JAL-2629 can now filter by sequence e-value or bit score

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c228c90..62165cd 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -532,6 +532,30 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+    JMenuItem filterByEValue = new JMenuItem(
+            MessageManager.getString("action.filter_by_evalue"));
+    filterByEValue.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        filterByEValue_actionPerformed();
+      }
+
+    });
+
+    JMenuItem filterByScore = new JMenuItem(
+            MessageManager.getString("action.filter_by_score"));
+    filterByScore.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        filterByScore_actionPerformed();
+      }
+
+    });
   
     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
             MessageManager.getString("action.pairwise_alignment"));
@@ -1744,6 +1768,18 @@ public class GAlignFrame extends JInternalFrame
         selectHighlightedColumns_actionPerformed(actionEvent);
       }
     };
+    JMenuItem Filter = new JMenuItem(
+            MessageManager.getString("action.select_highlighted_columns"));
+    selectHighlighted.setToolTipText(
+            MessageManager.getString("tooltip.select_highlighted_columns"));
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        selectHighlightedColumns_actionPerformed(actionEvent);
+      }
+    };
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
@@ -1805,6 +1841,9 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.add(justifyRightMenuItem);
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
+    editMenu.addSeparator();
+    editMenu.add(filterByEValue);
+    editMenu.add(filterByScore);
   
     showMenu.add(showAllColumns);
     showMenu.add(showAllSeqs);
@@ -2031,6 +2070,54 @@ public class GAlignFrame extends JInternalFrame
     // hmmSearch.add(addDatabase);
 
     /*
+     * jackhmmer
+     */
+    JMenu jackhmmer = new JMenu(
+            MessageManager.getString("label.jackhmmer"));
+    JMenuItem jackhmmerSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    jackhmmerSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        jackhmmer_actionPerformed(false);
+      }
+    });
+    JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "jackhmmer"));
+    jackhmmerRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        jackhmmer_actionPerformed(true);
+      }
+
+    });
+    /*
+    JMenuItem addDatabase = new JMenuItem(
+            MessageManager.getString("label.add_database"));
+    addDatabase.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed();
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
+    */
+    jackhmmer.add(jackhmmerRun);
+    jackhmmer.add(jackhmmerSettings);
+    // hmmSearch.add(addDatabase);
+
+    /*
      * top level menu
      */
     hmmerMenu.setText(MessageManager.getString("action.hmmer"));
@@ -2038,6 +2125,7 @@ public class GAlignFrame extends JInternalFrame
     hmmerMenu.add(hmmBuild);
     hmmerMenu.add(hmmAlign);
     hmmerMenu.add(hmmSearch);
+    hmmerMenu.add(jackhmmer);
 
   }
 
@@ -2538,6 +2626,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void jackhmmer_actionPerformed(boolean b)
+  {
+  }
+
   protected void addDatabase_actionPerformed()
           throws FileFormatException, IOException
   {
@@ -2603,6 +2695,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void filterByEValue_actionPerformed()
+  {
+  }
+
+  protected void filterByScore_actionPerformed()
+  {
+  }
+
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
   }