X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=a0fcacf26c4a3a20e5b7672126ed3bcb9cc13a5f;hb=55cae9b50608f760cbf6ae2627e1d79d16746186;hp=b4cb80c2cf2e972ed2c8512c0069340af04d8ab5;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index b4cb80c..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.
  * 
@@ -20,18 +20,55 @@
  */
 package MCview;
 
-import java.io.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.schemes.*;
+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;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.StrandColourScheme;
+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;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.BufferedReader;
+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;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.SwingUtilities;
+
 public class PDBViewer extends JInternalFrame implements Runnable
 {
 
@@ -81,8 +118,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
       try
       {
         tmpPDBFile = pdbentry.getFile();
-        PDBfile pdbfile = new PDBfile(tmpPDBFile,
-                jalview.io.AppletFormatAdapter.FILE);
+        PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
+                AppletFormatAdapter.FILE);
 
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 
@@ -123,7 +160,9 @@ public class PDBViewer extends JInternalFrame implements Runnable
               .getAbsolutePath());
 
       if (pdbentry.getFile() != null)
+      {
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+      }
     } catch (Exception ex)
     {
       pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
@@ -345,9 +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())
@@ -365,7 +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
@@ -373,7 +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);
               }
@@ -466,7 +505,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
    */
   public void eps_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.EPS);
+    makePDBImage(ImageMaker.TYPE.EPS);
   }
 
   /**
@@ -477,27 +516,34 @@ public class PDBViewer extends JInternalFrame implements Runnable
    */
   public void png_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.PNG);
+    makePDBImage(ImageMaker.TYPE.PNG);
   }
 
-  void makePDBImage(int 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.PNG)
+    if (type == ImageMaker.TYPE.PNG)
     {
-      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+      im = new ImageMaker(this, ImageMaker.TYPE.PNG,
               "Make PNG image from view", width, height, null, null);
     }
-    else
+    else if (type == ImageMaker.TYPE.EPS)
     {
-      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+      im = new ImageMaker(this, ImageMaker.TYPE.EPS,
               "Make EPS file from view", width, height, null,
               this.getTitle());
     }
+    else
+    {
+
+      im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+              "Make SVG file from PCA",
+              width, height, null, this.getTitle());
+    }
 
     if (im.getGraphics() != null)
     {
@@ -566,7 +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());
@@ -668,7 +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"));