X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=a2248f45f0be0e2674740fe550b623d3a38a920c;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=b3aae5130c3836b5158aa0f89a6060c6d3e5c6e6;hpb=28787d9646cca5dd77190930f59b7ff32cf995b4;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index b3aae51..a2248f4 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,41 +1,69 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
-import java.io.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
-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
 {
 
@@ -57,8 +85,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   String tmpPDBFile;
 
   public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap, String protocol) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
-
+          AlignmentPanel ap, String protocol)
   {
     this.pdbentry = pdbentry;
     this.seq = seq;
@@ -86,7 +113,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       try
       {
         tmpPDBFile = pdbentry.getFile();
-        PDBfile pdbfile = new PDBfile(tmpPDBFile,
+        PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
                 jalview.io.AppletFormatAdapter.FILE);
 
         pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
@@ -128,7 +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();
@@ -147,10 +176,10 @@ public class PDBViewer extends JInternalFrame implements Runnable
     });
 
     this.setJMenuBar(jMenuBar1);
-    fileMenu.setText("File");
-    coloursMenu.setText("Colours");
-    saveMenu.setActionCommand("Save Image");
-    saveMenu.setText("Save As");
+    fileMenu.setText(MessageManager.getString("action.file"));
+    coloursMenu.setText(MessageManager.getString("label.colours"));
+    saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
+    saveMenu.setText(MessageManager.getString("action.save_as"));
     png.setText("PNG");
     png.addActionListener(new ActionListener()
     {
@@ -167,7 +196,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         eps_actionPerformed(e);
       }
     });
-    mapping.setText("View Mapping");
+    mapping.setText(MessageManager.getString("label.view_mapping"));
     mapping.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -175,7 +204,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         mapping_actionPerformed(e);
       }
     });
-    wire.setText("Wireframe");
+    wire.setText(MessageManager.getString("label.wireframe"));
     wire.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -184,7 +213,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       }
     });
     depth.setSelected(true);
-    depth.setText("Depthcue");
+    depth.setText(MessageManager.getString("label.depthcue"));
     depth.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -193,7 +222,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       }
     });
     zbuffer.setSelected(true);
-    zbuffer.setText("Z Buffering");
+    zbuffer.setText(MessageManager.getString("label.z_buffering"));
     zbuffer.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -201,7 +230,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         zbuffer_actionPerformed(e);
       }
     });
-    charge.setText("Charge & Cysteine");
+    charge.setText(MessageManager.getString("label.charge_cysteine"));
     charge.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -209,7 +238,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         charge_actionPerformed(e);
       }
     });
-    chain.setText("By Chain");
+    chain.setText(MessageManager.getString("action.by_chain"));
     chain.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -218,7 +247,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       }
     });
     seqButton.setSelected(true);
-    seqButton.setText("By Sequence");
+    seqButton.setText(MessageManager.getString("action.by_sequence"));
     seqButton.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -227,7 +256,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
       }
     });
     allchains.setSelected(true);
-    allchains.setText("Show All Chains");
+    allchains.setText(MessageManager.getString("label.show_all_chains"));
     allchains.addItemListener(new ItemListener()
     {
       public void itemStateChanged(ItemEvent e)
@@ -235,7 +264,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         allchains_itemStateChanged(e);
       }
     });
-    zappo.setText("Zappo");
+    zappo.setText(MessageManager.getString("label.zappo"));
     zappo.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -243,7 +272,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         zappo_actionPerformed(e);
       }
     });
-    taylor.setText("Taylor");
+    taylor.setText(MessageManager.getString("label.taylor"));
     taylor.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -251,7 +280,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         taylor_actionPerformed(e);
       }
     });
-    hydro.setText("Hydro");
+    hydro.setText(MessageManager.getString("label.hydrophobicity"));
     hydro.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -259,7 +288,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         hydro_actionPerformed(e);
       }
     });
-    helix.setText("Helix");
+    helix.setText(MessageManager.getString("label.helix_propensity"));
     helix.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -267,7 +296,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         helix_actionPerformed(e);
       }
     });
-    strand.setText("Strand");
+    strand.setText(MessageManager.getString("label.strand_propensity"));
     strand.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -275,7 +304,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         strand_actionPerformed(e);
       }
     });
-    turn.setText("Turn");
+    turn.setText(MessageManager.getString("label.turn_propensity"));
     turn.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -283,7 +312,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         turn_actionPerformed(e);
       }
     });
-    buried.setText("Buried");
+    buried.setText(MessageManager.getString("label.buried_index"));
     buried.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -291,7 +320,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         buried_actionPerformed(e);
       }
     });
-    user.setText("User Defined...");
+    user.setText(MessageManager.getString("action.user_defined"));
     user.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -299,8 +328,9 @@ public class PDBViewer extends JInternalFrame implements Runnable
         user_actionPerformed(e);
       }
     });
-    viewMenu.setText("View");
-    background.setText("Background Colour...");
+    viewMenu.setText(MessageManager.getString("action.view"));
+    background
+            .setText(MessageManager.getString("action.background_colour"));
     background.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -308,7 +338,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
         background_actionPerformed(e);
       }
     });
-    savePDB.setText("PDB File");
+    savePDB.setText(MessageManager.getString("label.pdb_file"));
     savePDB.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -370,8 +400,10 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
               int option = JOptionPane.showInternalConfirmDialog(
                       jalview.gui.Desktop.desktop,
-                      "Remove from default list?",
-                      "Remove user defined colour",
+                      MessageManager
+                              .getString("label.remove_from_default_list"),
+                      MessageManager
+                              .getString("label.remove_user_defined_colour"),
                       JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
@@ -468,7 +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);
   }
 
   /**
@@ -479,26 +511,34 @@ 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,
-              "Make PNG image from view", width, height, null, null);
+      im = new jalview.util.ImageMaker(this,
+              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+              width, height, null, null);
+    }
+    else if (type == jalview.util.ImageMaker.TYPE.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.EPS,
-              "Make EPS file from view", width, height, null,
-              this.getTitle());
+
+      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)
@@ -572,7 +612,9 @@ public class PDBViewer extends JInternalFrame implements Runnable
     try
     {
       cap.setText(pdbcanvas.mappingDetails.toString());
-      Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
+      Desktop.addInternalFrame(cap,
+              MessageManager.getString("label.pdb_sequence_mapping"), 550,
+              600);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("Opening sequence to structure mapping report", oom);
@@ -635,7 +677,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
   public void user_actionPerformed(ActionEvent e)
   {
-    if (e.getActionCommand().equals("User Defined..."))
+    if (e.getActionCommand().equals(
+            MessageManager.getString("action.user_defined")))
     {
       // new UserDefinedColours(pdbcanvas, null);
     }
@@ -653,7 +696,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
   public void background_actionPerformed(ActionEvent e)
   {
     java.awt.Color col = JColorChooser.showDialog(this,
-            "Select Background Colour", pdbcanvas.backgroundColour);
+            MessageManager.getString("label.select_backgroud_colour"),
+            pdbcanvas.backgroundColour);
 
     if (col != null)
     {
@@ -669,8 +713,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save PDB File");
-    chooser.setToolTipText("Save");
+    chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+    chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);