11016  3.64379  3.74448  2.38547  3.30891  4.11909  2.80952  3.78509  2.79112  2.97996  2.54099  2.92358  3.37653  5.51637  4.13250 129 - -
           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
-    122   2.37074  5.20065  2.03752  1.62561  4.52764  2.94012  3.68254  3.99698  2.59389  3.53203  4.34713  2.73405  3.79399  2.83254  3.13133  2.70217  3.03318  3.59496  5.71621  4.27884    130 - -
+    122   2.37074  5.20065  2.03752  1.62561  4.52764  2.94012  3.68254  3.99698  2.59389  3.53203  4.34713  2.73405  3.79399  2.83254  3.13133  2.70217  3.03318  3.59496  5.71621  4.27884 130 - -
           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
-    123   2.76891  4.53595  3.45942  3.36936  4.50963  0.61326  4.48439  4.12940  3.56175  3.77320  4.74981  3.62373  3.92970  3.87945  3.78857  2.94321  3.25651  3.64192  5.58291  4.61439    131 - -
+    123   2.76891  4.53595  3.45942  3.36936  4.50963  0.61326  4.48439  4.12940  3.56175  3.77320  4.74981  3.62373  3.92970  3.87945  3.78857  2.94321  3.25651  3.64192  5.58291  4.61439 131 - -
           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
-    124   3.45280  4.72560  4.55948  4.18538  1.45983  4.27876  3.45556  3.19175  4.01502  2.56322  3.77632  3.99268  4.58568  4.02082  4.06587  3.62371  3.67122  3.09770  1.76510  1.80304    132 - -
+    124   3.45280  4.72560  4.55948  4.18538  1.45983  4.27876  3.45556  3.19175  4.01502  2.56322  3.77632  3.99268  4.58568  4.02082  4.06587  3.62371  3.67122  3.09770  1.76510  1.80304 132 - -
           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
-    125   2.87283  4.39315  4.23821  3.90420  3.61058  3.80809  4.69198  2.04849  3.77322  2.28363  3.56364  4.08078  4.36427  4.12727  3.97777  3.31702  3.23254  0.92773  5.40873  4.14528    133 - -
+    125   2.87283  4.39315  4.23821  3.90420  3.61058  3.80809  4.69198  2.04849  3.77322  2.28363  3.56364  4.08078  4.36427  4.12727  3.97777  3.31702  3.23254  0.92773  5.40873  4.14528 133 - -
           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
-    126   3.24760  4.68579  4.32075  3.96132  3.16793  4.08580  4.59138  2.37683  3.72825  0.78064  3.16594  4.22883  4.50730  4.07699  3.89079  3.66669  3.53825  2.43535  5.07658  3.81868    134 - -
+    126   3.24760  4.68579  4.32075  3.96132  3.16793  4.08580  4.59138  2.37683  3.72825  0.78064  3.16594  4.22883  4.50730  4.07699  3.89079  3.66669  3.53825  2.43535  5.07658  3.81868 134 - -
           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
-    127   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    135 - -
+    127   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 135 - -
           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
-    128   2.68154  0.78852  4.21932  3.97783  3.95068  3.28696  4.60693  3.10838  3.80528  3.02007  4.14415  3.94300  4.00035  4.14805  3.91507  2.95331  3.15521  2.84739  5.34926  4.23772    136 - -
+    128   2.68154  0.78852  4.21932  3.97783  3.95068  3.28696  4.60693  3.10838  3.80528  3.02007  4.14415  3.94300  4.00035  4.14805  3.91507  2.95331  3.15521  2.84739  5.34926  4.23772 136 - -
           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
-    129   2.02617  4.29048  3.42265  2.94627  3.54036  3.40652  3.31257  2.77872  2.86355  2.59741  3.53948  3.30371  3.90044  3.21666  3.18816  2.73904  2.82169  1.86270  5.00831  3.74432    137 - -
+    129   2.02617  4.29048  3.42265  2.94627  3.54036  3.40652  3.31257  2.77872  2.86355  2.59741  3.53948  3.30371  3.90044  3.21666  3.18816  2.73904  2.82169  1.86270  5.00831  3.74432 137 - -
           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
-    130   0.90195  4.23400  3.54659  3.34205  4.13472  3.05626  4.35430  3.27256  3.36043  3.15035  4.17350  3.47069  3.80326  3.69417  3.60509  2.58374  2.86679  2.91280  5.55371  4.36315    138 - -
+    130   0.90195  4.23400  3.54659  3.34205  4.13472  3.05626  4.35430  3.27256  3.36043  3.15035  4.17350  3.47069  3.80326  3.69417  3.60509  2.58374  2.86679  2.91280  5.55371  4.36315 138 - -
           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
-    131   3.44381  4.80306  4.30117  3.95207  1.85364  4.19548  3.48537  3.22033  3.81418  2.60484  3.85318  3.90681  4.54641  3.92239  3.94488  3.57229  3.68268  3.12961  3.68006  0.97942    139 - -
+    131   3.44381  4.80306  4.30117  3.95207  1.85364  4.19548  3.48537  3.22033  3.81418  2.60484  3.85318  3.90681  4.54641  3.92239  3.94488  3.57229  3.68268  3.12961  3.68006  0.97942 139 - -
