X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=1f1f94dd35cb6add225ca5ddced9a60a0ca4c48f;hb=284dc3090d93f4b149b38bb5106d93eb1a4ae7b2;hp=082ce6e1f0b9d7cddc0d1a373e441f55896d3305;hpb=8893c2ac9824d4c566ae69c73d34889c5316b058;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 082ce6e..1f1f94d 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,31 +1,47 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package MCview;
 
 import javax.swing.*;
 import java.awt.event.*;
 import jalview.datamodel.*;
+import jalview.schemes.*;
 import jalview.gui.*;
 import jalview.io.EBIFetchClient;
 import java.awt.event.ActionListener;
 import java.awt.event.ActionEvent;
+import java.io.*;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 
 public class PDBViewer extends JInternalFrame implements Runnable
 {
   PDBEntry pdb;
   Sequence sequence;
   PDBCanvas pdbcanvas;
+  String tmpPDBFile;
 
 
   public PDBViewer(PDBEntry entry,
                    Sequence seq,
                    SeqCanvas seqcanvas)
   {
-
-    pdb = entry;
-    sequence = seq;
-
-    Thread worker = new Thread(this);
-    worker.start();
-
     try
     {
       jbInit();
@@ -35,18 +51,49 @@ public class PDBViewer extends JInternalFrame implements Runnable
       ex.printStackTrace();
     }
 
-    pdbcanvas = new PDBCanvas(seqcanvas, seq);
+
+    if (entry==null)
+      return;
+    pdb = entry;
+    sequence = seq;
+    pdbcanvas = new PDBCanvas(seqcanvas, sequence);
+
+    if(pdb.getFile()!=null)
+    {
+        try{
+          tmpPDBFile = pdb.getFile();
+          PDBfile pdbfile = new PDBfile(tmpPDBFile,
+                                        jalview.io.AppletFormatAdapter.FILE);
+          pdbcanvas.setPDBFile(pdbfile);
+
+        }catch(java.io.IOException ex)
+        {
+          ex.printStackTrace();
+        }
+    }
+    else
+    {
+      Thread worker = new Thread(this);
+      worker.start();
+    }
+
+
 
     setContentPane(pdbcanvas);
     StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
     if(pdb.getProperty()!=null)
     {
-      title.append( " Method: " );
-      title.append(pdb.getProperty().get("method"));
-      title.append( " Chain:" );
-      title.append( pdb.getProperty().get("chains"));
+      if (pdb.getProperty().get("method")!=null)
+      {
+        title.append(" Method: ");
+        title.append(pdb.getProperty().get("method"));
+      }
+      if (pdb.getProperty().get("chains") != null)
+      {
+        title.append(" Chain:");
+        title.append(pdb.getProperty().get("chains"));
+      }
     }
-
      Desktop.addInternalFrame(this,title.toString(),400, 400);
   }
 
@@ -54,17 +101,24 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     try
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");
-
-      PDBfile pdbfile = new PDBfile(result);
-
-      pdbcanvas.setPDBFile(pdbfile);
-
+        EBIFetchClient ebi = new EBIFetchClient();
+        String query = "pdb:" + pdb.getId();
+        tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
+        if (tmpPDBFile != null)
+        {
+          PDBfile pdbfile = new PDBfile(tmpPDBFile, jalview.io.AppletFormatAdapter.FILE);
+          pdbcanvas.setPDBFile(pdbfile);
+        }
+        else
+        {
+          throw new Exception("Empty result for WSDbFetch Query: " + query);
+        }
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
+      showErrorMessage("Failed to retrieve PDB structure.");
+//      this.dispose();
     }
   }
 
@@ -142,14 +196,6 @@ public class PDBViewer extends JInternalFrame implements Runnable
         charge_actionPerformed(e);
       }
     });
-    hydro.setText("Hydrophobicity");
-    hydro.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydro_actionPerformed(e);
-      }
-    });
     chain.setText("By Chain");
     chain.addActionListener(new ActionListener()
     {
@@ -167,14 +213,6 @@ public class PDBViewer extends JInternalFrame implements Runnable
         seqButton_actionPerformed(e);
       }
     });
-    molecule.setText("By Molecule");
-    molecule.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        molecule_actionPerformed(e);
-      }
-    });
     allchains.setSelected(true);
     allchains.setText("Show All Chains");
     allchains.addItemListener(new ItemListener()
@@ -184,27 +222,175 @@ public class PDBViewer extends JInternalFrame implements Runnable
         allchains_itemStateChanged(e);
       }
     });
+    zappo.setText("Zappo");
+    zappo.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappo_actionPerformed(e);
+      }
+    });
+    taylor.setText("Taylor");
+    taylor.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylor_actionPerformed(e);
+      }
+    });
+    hydro.setText("Hydro");
+    hydro.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hydro_actionPerformed(e);
+      }
+    });
+    helix.setText("Helix");
+    helix.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helix_actionPerformed(e);
+      }
+    });
+    strand.setText("Strand");
+    strand.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strand_actionPerformed(e);
+      }
+    });
+    turn.setText("Turn");
+    turn.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turn_actionPerformed(e);
+      }
+    });
+    buried.setText("Buried");
+    buried.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buried_actionPerformed(e);
+      }
+    });
+    user.setText("User Defined...");
+    user.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        user_actionPerformed(e);
+      }
+    });
+    viewMenu.setText("View");
+    background.setText("Background Colour...");
+    background.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        background_actionPerformed(e);
+      }
+    });
+    savePDB.setText("PDB File");
+    savePDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        savePDB_actionPerformed(e);
+      }
+    });
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(coloursMenu);
+    jMenuBar1.add(viewMenu);
     fileMenu.add(saveMenu);
     fileMenu.add(mapping);
+    saveMenu.add(savePDB);
     saveMenu.add(png);
     saveMenu.add(eps);
     coloursMenu.add(seqButton);
     coloursMenu.add(chain);
-    coloursMenu.add(hydro);
     coloursMenu.add(charge);
-    coloursMenu.addSeparator();
-    coloursMenu.add(wire);
-    coloursMenu.add(depth);
-    coloursMenu.add(zbuffer);
-    coloursMenu.add(molecule);
-    coloursMenu.add(allchains);
+    coloursMenu.add(zappo);
+    coloursMenu.add(taylor);
+    coloursMenu.add(hydro);
+    coloursMenu.add(helix);
+    coloursMenu.add(strand);
+    coloursMenu.add(turn);
+    coloursMenu.add(buried);
+    coloursMenu.add(user);
+    coloursMenu.add(background);
     ButtonGroup bg = new ButtonGroup();
     bg.add(seqButton);
     bg.add(chain);
-    bg.add(hydro);
     bg.add(charge);
+    bg.add(zappo);
+    bg.add(taylor);
+    bg.add(hydro);
+    bg.add(helix);
+    bg.add(strand);
+    bg.add(turn);
+    bg.add(buried);
+    bg.add(user);
+
+
+    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+            nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+            {
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                    coloursMenu.remove(radioItem);
+                  }
+                  else
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        user_actionPerformed(evt);
+                      }
+                    });
+                }
+              }
+            });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            user_actionPerformed(evt);
+          }
+        });
+        coloursMenu.add(radioItem);
+        bg.add(radioItem);
+      }
+    }
+
+    viewMenu.add(wire);
+    viewMenu.add(depth);
+    viewMenu.add(zbuffer);
+    viewMenu.add(allchains);
   }
 
   JMenuBar jMenuBar1 = new JMenuBar();
@@ -217,12 +403,22 @@ public class PDBViewer extends JInternalFrame implements Runnable
   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
+
   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
-  JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
-  JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
+  JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem zappo = new  JRadioButtonMenuItem();
+  JRadioButtonMenuItem user = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
+  JMenu viewMenu = new JMenu();
+  JMenuItem background = new JMenuItem();
+  JMenuItem savePDB = new JMenuItem();
 
   /**
    * DOCUMENT ME!
@@ -272,7 +468,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   }
   public void charge_actionPerformed(ActionEvent e)
   {
-    clearButtonGroup();
+    pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setChargeColours();
     pdbcanvas.redrawneeded=true;
     pdbcanvas.repaint();
@@ -280,15 +476,15 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
   public void hydro_actionPerformed(ActionEvent e)
   {
-    clearButtonGroup();
-    pdbcanvas.pdb.setHydrophobicityColours();
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
     pdbcanvas.redrawneeded=true;
     pdbcanvas.repaint();
   }
 
   public void chain_actionPerformed(ActionEvent e)
   {
-    clearButtonGroup();
+    pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setChainColours();
     pdbcanvas.redrawneeded=true;
     pdbcanvas.repaint();
@@ -324,16 +520,10 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
   public void seqButton_actionPerformed(ActionEvent e)
   {
-    clearButtonGroup();
-    pdbcanvas.bysequence = seqButton.isSelected();
+    pdbcanvas.bysequence = true;
     pdbcanvas.updateSeqColours();
   }
 
-  void clearButtonGroup()
-  {
-   pdbcanvas.bysequence = false;
-   pdbcanvas.bymolecule = false;
-  }
 
   public void mapping_actionPerformed(ActionEvent e)
   {
@@ -346,4 +536,123 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.setAllchainsVisible(allchains.getState());
   }
+  void showErrorMessage(String error)
+  {
+    JOptionPane.showInternalMessageDialog(Desktop.desktop,
+         error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
+  }
+
+
+  public void zappo_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new ZappoColourScheme());
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void taylor_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new TaylorColourScheme());
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void helix_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new HelixColourScheme());
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void strand_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new StrandColourScheme());
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void turn_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new TurnColourScheme());
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void buried_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = false;
+    pdbcanvas.pdb.setColours(new BuriedColourScheme());
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void user_actionPerformed(ActionEvent e)
+  {
+    if (e.getActionCommand().equals("User Defined..."))
+    {
+      new UserDefinedColours(pdbcanvas, null);
+    }
+    else
+    {
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+          getUserColourSchemes().get(e.getActionCommand());
+
+      pdbcanvas.pdb.setColours(udc);
+      pdbcanvas.redrawneeded=true;
+      pdbcanvas.repaint();
+    }
+  }
+
+  public void background_actionPerformed(ActionEvent e)
+  {
+      java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",
+                pdbcanvas.backgroundColour);
+
+      if(col!=null)
+       {
+         pdbcanvas.backgroundColour = col;
+         pdbcanvas.redrawneeded = true;
+         pdbcanvas.repaint();
+       }
+  }
+
+  public void savePDB_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+        jalview.bin.Cache.getProperty(
+            "LAST_DIRECTORY"));
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save PDB File");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+        try
+        {
+          BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
+          File outFile = chooser.getSelectedFile();
+
+          PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+          String data;
+          while ( (data = in.readLine()) != null)
+          {
+            if (data.indexOf("<PRE>") == -1 && data.indexOf("</PRE>") == -1)
+              out.println(data);
+          }
+          out.close();
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+  }
 }