JAL-2629 add sort by evalue and bit score

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bc71566..579da08 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,6 +21,8 @@
 package jalview.jbgui;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
@@ -28,13 +30,13 @@ import jalview.gui.Preferences;
 import jalview.hmmer.HmmerCommand;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
-import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
@@ -80,7 +82,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sortByAnnotScore = new JMenu();
 
-  public JLabel statusBar = new JLabel();
+  protected JLabel statusBar = new JLabel();
 
   protected JMenu outputTextboxMenu = new JMenu();
 
@@ -128,7 +130,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
@@ -142,7 +144,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 
-  protected JMenuItem showTranslation = new JMenuItem();
+  protected JMenu showTranslation = new JMenu();
 
   protected JMenuItem showReverse = new JMenuItem();
 
@@ -274,14 +276,14 @@ public class GAlignFrame extends JInternalFrame
   
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
   
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -307,7 +309,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -334,7 +336,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -370,7 +372,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -384,7 +386,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -398,7 +400,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -412,8 +414,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -516,11 +518,31 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
+    JMenuItem sortEValueMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_evalue"));
+    sortEValueMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortEValueMenuItem_actionPerformed(e);
+      }
+    });
+    JMenuItem sortBitScoreMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_bit_score"));
+    sortBitScoreMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortBitScoreMenuItem_actionPerformed(e);
+      }
+    });
   
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -530,6 +552,30 @@ 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"));
@@ -698,7 +744,7 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -712,7 +758,7 @@ public class GAlignFrame extends JInternalFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -736,7 +782,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -762,7 +808,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -924,7 +970,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -949,7 +995,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -963,8 +1009,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -978,7 +1024,7 @@ public class GAlignFrame extends JInternalFrame
   
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 
     al = new ActionListener()
     {
@@ -992,7 +1038,7 @@ public class GAlignFrame extends JInternalFrame
   
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1018,8 +1064,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1041,7 +1087,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1252,16 +1298,33 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation
-            .setText(MessageManager.getString("label.translate_cDNA"));
-    showTranslation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
+
+    /*
+     * Translate as cDNA with sub-menu of translation tables
+     */
+    showTranslation.setText(MessageManager
+            .getString("label.translate_cDNA"));
+    boolean first = true;
+    for (final GeneticCodeI table : GeneticCodes.getInstance()
+            .getCodeTables())
+    {
+      JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+      showTranslation.add(item);
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          showTranslation_actionPerformed(table);
+        }
+      });
+      if (first)
       {
-        showTranslation_actionPerformed(e);
+        showTranslation.addSeparator();
       }
-    });
+      first = false;
+    }
+
     showReverse.setText(MessageManager.getString("label.reverse"));
     showReverse.addActionListener(new ActionListener()
     {
@@ -1549,8 +1612,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.ALT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1613,7 +1676,7 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1638,7 +1701,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1725,6 +1788,18 @@ 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"));
@@ -1786,6 +1861,9 @@ 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);
@@ -1841,6 +1919,8 @@ public class GAlignFrame extends JInternalFrame
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
+    sort.add(sortEValueMenuItem);
+    sort.add(sortBitScoreMenuItem);
     sort.add(sortByTreeMenu);
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
@@ -2007,9 +2087,57 @@ public class GAlignFrame extends JInternalFrame
         }
       }
     });
-    hmmSearch.add(hmmSearchSettings);
     hmmSearch.add(hmmSearchRun);
-    hmmSearch.add(addDatabase);
+    hmmSearch.add(hmmSearchSettings);
+    // 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
@@ -2019,6 +2147,7 @@ public class GAlignFrame extends JInternalFrame
     hmmerMenu.add(hmmBuild);
     hmmerMenu.add(hmmAlign);
     hmmerMenu.add(hmmSearch);
+    hmmerMenu.add(jackhmmer);
 
   }
 
@@ -2097,8 +2226,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColour = new JMenuItem(
+    annotationColour = new JRadioButtonMenuItem(
             MessageManager.getString("action.by_annotation"));
+    annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
     annotationColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2436,6 +2566,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -2518,6 +2656,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void jackhmmer_actionPerformed(boolean b)
+  {
+  }
+
   protected void addDatabase_actionPerformed()
           throws FileFormatException, IOException
   {
@@ -2583,6 +2725,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void filterByEValue_actionPerformed()
+  {
+  }
+
+  protected void filterByScore_actionPerformed()
+  {
+  }
+
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
   }
@@ -2613,7 +2763,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }