JAL-2629 refactoring of Hmmer preferences

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 126196f..9755729 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -68,6 +68,7 @@ import jalview.hmmer.HMMBuildThread;
 import jalview.hmmer.HMMERParamStore;
 import jalview.hmmer.HMMERPreset;
 import jalview.hmmer.HMMSearchThread;
+import jalview.hmmer.HmmerCommand;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
@@ -400,7 +401,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     });
     buildColourMenu();
-    buildHMMERMenu();
 
     if (Desktop.desktop != null)
     {
@@ -508,18 +508,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Adds all menu items to the HMMER menu
-   */
-  private void buildHMMERMenu()
-  {
-    hmmerMenu.removeAll();
-
-    hmmerMenu.add(hmmAlign);
-    hmmerMenu.add(hmmBuild);
-    hmmerMenu.add(hmmSearch);
-  }
-
-  /**
    * Change the filename and format for the alignment, and enable the 'reload'
    * button functionality.
    * 
@@ -1036,8 +1024,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void hmmBuildSettings_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  public void hmmBuildSettings_actionPerformed()
   {
     if (!(alignmentIsSufficient(1)))
     {
@@ -1057,8 +1044,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void hmmAlignSettings_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  public void hmmAlignSettings_actionPerformed()
   {
     if (!(checkForHMM() && alignmentIsSufficient(2)))
     {
@@ -1078,7 +1064,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void hmmSearchSettings_actionPerformed(ActionEvent e)
+  public void hmmSearchSettings_actionPerformed()
   {
     if (!checkForHMM())
     {
@@ -1098,8 +1084,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void hmmBuildRun_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  public void hmmBuildRun_actionPerformed()
   {
     if (!alignmentIsSufficient(1))
     {
@@ -1107,13 +1092,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     new Thread(new HMMBuildThread(this, null))
             .start();
-    alignPanel.repaint();
-
   }
 
   @Override
-  public void hmmAlignRun_actionPerformed(ActionEvent e)
-          throws IOException, InterruptedException
+  public void hmmAlignRun_actionPerformed()
   {
     if (!(checkForHMM() && alignmentIsSufficient(2)))
     {
@@ -1121,11 +1103,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     new Thread(new HMMAlignThread(this, true, null))
             .start();
-    alignPanel.repaint();
   }
 
   @Override
-  public void hmmSearchRun_actionPerformed(ActionEvent e)
+  public void hmmSearchRun_actionPerformed()
   {
     if (!checkForHMM())
     {
@@ -1133,7 +1114,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     new Thread(new HMMSearchThread(this, true, null))
             .start();
-    alignPanel.repaint();
   }
 
   /**
@@ -1170,7 +1150,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void addDatabase_actionPerformed(ActionEvent e) throws IOException
+  public void addDatabase_actionPerformed() throws IOException
   {
     if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
     {
@@ -1191,7 +1171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
         currentDbPaths += " " + path;
 
-        String fileName = StringUtils.getLastToken(path, new String("/"));
+        String fileName = StringUtils.getLastToken(path, File.separator);
         Scanner scanner = new Scanner(fileName).useDelimiter(".");
         String name = scanner.next();
         scanner.close();
@@ -5858,12 +5838,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Sets the status of the HMMER menu
-   * 
-   * @param status
    */
-  public void updateHMMERStatus(boolean status)
+  public void updateHMMERStatus()
   {
-    hmmerMenu.setEnabled(status);
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
   }
 
   /**