           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
-    132   2.86235  4.60578  3.47842  3.32948  4.31715  3.28867  4.39999  3.88386  3.39382  3.50174  4.55528  3.62780  0.68858  3.78012  3.62986  3.03247  3.31042  3.51987  5.48103  4.43903    140 - -
+    132   2.86235  4.60578  3.47842  3.32948  4.31715  3.28867  4.39999  3.88386  3.39382  3.50174  4.55528  3.62780  0.68858  3.78012  3.62986  3.03247  3.31042  3.51987  5.48103  4.43903 140 - -
           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
-    133   2.60256  4.60991  3.08123  2.59418  3.90705  3.39886  3.69738  3.25085  2.27951  2.91739  3.78849  3.05676  3.84470  2.63540  2.79735  2.69573  1.94572  2.76699  5.21418  3.93668    141 - -
+    133   2.60256  4.60991  3.08123  2.59418  3.90705  3.39886  3.69738  3.25085  2.27951  2.91739  3.78849  3.05676  3.84470  2.63540  2.79735  2.69573  1.94572  2.76699  5.21418  3.93668 141 - -
           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
-    134   2.16968  3.47307  3.59233  3.22260  4.15866  2.47411  4.19438  3.56363  3.18625  3.27458  4.10858  3.32406  3.66022  3.48496  3.48055  1.23700  2.65371  3.05043  5.52336  4.31592    142 - -
+    134   2.16968  3.47307  3.59233  3.22260  4.15866  2.47411  4.19438  3.56363  3.18625  3.27458  4.10858  3.32406  3.66022  3.48496  3.48055  1.23700  2.65371  3.05043  5.52336  4.31592 142 - -
           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
-    135   3.07859  5.21813  0.80740  2.38838  4.60638  3.27362  4.00471  4.21341  3.10456  3.80732  4.78755  2.94873  3.93224  3.24424  3.63163  3.03196  3.41903  3.84400  5.75900  4.46621    143 - -
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           0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
-    136   2.87283  4.39315  4.23821  3.90420  3.61058  3.80809  4.69198  2.04849  3.77322  2.28363  3.56364  4.08078  4.36427  4.12727  3.97777  3.31702  3.23254  0.92773  5.40873  4.14528    144 - -
+    136   2.87283  4.39315  4.23821  3.90420  3.61058  3.80809  4.69198  2.04849  3.77322  2.28363  3.56364  4.08078  4.36427  4.12727  3.97777  3.31702  3.23254  0.92773  5.40873  4.14528 144 - -
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           0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
-    137   2.50102  4.23694  3.76525  3.33965  3.72246  3.37067  4.24809  2.46042  3.23911  2.55924  3.64161  3.56053  3.97799  3.58142  3.52035  2.77764  1.69802  1.75863  5.30971  4.08018    145 - -
+    137   2.50102  4.23694  3.76525  3.33965  3.72246  3.37067  4.24809  2.46042  3.23911  2.55924  3.64161  3.56053  3.97799  3.58142  3.52035  2.77764  1.69802  1.75863  5.30971  4.08018 145 - -
           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 - -
+    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 - -
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           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 - -
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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
-    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 - -
+    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 - -
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           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 - -
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           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 - -
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-    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 - -
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           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 - -
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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
-    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 - -
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           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 - -
+    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 - -
+    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/FileFormat.java b/src/jalview/io/FileFormat.java
index 50d2aa7..11e06a2 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -354,7 +354,7 @@ public enum FileFormat implements FileFormatI
       return false;
     }
   },
-  HMMER3("HMMER3", "hmm", false, false)
+  HMMER3("HMMER3", "hmm", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)

diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java
index e7f8030..02d9229 100644 (file)
--- a/src/jalview/io/HMMFile.java
+++ b/src/jalview/io/HMMFile.java
@@ -27,9 +27,6 @@ public class HMMFile extends AlignFile
   // HMM to store file data
   private HiddenMarkovModel hmm = new HiddenMarkovModel();
 
-
-
-
   // number of possible transitions
   private final int NUMBER_OF_TRANSITIONS = 7;
 
@@ -48,13 +45,15 @@ public class HMMFile extends AlignFile
   private static final String TRANSITIONTYPELINE = "m->m     m->i     m->d     i->m     i->i     d->m     d->d";
 
   /**
-   * Constructor for HMMFile
+   * Constructor for HMMFile, parses immediately
+   * 
    * @param source
    * @throws IOException
    */
   public HMMFile(FileParse source) throws IOException
   {
     super(false, source);
+    parse();
   }
 
   /**

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index b3ccb45..96a35f9 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -80,8 +80,8 @@ import java.util.Map;
  * @author jimp
  * 
  */
-public abstract class AlignmentViewport implements AlignViewportI,
-        CommandListener, VamsasSource
+public abstract class AlignmentViewport
+        implements AlignViewportI, CommandListener, VamsasSource
 {
   final protected ViewportRanges ranges;
 
@@ -98,7 +98,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected Deque<CommandI> historyList = new ArrayDeque<>();
 
   protected Deque<CommandI> redoList = new ArrayDeque<>();
-  
 
   /**
    * alignment displayed in the viewport. Please use get/setter
@@ -571,8 +570,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setSeqNameItalics(default1);
   }
 
-
-
   @Override
   public AlignmentI getAlignment()
   {
@@ -668,8 +665,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
         sg.setColourScheme(cs);
         if (cs != null)
         {
-          sg.getGroupColourScheme()
-                  .alignmentChanged(sg, hiddenRepSequences);
+          sg.getGroupColourScheme().alignmentChanged(sg,
+                  hiddenRepSequences);
         }
       }
     }
@@ -678,8 +675,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public ColourSchemeI getGlobalColourScheme()
   {
-    return residueShading == null ? null : residueShading
-            .getColourScheme();
+    return residueShading == null ? null : residueShading.getColourScheme();
   }
 
   @Override
@@ -837,7 +833,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return information.get(index);
   }
 
-
   @Override
   public AlignmentAnnotation getAlignmentGapAnnotation()
   {
@@ -870,11 +865,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator
-            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
+    if (calculator.getRegisteredWorkersOfClass(
+            jalview.workers.ConservationThread.class) == null)
     {
-      calculator.registerWorker(new jalview.workers.ConservationThread(
-              this, ap));
+      calculator.registerWorker(
+              new jalview.workers.ConservationThread(this, ap));
     }
   }
 
@@ -888,7 +883,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+    if (calculator
+            .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -919,8 +915,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
       if (doConsensus)
       {
-        if (calculator
-                .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+        if (calculator.getRegisteredWorkersOfClass(
+                ComplementConsensusThread.class) == null)
         {
           calculator
                   .registerWorker(new ComplementConsensusThread(this, ap));
@@ -957,7 +953,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
+    if (calculator.getRegisteredWorkersOfClass(
+            StrucConsensusThread.class) == null)
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -1300,8 +1297,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (sequenceSetID != null)
     {
-      System.err
-              .println("Warning - overwriting a sequenceSetId for a viewport!");
+      System.err.println(
+              "Warning - overwriting a sequenceSetId for a viewport!");
     }
     sequenceSetID = new String(newid);
   }
@@ -1531,8 +1528,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup = new SequenceGroup();
         selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
-              hiddenRepSequences);
+      List<SequenceI> tmp = alignment.getHiddenSequences()
+              .showAll(hiddenRepSequences);
       for (SequenceI seq : tmp)
       {
         selectionGroup.addSequence(seq, false);
@@ -1550,8 +1547,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void showSequence(int index)
   {
-    List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
-            index, hiddenRepSequences);
+    List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
+            hiddenRepSequences);
     if (tmp.size() > 0)
     {
       if (selectionGroup == null)
@@ -1622,8 +1619,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
 
     int gsize = selectionGroup.getSize();
-    SequenceI[] hseqs = selectionGroup.getSequences().toArray(
-            new SequenceI[gsize]);
+    SequenceI[] hseqs = selectionGroup.getSequences()
+            .toArray(new SequenceI[gsize]);
 
     hideSequence(hseqs);
     setSelectionGroup(null);
@@ -1713,8 +1710,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return (hiddenRepSequences != null && hiddenRepSequences
-            .containsKey(seq));
+    return (hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(seq));
   }
 
