JAL-2629 add ability to select hmmer binaries folder

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 5291493..339a764 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1315,11 +1315,13 @@ label.occupancy_descr = Number of aligned positions
 label.show_experimental = Enable experimental features
 label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
 label.warning_hidden = Warning: {0} {1} is currently hidden
-label.change_hmmer_directory = Change HMMER suite location
 label.auto_align_seqs = Automatically Align New Sequences
 label.hmmalign = Align Sequences to HMM
 label.hmmbuild = Build HMM from Alignment
 label.hmmsearch = Search for Related Sequences
+label.change_hmmer_location = Set HMMER Installation Location
 warn.null_hmm = Please ensure the alignment contains a hidden Markov model.
 label.ignore_below_background_frequency = Ignore Below Background Frequency
 label.information_description = Information content, measured in bits
+label.enter_location = Please enter the path of your HMMER binaries folder.
+label.invalid_hmmer_folder = The folder that you selected does not contain the necessary HMMER binaries.

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index da3cb92..4b890cc 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -260,6 +260,8 @@ public class Cache
   private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
           .toString();
 
+  private static String HMMER_PATH;
+
   /*
    * a date formatter using a fixed (rather than the user's) locale; 
    * this ensures that date properties can be written and re-read successfully
@@ -281,7 +283,7 @@ public class Cache
     @Override
     public synchronized Enumeration<Object> keys()
     {
-      return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+      return Collections.enumeration(new TreeSet<>(super.keySet()));
     }
   };
 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index dba6717..9b5681b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -146,6 +146,7 @@ import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
@@ -339,6 +340,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     init();
   }
 
+  public void setIsRecurring(boolean status)
+  {
+    recurring = status;
+  }
+
   /**
    * initalise the alignframe from the underlying viewport data and the
    * configurations
@@ -501,6 +507,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     hmmerMenu.removeAll();
 
+    hmmerMenu.add(changeHMMERLocation);
+    hmmerMenu.addSeparator();
+
     hmmerMenu.add(autoAlignSeqs);
     hmmerMenu.addSeparator();
 
@@ -1053,13 +1062,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hmmAlign_actionPerformed(ActionEvent e)
           throws IOException, InterruptedException
   {
-    SequenceI seq = getViewport().getAlignment()
-            .getHMMConsensusSequences(false).get(0);
     new Thread(new HMMAlignThread(this, true)).start();
     alignPanel.repaint();
   }
 
   @Override
+  public void changeHMMERLocation_actionPerformed(ActionEvent e)
+  {
+    String location = JOptionPane.showInputDialog(
+            MessageManager.getString("label.enter_location"));
+    Cache.setProperty(Preferences.HMMER_PATH, location);
+  }
+
+  @Override
   public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
   {
     autoAlignNewSequences = autoAlignSeqs;
@@ -4759,6 +4774,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           else
           {
             new FileLoader().LoadFile(viewport, file, sourceType, format);
+            if (autoAlignNewSequences && !recurring)
+            {
+              new Thread(new HMMAlignThread(this, false)).start();
+            }
           }
         }
       }
@@ -4788,14 +4807,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       + (format != null ? "(parsing as '" + format
                               + "' file)" : ""), oom, Desktop.desktop);
     }
-    if (autoAlignNewSequences && !recurring)
-    {
-      recurring = true;
-      HiddenMarkovModel hmm = getViewport().getAlignment()
-              .getHMMConsensusSequences(false).get(0).getHMM();
-      new Thread(new HMMAlignThread(this, false)).start();
-    }
-    recurring = false;
   }
 
   /**
@@ -5752,4 +5763,5 @@ class PrintThread extends Thread
     }
   }
 
+
 }

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8b4f85f..b5fa4e8 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -102,6 +102,8 @@ public class Preferences extends GPreferences
   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 
   public static final String CHIMERA_PATH = "CHIMERA_PATH";
+  
+  public static final String HMMER_PATH = "HMMER_PATH";
 
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 
@@ -1094,6 +1096,28 @@ public class Preferences extends GPreferences
     }
     return true;
   }
+  
+  /**
+   * Returns true if hmmer path contains the necessary valid executables, else show an error
+   * dialog.
+   */
+  private boolean validateHMMERPath()
+  {
+    String path = Cache.getProperty("HMMERPATH");
+    if (path.length() > 0)
+    {
+      File f = new File(path);
+      if (!f.canExecute())
+      {
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                MessageManager.getString("label.invalid_hmmer_folder"),
+                MessageManager.getString("Invalid folder"),
+                JvOptionPane.ERROR_MESSAGE);
+        return false;
+      }
+    }
+    return true;
+  }
 
