JAL-1620 version bump and release notes

[jalview.git] / src / MCview / PDBViewer.java

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index a297892..e16241b 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,18 +20,50 @@
  */
 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.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.OOMWarning;
+import jalview.gui.UserDefinedColours;
+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.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 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
 {
 
@@ -81,7 +113,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       try
       {
         tmpPDBFile = pdbentry.getFile();
-        PDBfile pdbfile = new PDBfile(false,false,tmpPDBFile,
+        PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
                 jalview.io.AppletFormatAdapter.FILE);
 
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
@@ -123,7 +155,9 @@ 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();
@@ -466,7 +500,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
    */
   public void eps_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.EPS);
+    makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
   }
 
   /**
@@ -477,27 +511,36 @@ public class PDBViewer extends JInternalFrame implements Runnable
    */
   public void png_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.PNG);
+    makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
   }
 
-  void makePDBImage(int type)
+  void makePDBImage(jalview.util.ImageMaker.TYPE type)
   {
     int width = pdbcanvas.getWidth();
     int height = pdbcanvas.getHeight();
 
     jalview.util.ImageMaker im;
 
-    if (type == jalview.util.ImageMaker.PNG)
+    if (type == jalview.util.ImageMaker.TYPE.PNG)
     {
-      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.PNG,
               "Make PNG image from view", width, height, null, null);
     }
-    else
+    else if (type == jalview.util.ImageMaker.TYPE.EPS)
     {
-      im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.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",
+              width, height, null, this.getTitle());
+    }
 
     if (im.getGraphics() != null)
     {