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Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6aaba84..ffa586e 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,18 +20,6 @@
  */
 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;
-import jalview.gui.Preferences;
-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;
@@ -61,6 +49,18 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+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;
+import jalview.gui.Preferences;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 @SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
@@ -102,6 +102,8 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
+  public JCheckBoxMenuItem showSeqFeatureCounts = new JCheckBoxMenuItem();
+
   JMenuItem copy = new JMenuItem();
 
   JMenuItem cut = new JMenuItem();
@@ -283,7 +285,9 @@ public class GAlignFrame extends JInternalFrame
 
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -306,7 +310,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -333,7 +339,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -369,7 +377,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -383,7 +393,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -397,7 +409,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -519,7 +533,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -694,7 +710,9 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -708,7 +726,9 @@ public class GAlignFrame extends JInternalFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -732,7 +752,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -758,7 +780,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -781,6 +805,16 @@ public class GAlignFrame extends JInternalFrame
         showSeqFeatures_actionPerformed(actionEvent);
       }
     });
+    showSeqFeatureCounts.setText(
+            MessageManager.getString("label.show_sequence_feature_counts"));
+    showSeqFeatureCounts.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        showSeqFeatureCounts_actionPerformed(actionEvent);
+      }
+    });
     /*
      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
@@ -919,7 +953,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -944,7 +980,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -973,7 +1011,9 @@ public class GAlignFrame extends JInternalFrame
 
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
 
     al = new ActionListener()
     {
@@ -987,7 +1027,9 @@ public class GAlignFrame extends JInternalFrame
 
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1029,7 +1071,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1213,8 +1257,7 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
-    padGapsMenuitem
-            .setState(Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       @Override
@@ -1357,8 +1400,7 @@ public class GAlignFrame extends JInternalFrame
     });
     autoCalculate.setText(
             MessageManager.getString("label.autocalculate_consensus"));
-    autoCalculate.setState(
-            Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1371,8 +1413,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.sort_alignment_new_tree"));
     sortByTree.setToolTipText("<html>" + MessageManager.getString(
             "label.enable_automatically_sort_alignment_when_open_new_tree"));
-    sortByTree
-            .setState(Cache.getDefault("SORT_BY_TREE", false));
+    sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
     {
       @Override
@@ -1610,7 +1651,9 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1635,7 +1678,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1830,6 +1875,7 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showAutoFirst);
     autoAnnMenu.add(showAutoLast);
     autoAnnMenu.addSeparator();
+    autoAnnMenu.add(showSeqFeatureCounts);
     autoAnnMenu.add(applyAutoAnnotationSettings);
     autoAnnMenu.add(showConsensusHistogram);
     autoAnnMenu.add(showSequenceLogo);
@@ -1918,6 +1964,13 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void showSeqFeatureCounts_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   protected void loadVcf_actionPerformed()
   {
   }