X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=a0fcacf26c4a3a20e5b7672126ed3bcb9cc13a5f;hb=55cae9b50608f760cbf6ae2627e1d79d16746186;hp=bf285b9ea9b14c9c45df14a6f5a04ce0be19e8e9;hpb=13317fa1bc7bf640dc1967ce4438676e89390ad3;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index bf285b9..a0fcacf 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,12 +20,15 @@
  */
 package MCview;
 
+import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
 import jalview.gui.Desktop;
 import jalview.gui.OOMWarning;
 import jalview.gui.UserDefinedColours;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.schemes.BuriedColourScheme;
@@ -36,6 +39,7 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 
@@ -52,6 +56,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.FileReader;
 import java.io.PrintWriter;
+import java.util.Enumeration;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
@@ -114,7 +119,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       {
         tmpPDBFile = pdbentry.getFile();
         PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
-                jalview.io.AppletFormatAdapter.FILE);
+                AppletFormatAdapter.FILE);
 
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 
@@ -379,9 +384,9 @@ public class PDBViewer extends JInternalFrame implements Runnable
     bg.add(buried);
     bg.add(user);
 
-    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())
@@ -399,7 +404,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
               int option = JOptionPane.showInternalConfirmDialog(
-                      jalview.gui.Desktop.desktop,
+                      Desktop.desktop,
                       MessageManager
                               .getString("label.remove_from_default_list"),
                       MessageManager
@@ -407,7 +412,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
                       JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
-                jalview.gui.UserDefinedColours
+                UserDefinedColours
                         .removeColourFromDefaults(radioItem.getText());
                 coloursMenu.remove(radioItem);
               }
@@ -500,7 +505,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
    */
   public void eps_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
+    makePDBImage(ImageMaker.TYPE.EPS);
   }
 
   /**
@@ -511,34 +516,32 @@ public class PDBViewer extends JInternalFrame implements Runnable
    */
   public void png_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
+    makePDBImage(ImageMaker.TYPE.PNG);
   }
 
-  void makePDBImage(jalview.util.ImageMaker.TYPE type)
+  void makePDBImage(ImageMaker.TYPE type)
   {
     int width = pdbcanvas.getWidth();
     int height = pdbcanvas.getHeight();
 
-    jalview.util.ImageMaker im;
+    ImageMaker im;
 
-    if (type == jalview.util.ImageMaker.TYPE.PNG)
+    if (type == ImageMaker.TYPE.PNG)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG,
+      im = new ImageMaker(this, ImageMaker.TYPE.PNG,
               "Make PNG image from view", width, height, null, null);
     }
-    else if (type == jalview.util.ImageMaker.TYPE.EPS)
+    else if (type == ImageMaker.TYPE.EPS)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS,
+      im = new ImageMaker(this, ImageMaker.TYPE.EPS,
               "Make EPS file from view", width, height, null,
               this.getTitle());
     }
     else
     {
 
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+      im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+              "Make SVG file from PCA",
               width, height, null, this.getTitle());
     }
 
@@ -609,7 +612,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
   public void mapping_actionPerformed(ActionEvent e)
   {
-    jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
       cap.setText(pdbcanvas.mappingDetails.toString());
@@ -711,7 +714,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   public void savePDB_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));