JAL-2092 hide columns with/without feature

[jalview.git] / src / jalview / appletgui / FeatureSettings.java

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 584a69a..7ae318c 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -59,8 +59,8 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.util.Arrays;
 import java.util.Enumeration;
-import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 public class FeatureSettings extends Panel implements ItemListener,
@@ -95,14 +95,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     transparency = new Scrollbar(Scrollbar.HORIZONTAL,
             100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
 
-    if (fr.isTransparencyAvailable())
-    {
-      transparency.addAdjustmentListener(this);
-    }
-    else
-    {
-      transparency.setEnabled(false);
-    }
+    transparency.addAdjustmentListener(this);
 
     java.net.URL url = getClass().getResource("/images/link.gif");
     if (url != null)
@@ -134,17 +127,8 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     Panel tPanel = new Panel(new BorderLayout());
 
-    if (fr.isTransparencyAvailable())
-    {
-      tPanel.add(transparency, BorderLayout.CENTER);
-      tPanel.add(new Label("Transparency"), BorderLayout.EAST);
-    }
-    else
-    {
-      tPanel.add(
-              new Label("Transparency not available in this web browser"),
-              BorderLayout.CENTER);
-    }
+    tPanel.add(transparency, BorderLayout.CENTER);
+    tPanel.add(new Label("Transparency"), BorderLayout.EAST);
 
     lowerPanel.add(tPanel, BorderLayout.SOUTH);
 
@@ -201,7 +185,8 @@ public class FeatureSettings extends Panel implements ItemListener,
             60);
   }
 
-  protected void popupSort(final MyCheckbox check, final Hashtable minmax,
+  protected void popupSort(final MyCheckbox check,
+          final Map<String, float[][]> minmax,
           int x, int y)
   {
     final String type = check.type;
@@ -237,9 +222,10 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     });
     men.add(dens);
+
     if (minmax != null)
     {
-      final Object typeMinMax = minmax.get(type);
+      final float[][] typeMinMax = minmax.get(type);
       /*
        * final java.awt.CheckboxMenuItem chb = new
        * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
@@ -252,7 +238,7 @@ public class FeatureSettings extends Panel implements ItemListener,
        * 
        * }); men.add(chb);
        */
-      if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+      if (typeMinMax != null && typeMinMax[0] != null)
       {
         // graduated colourschemes for those where minmax exists for the
         // positional features
@@ -282,6 +268,57 @@ public class FeatureSettings extends Panel implements ItemListener,
         });
       }
     }
+
+    MenuItem selectContaining = new MenuItem(
+            MessageManager.getString("label.select_columns_containing"));
+    selectContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+                false, type);
+      }
+    });
+    men.add(selectContaining);
+
+    MenuItem selectNotContaining = new MenuItem(
+            MessageManager.getString("label.select_columns_not_containing"));
+    selectNotContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+                false, type);
+      }
+    });
+    men.add(selectNotContaining);
+
+    MenuItem hideContaining = new MenuItem(
+            MessageManager.getString("label.hide_columns_containing"));
+    hideContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideFeatureColumns(type, true);
+      }
+    });
+    men.add(hideContaining);
+
+    MenuItem hideNotContaining = new MenuItem(
+            MessageManager.getString("label.hide_columns_not_containing"));
+    hideNotContaining.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideFeatureColumns(type, false);
+      }
+    });
+    men.add(hideNotContaining);
+
     this.featurePanel.add(men);
     men.show(this.featurePanel, x, y);
   }
@@ -338,7 +375,7 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
     SequenceFeature[] tmpfeatures;
     String group = null, type;
-    Vector visibleChecks = new Vector();
+    Vector<String> visibleChecks = new Vector<String>();
     AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
     {
@@ -404,7 +441,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     // now add checkboxes which should be visible,
     // if they have not already been added
-    Enumeration en = visibleChecks.elements();
+    Enumeration<String> en = visibleChecks.elements();
 
     while (en.hasMoreElements())
     {
@@ -793,4 +830,24 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
   }
 
+  /**
+   * Hide columns containing (or not containing) a given feature type
+   * 
+   * @param type
+   * @param columnsContaining
+   */
+  void hideFeatureColumns(final String type,
+          boolean columnsContaining)
+  {
+    if (ap.alignFrame.avc.markColumnsContainingFeatures(
+            columnsContaining, false, false, type))
+    {
+      if (ap.alignFrame.avc.markColumnsContainingFeatures(
+              !columnsContaining, false, false, type))
+      {
+        ap.alignFrame.viewport.hideSelectedColumns();
+      }
+    }
+  }
+
 }