X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=721b6a714820ae55ef2c297a83237d03f4792138;hb=94379c810f9115b8564ee7bac46ed119218d5fd2;hp=eaa33df3ad84ea048847b2501b55415d4773871b;hpb=8546ee20c998cd48567d324027d1885a771e688f;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index eaa33df..721b6a7 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -24,8 +24,10 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
 import jalview.gui.OOMWarning;
 import jalview.gui.UserDefinedColours;
+import jalview.io.DataSourceType;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.schemes.BuriedColourScheme;
@@ -39,6 +41,7 @@ import jalview.schemes.ZappoColourScheme;
 import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 
+import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
@@ -52,6 +55,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.FileReader;
 import java.io.PrintWriter;
+import java.util.Map;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
@@ -60,7 +64,6 @@ import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JRadioButtonMenuItem;
 
 public class PDBViewer extends JInternalFrame implements Runnable
@@ -79,12 +82,12 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
   AlignmentPanel ap;
 
-  String protocol;
+  DataSourceType protocol;
 
   String tmpPDBFile;
 
   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap, String protocol)
+          AlignmentPanel ap, DataSourceType protocol)
   {
     this.pdbentry = pdbentry;
     this.seq = seq;
@@ -113,7 +116,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       {
         tmpPDBFile = pdbentry.getFile();
         PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
-                jalview.io.AppletFormatAdapter.FILE);
+                DataSourceType.FILE);
 
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
 
@@ -150,7 +153,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     {
       EBIFetchClient ebi = new EBIFetchClient();
       String query = "pdb:" + pdbentry.getId();
-      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
+      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "xml")
               .getAbsolutePath());
 
       if (pdbentry.getFile() != null)
@@ -274,7 +277,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         allchains_itemStateChanged(e);
       }
     });
-    zappo.setText(MessageManager.getString("label.zappo"));
+    zappo.setText(MessageManager.getString("label.colourScheme_zappo"));
     zappo.addActionListener(new ActionListener()
     {
       @Override
@@ -283,7 +286,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         zappo_actionPerformed(e);
       }
     });
-    taylor.setText(MessageManager.getString("label.taylor"));
+    taylor.setText(MessageManager.getString("label.colourScheme_taylor"));
     taylor.addActionListener(new ActionListener()
     {
       @Override
@@ -292,7 +295,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
         taylor_actionPerformed(e);
       }
     });
-    hydro.setText(MessageManager.getString("label.hydrophobicity"));
+    hydro.setText(MessageManager
+            .getString("label.colourScheme_hydrophobic"));
     hydro.addActionListener(new ActionListener()
     {
       @Override
@@ -301,7 +305,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
         hydro_actionPerformed(e);
       }
     });
-    helix.setText(MessageManager.getString("label.helix_propensity"));
+    helix.setText(MessageManager
+            .getString("label.colourScheme_helix_propensity"));
     helix.addActionListener(new ActionListener()
     {
       @Override
@@ -310,7 +315,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
         helix_actionPerformed(e);
       }
     });
-    strand.setText(MessageManager.getString("label.strand_propensity"));
+    strand.setText(MessageManager
+            .getString("label.colourScheme_strand_propensity"));
     strand.addActionListener(new ActionListener()
     {
       @Override
@@ -319,7 +325,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
         strand_actionPerformed(e);
       }
     });
-    turn.setText(MessageManager.getString("label.turn_propensity"));
+    turn.setText(MessageManager
+            .getString("label.colourScheme_turn_propensity"));
     turn.addActionListener(new ActionListener()
     {
       @Override
@@ -328,7 +335,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
         turn_actionPerformed(e);
       }
     });
-    buried.setText(MessageManager.getString("label.buried_index"));
+    buried.setText(MessageManager
+            .getString("label.colourScheme_buried_index"));
     buried.addActionListener(new ActionListener()
     {
       @Override
@@ -399,15 +407,14 @@ public class PDBViewer extends JInternalFrame implements Runnable
     bg.add(buried);
     bg.add(user);
 
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
+            .getUserColourSchemes();
+    if (userColourSchemes != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
-              .getUserColourSchemes().keys();
-
-      while (userColours.hasMoreElements())
+      for (String userColour : userColourSchemes.keySet())
       {
         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-                userColours.nextElement().toString());
+                userColour);
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
@@ -436,13 +443,13 @@ public class PDBViewer extends JInternalFrame implements Runnable
           {
             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-            int option = JOptionPane.showInternalConfirmDialog(
+            int option = JvOptionPane.showInternalConfirmDialog(
                     jalview.gui.Desktop.desktop, MessageManager
                             .getString("label.remove_from_default_list"),
                     MessageManager
                             .getString("label.remove_user_defined_colour"),
-                    JOptionPane.YES_NO_OPTION);
-            if (option == JOptionPane.YES_OPTION)
+                    JvOptionPane.YES_NO_OPTION);
+            if (option == JvOptionPane.YES_OPTION)
             {
               jalview.gui.UserDefinedColours
                       .removeColourFromDefaults(radioItem.getText());
@@ -722,7 +729,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+      UserColourScheme udc = UserDefinedColours
               .getUserColourSchemes().get(e.getActionCommand());
 
       pdbcanvas.pdb.setColours(udc);
@@ -733,8 +740,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
   public void background_actionPerformed(ActionEvent e)
   {
-    java.awt.Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_backgroud_colour"),
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_background_colour"),
             pdbcanvas.backgroundColour);
 
     if (col != null)