   /**
@@ -1732,8 +1729,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(
-            alignmentIndex);
+    return alignment.getHiddenSequences()
+            .adjustForHiddenSeqs(alignmentIndex);
   }
 
   @Override
@@ -1805,8 +1802,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return new AlignmentView(alignment, alignment.getHiddenColumns(),
             selectionGroup, alignment.getHiddenColumns() != null
                     && alignment.getHiddenColumns().hasHiddenColumns(),
-            selectedOnly,
-            markGroups);
+            selectedOnly, markGroups);
   }
 
   @Override
@@ -1852,8 +1848,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     if (alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
-              start, end, seqs);
+      selection = alignment.getHiddenColumns()
+              .getVisibleSequenceStrings(start, end, seqs);
     }
     else
     {
@@ -1922,8 +1918,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
         if (selectedOnly && selectionGroup != null)
         {
           alignment.getHiddenColumns().makeVisibleAnnotation(
-                  selectionGroup.getStartRes(),
-                  selectionGroup.getEndRes(), clone);
+                  selectionGroup.getStartRes(), selectionGroup.getEndRes(),
+                  clone);
         }
         else
         {
@@ -2064,7 +2060,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
-
   /**
    * If this is a protein alignment and there are mappings to cDNA, adds the
    * cDNA consensus annotation and returns true, else returns false.
@@ -2127,6 +2122,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     information.hasText = true;
     information.autoCalculated = false;
     information.sequenceRef = hmmSequence;
+    information.setCalcId("HMM annotation");
     this.information.add(information);
     hinformation.add(new Profiles(new ProfileI[1]));
     alignment.addAnnotation(information);
@@ -2140,8 +2136,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       gapcounts = new AlignmentAnnotation("Occupancy",
               MessageManager.getString("label.occupancy_descr"),
-              new Annotation[1], 0f,
-              alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+              new Annotation[1], 0f, alignment.getHeight(),
+              AlignmentAnnotation.BAR_GRAPH);
       gapcounts.hasText = true;
       gapcounts.autoCalculated = true;
       gapcounts.scaleColLabel = true;
@@ -2159,8 +2155,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         conservation = new AlignmentAnnotation("Conservation",
                 MessageManager.formatMessage("label.conservation_descr",
-                        getConsPercGaps()), new Annotation[1],
-                0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+                        getConsPercGaps()),
+                new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
         alignment.addAnnotation(conservation);
@@ -2646,8 +2642,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle = new ViewStyle(settingsForView);
     if (residueShading != null)
     {
-      residueShading.setConservationApplied(settingsForView
-              .isConservationColourSelected());
+      residueShading.setConservationApplied(
+              settingsForView.isConservationColourSelected());
     }
   }
 
@@ -2815,7 +2811,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sortAnnotationsBy;
   }
 
-  public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+  public void setSortAnnotationsBy(
+          SequenceAnnotationOrder sortAnnotationsBy)
   {
     this.sortAnnotationsBy = sortAnnotationsBy;
   }
@@ -2893,8 +2890,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return 0;
     }
     boolean iAmProtein = !getAlignment().isNucleotide();
-    AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
-            .getAlignment();
+    AlignmentI proteinAlignment = iAmProtein ? getAlignment()
+            : complement.getAlignment();
     if (proteinAlignment == null)
     {
       return 0;
@@ -2925,7 +2922,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
-    for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+    for (int seqNo = ranges
+            .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2936,9 +2934,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         continue;
       }
-      seqMappings = MappingUtils
-              .findMappingsForSequenceAndOthers(sequence, mappings,
-                      getCodingComplement().getAlignment().getSequences());
+      seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
+              mappings,
+              getCodingComplement().getAlignment().getSequences());
       if (!seqMappings.isEmpty())
       {
         break;
@@ -3038,6 +3036,5 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
-  
 
 }