   /**
    * If Chimera is selected, check it can be found on default or user-specified

diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java
index 8cd4270..3879a87 100644 (file)
--- a/src/jalview/hmmer/HMMAlignThread.java
+++ b/src/jalview/hmmer/HMMAlignThread.java
@@ -1,9 +1,12 @@
 package jalview.hmmer;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileLoader;
@@ -11,6 +14,7 @@ import jalview.util.MessageManager;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.util.HashMap;
 import java.util.Map;
 
 public class HMMAlignThread implements Runnable
@@ -42,7 +46,7 @@ public class HMMAlignThread implements Runnable
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
             barID);
-
+    HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
     try
     {
       try
@@ -73,7 +77,7 @@ public class HMMAlignThread implements Runnable
       }
     } catch (Exception e)
     {
-
+      e.printStackTrace();
     } finally
     {
       af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
@@ -83,7 +87,7 @@ public class HMMAlignThread implements Runnable
 
   private void runCommand() throws IOException, InterruptedException
   {
-    String command = HMMERCommands.HMMALIGN;
+    String command = HMMERCommands.HMMERFOLDER + HMMERCommands.HMMALIGN;
     if (!hmm.getFileHeader().contains("HMMER3/f"))
     {
       command += HMMERCommands.ALLCOL;
@@ -100,22 +104,31 @@ public class HMMAlignThread implements Runnable
     if (newFrame)
     {
       FileLoader loader = new FileLoader();
+      AlignmentOrder order = new AlignmentOrder(alignment);
       AlignFrame newAFrame = loader.LoadFileWaitTillLoaded(
               HMMERCommands.ALIGNMENTINPUT, DataSourceType.FILE);
-      addSeqs(newAFrame);
+      Map<Integer, SequenceI> copy = new HashMap<>(
+              hmmSeqs);
+      addSeqs(newAFrame, copy);
+      SequenceI seq = newAFrame.getViewport().getAlignment()
+              .getSequenceAt(0);
+      hmm.mapToReferenceAnnotation(newAFrame, seq);
+      addSeqs(af, hmmSeqs);
     }
     else
     {
       af.getViewport().getAlignment().getSequences().clear();
+      af.setIsRecurring(true);
       af.loadJalviewDataFile(HMMERCommands.ALIGNMENTBUFFER,
               DataSourceType.FILE, FileFormat.Stockholm, null);
-      addSeqs(af);
+      af.setIsRecurring(false);
+      addSeqs(af, hmmSeqs);
     }
   }
 
-  private void addSeqs(AlignFrame alignFrame)
+  private void addSeqs(AlignFrame alignFrame, Map<Integer, SequenceI> map)
   {
-    for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
+    for (Map.Entry<Integer, SequenceI> entry : map.entrySet())
     {
       SequenceI seq = entry.getValue();
       Integer pos = entry.getKey();

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index c66e53d..e48dce3 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -1,9 +1,11 @@
 package jalview.hmmer;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.util.MessageManager;
@@ -34,6 +36,7 @@ public class HMMBuildThread implements Runnable
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
             barID);
+    HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
 
     try
     {
@@ -79,7 +82,8 @@ public class HMMBuildThread implements Runnable
   
   private void runCommand() throws IOException, InterruptedException
   {
-    final String command = HMMERCommands.HMMBUILD + HMMERCommands.NAME
+    final String command = HMMERCommands.HMMERFOLDER
+            + HMMERCommands.HMMBUILD + HMMERCommands.NAME
             + af.getName() + HMMERCommands.SPACE
             + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
             + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index 56f7e3a..54516b5 100644 (file)
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -17,15 +17,16 @@ import java.util.List;
 public class HMMERCommands
 {
   // Path of hmmer binaries directory
-  static final String HMMERFOLDER = "H:/Documents/";
+  static String HMMERFOLDER = "/Documents/";
 
-  static final String HMMALIGN = HMMERFOLDER + "hmmalign ";
+  static final String JALVIEWDIRECTORY = System.getProperty("user.dir")
+          + "/";
 
-  static final String HMMBUILD = HMMERFOLDER + "hmmbuild ";
+  static String HMMALIGN = "/hmmalign ";
 
-  static final String HMMSEARCH = HMMERFOLDER + "hmmsearch ";
+  static String HMMBUILD = "/hmmbuild ";
 
-  static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/";
+  static String HMMSEARCH = "/hmmsearch ";
 
   static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm ";
 

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 0dc82cc..6e3c517 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -72,6 +72,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem autoAlignSeqs = new JCheckBoxMenuItem();
 
+  protected JMenuItem changeHMMERLocation = new JCheckBoxMenuItem();
+
   protected JMenuItem hmmAlign = new JMenuItem();
 
   protected JMenuItem hmmSearch = new JMenuItem();
@@ -1756,6 +1758,18 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
+    changeHMMERLocation.setText(
+            MessageManager.getString("label.change_hmmer_location"));
+    changeHMMERLocation.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        changeHMMERLocation_actionPerformed(e);
+      }
+
+    });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
@@ -2449,6 +2463,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void changeHMMERLocation_actionPerformed(ActionEvent e)
+  {
+  }
+
   protected void hmmBuild_actionPerformed(ActionEvent e)
           throws IOException, InterruptedException
   {