JAL-1807 explicit imports (jalview.gui)

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ad3d6af..c9d9e50 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,31 +20,11 @@
  */
 package jalview.gui;
 
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
+import jalview.bin.Cache;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -58,7 +38,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
+import jalview.io.JalviewFileChooser;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.Blosum62ColourScheme;
@@ -75,10 +57,35 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.util.BrowserLauncher;
+import jalview.util.DBRefUtils;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
+import jalview.ws.DBRefFetcher;
+
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
 
 /**
  * DOCUMENT ME!
@@ -263,10 +270,10 @@ public class PopupMenu extends JPopupMenu
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    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 java.awt.event.ActionListener()
       {
@@ -618,14 +625,14 @@ public class PopupMenu extends JPopupMenu
           urlLink = new UrlLink(link);
         } catch (Exception foo)
         {
-          jalview.bin.Cache.log.error("Exception for URLLink '" + link
+          Cache.log.error("Exception for URLLink '" + link
                   + "'", foo);
           continue;
         }
         ;
         if (!urlLink.isValid())
         {
-          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+          Cache.log.error(urlLink.getInvalidMessage());
           continue;
         }
         final String label = urlLink.getLabel();
@@ -633,7 +640,7 @@ public class PopupMenu extends JPopupMenu
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+          DBRefEntry[] dbr = DBRefUtils.selectRefs(
                   seq.getDBRef(), new String[]
                   { urlLink.getTarget() });
           // collect id string too
@@ -896,7 +903,7 @@ public class PopupMenu extends JPopupMenu
       {
         for (int d = 0; d < dbr.length; d++)
         {
-          String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = dbr[d].getSource(); // DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
           Object[] sarray = (Object[]) commonDbrefs.get(src);
           if (sarray == null)
           {
@@ -932,20 +939,20 @@ public class PopupMenu extends JPopupMenu
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+        Cache.log.error("Exception for GroupURLLink '" + link
                 + "'", foo);
         continue;
       }
       ;
       if (!urlLink.isValid())
       {
-        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+        Cache.log.error(urlLink.getInvalidMessage());
         continue;
       }
       final String label = urlLink.getLabel();
       boolean usingNames = false;
       // Now see which parts of the group apply for this URL
-      String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+      String ltarget = urlLink.getTarget(); // DBRefUtils.getCanonicalName(urlLink.getTarget());
       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
       String[] seqstr, ids; // input to makeUrl
       if (idset != null)
@@ -1452,9 +1459,9 @@ public class PopupMenu extends JPopupMenu
     }
     colourMenu.add(userDefinedColour);
 
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    if (UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+      Enumeration userColours = UserDefinedColours
               .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
@@ -2292,7 +2299,7 @@ public class PopupMenu extends JPopupMenu
   {
     try
     {
-      jalview.util.BrowserLauncher.openURL(url);
+      BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -2403,8 +2410,8 @@ public class PopupMenu extends JPopupMenu
 
   public void pdbFromFile_actionPerformed()
   {
-    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(MessageManager.formatMessage(
             "label.select_pdb_file_for", new Object[]
@@ -2415,12 +2422,12 @@ public class PopupMenu extends JPopupMenu
 
     int value = chooser.showOpenDialog(null);
 
-    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      Cache.setProperty("LAST_DIRECTORY", choice);
       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
-              jalview.io.AppletFormatAdapter.FILE, sequence, true,
+              AppletFormatAdapter.FILE, sequence, true,
               Desktop.instance);
     }
 
@@ -2454,7 +2461,7 @@ public class PopupMenu extends JPopupMenu
       public void run()
       {
 
-        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+        new DBRefFetcher(sequences, ap.alignFrame)
                 .fetchDBRefs(false);
       }