JAL-1807 explicit imports (jalview.jbgui)

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c6a042b..614c383 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,10 +23,14 @@ package jalview.jbgui;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
+import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.gui.UserDefinedColours;
+import jalview.io.FormatAdapter;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -39,6 +43,7 @@ import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -241,10 +246,10 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      for (int i = 0; i < FormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
         JMenuItem item = new JMenuItem(
-                jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+                FormatAdapter.WRITEABLE_FORMATS[i]);
 
         item.addActionListener(new ActionListener()
         {
@@ -262,7 +267,7 @@ public class GAlignFrame extends JInternalFrame
       System.err.println(e.toString());
     }
 
-    if (!jalview.util.Platform.isAMac())
+    if (!Platform.isAMac())
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -274,10 +279,10 @@ public class GAlignFrame extends JInternalFrame
       reload.setMnemonic('R');
     }
 
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    if (UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
-              .getUserColourSchemes().keys();
+      Enumeration userColours = UserDefinedColours.getUserColourSchemes()
+              .keys();
 
       while (userColours.hasMoreElements())
       {
@@ -295,7 +300,7 @@ public class GAlignFrame extends JInternalFrame
               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
               int option = JOptionPane.showInternalConfirmDialog(
-                      jalview.gui.Desktop.desktop,
+                      Desktop.desktop,
                       MessageManager
                               .getString("label.remove_from_default_list"),
                       MessageManager
@@ -303,8 +308,8 @@ public class GAlignFrame extends JInternalFrame
                       JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
-                jalview.gui.UserDefinedColours
-                        .removeColourFromDefaults(radioItem.getText());
+                UserDefinedColours.removeColourFromDefaults(radioItem
+                        .getText());
                 colourMenu.remove(radioItem);
               }
               else
@@ -350,7 +355,7 @@ public class GAlignFrame extends JInternalFrame
     // colours.add(covariationColour);
     colours.add(tcoffeeColour);
     colours.add(RNAInteractionColour);
-    setColourSelected(jalview.bin.Cache.getDefault(
+    setColourSelected(Cache.getDefault(
             Preferences.DEFAULT_COLOUR, "None"));
   }
 
@@ -1484,7 +1489,7 @@ public class GAlignFrame extends JInternalFrame
     });
     seqLimits.setText(MessageManager
             .getString("label.show_sequence_limits"));
-    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new ActionListener()
     {
       @Override
@@ -1654,7 +1659,7 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("action.calculate_tree"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
-    padGapsMenuitem.setState(jalview.bin.Cache
+    padGapsMenuitem.setState(Cache
             .getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
@@ -1768,7 +1773,7 @@ public class GAlignFrame extends JInternalFrame
     });
     autoCalculate.setText(MessageManager
             .getString("label.autocalculate_consensus"));
-    autoCalculate.setState(jalview.bin.Cache.getDefault(
+    autoCalculate.setState(Cache.getDefault(
             "AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
@@ -1785,7 +1790,7 @@ public class GAlignFrame extends JInternalFrame
                     + MessageManager
                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
     sortByTree
-            .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+            .setState(Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
     {
       @Override