JAL-1807 explicit imports (jalview.jbgui)

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

diff --git a/src/jalview/jbgui/GDasSourceBrowser.java b/src/jalview/jbgui/GDasSourceBrowser.java
index d74900a..7443de1 100755 (executable)
--- a/src/jalview/jbgui/GDasSourceBrowser.java
+++ b/src/jalview/jbgui/GDasSourceBrowser.java
@@ -20,13 +20,33 @@
  */
 package jalview.jbgui;
 
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JEditorPane;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
 
 public class GDasSourceBrowser extends JPanel
 {
@@ -210,7 +230,7 @@ public class GDasSourceBrowser extends JPanel
 
       if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
       {
-        jalview.util.BrowserLauncher.openURL(e.getURL().toString());
+        BrowserLauncher.openURL(e.getURL().toString());
       }
     } catch (Exception ex)
     {

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 7bb688c..301c29b 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -20,7 +20,9 @@
  */
 package jalview.jbgui;
 
+import jalview.gui.AlignViewport;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.FlowLayout;
 import java.awt.Toolkit;
@@ -116,7 +118,7 @@ public class GDesktop extends JFrame
       e.printStackTrace();
     }
 
-    if (!new jalview.util.Platform().isAMac())
+    if (!Platform.isAMac())
     {
       FileMenu.setMnemonic('F');
       inputLocalFileMenuItem.setMnemonic('L');
@@ -435,8 +437,7 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  protected void inputLocalFileMenuItem_actionPerformed(
-          jalview.gui.AlignViewport av)
+  protected void inputLocalFileMenuItem_actionPerformed(AlignViewport av)
   {
   }
 
@@ -446,8 +447,7 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  protected void inputURLMenuItem_actionPerformed(
-          jalview.gui.AlignViewport av)
+  protected void inputURLMenuItem_actionPerformed(AlignViewport av)
   {
   }
 
@@ -457,8 +457,7 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  protected void inputTextboxMenuItem_actionPerformed(
-          jalview.gui.AlignViewport av)
+  protected void inputTextboxMenuItem_actionPerformed(AlignViewport av)
   {
   }
 

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 0b2e6be..1e748ce 100755 (executable)
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -20,8 +20,10 @@
  */
 package jalview.jbgui;
 
+import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentI;
 import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -220,8 +222,8 @@ public class GFinder extends JPanel
           }
           if (al != null && al.getHeight() > 0)
           {
-            str = jalview.analysis.AlignSeq.extractGaps(
-                    jalview.util.Comparison.GapChars, al.getSequenceAt(0)
+            str = AlignSeq.extractGaps(
+                    Comparison.GapChars, al.getSequenceAt(0)
                             .getSequenceAsString());
 
             textfield.setText(str);

diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index ed74f02..9e32766 100755 (executable)
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -20,13 +20,26 @@
  */
 package jalview.jbgui;
 
+import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
 
 public class GSequenceLink extends Panel
 {
@@ -119,9 +132,8 @@ public class GSequenceLink extends Panel
     }
 
     JOptionPane
-            .showInternalMessageDialog(
-                    jalview.gui.Desktop.desktop,
-                    MessageManager.getString("warn.url_must_contain"),
+.showInternalMessageDialog(Desktop.desktop,
+            MessageManager.getString("warn.url_must_contain"),
                     MessageManager.getString("label.invalid_url"), JOptionPane.WARNING_MESSAGE);
     return false;
   }

diff --git a/src/jalview/jbgui/GWsPreferences.java b/src/jalview/jbgui/GWsPreferences.java
index 1eae7fc..7f073cc 100644 (file)
--- a/src/jalview/jbgui/GWsPreferences.java
+++ b/src/jalview/jbgui/GWsPreferences.java
@@ -20,6 +20,7 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -409,7 +410,7 @@ public class GWsPreferences extends JPanel
     wsMenuRefreshButs.add(resetWs, null);
     wsMenuRefreshButs.add(progressBar, null);
     myBorderlayout.setHgap(3);
-    if (jalview.bin.Cache.getDefault("ENABLE_RSBS_EDITOR", false))
+    if (Cache.getDefault("ENABLE_RSBS_EDITOR", false))
     {
       JTabbedPane listPanels = new JTabbedPane();
       listPanels.addTab("JABAWS Servers", wsListPanel);