X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=8bfd7b51eb3147c355d1fd42e5a5b0844eae9166;hb=02e9934037787599aefda03a6af9b7501e867dc3;hp=d71e9bcbf9b3166500731e8269e701329175b242;hpb=13b72a19a32edf45b82976ad2984c5ca3e40f37d;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index d71e9bc..8bfd7b5 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,78 +1,92 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * 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
+ * 
+ * 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.
+ *  
+ * 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/>.
  */
 package MCview;
 
-import javax.swing.*;
+import java.io.*;
+
 import java.awt.event.*;
+import javax.swing.*;
+
 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;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.ws.ebi.EBIFetchClient;
 
 public class PDBViewer extends JInternalFrame implements Runnable
 {
-  PDBEntry pdb;
+
   /**
    * The associated sequence in an alignment
    */
-  Sequence sequence;
   PDBCanvas pdbcanvas;
+
+  PDBEntry pdbentry;
+
+  SequenceI[] seq;
+
+  String[] chains;
+
+  AlignmentPanel ap;
+
+  String protocol;
+
   String tmpPDBFile;
 
+  public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+          AlignmentPanel ap, String protocol)
 
-  public PDBViewer(PDBEntry entry,
-                   Sequence seq,
-                   SeqCanvas seqcanvas)
   {
+    this.pdbentry = pdbentry;
+    this.seq = seq;
+    this.chains = chains;
+    this.ap = ap;
+    this.protocol = protocol;
+
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
+    StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+            + pdbentry.getFile());
 
-    if (entry==null)
-      return;
-    pdb = entry;
-    sequence = seq;
-    pdbcanvas = new PDBCanvas(seqcanvas, sequence);
+    pdbcanvas = new PDBCanvas();
 
-    if(pdb.getFile()!=null)
+    setContentPane(pdbcanvas);
+
+    if (pdbentry.getFile() != null)
     {
-        try{
-          tmpPDBFile = pdb.getFile();
-          PDBfile pdbfile = new PDBfile(tmpPDBFile,
-                                        jalview.io.AppletFormatAdapter.FILE);
-          pdbcanvas.setPDBFile(pdbfile);
+      try
+      {
+        tmpPDBFile = pdbentry.getFile();
+        PDBfile pdbfile = new PDBfile(tmpPDBFile,
+                jalview.io.AppletFormatAdapter.FILE);
 
-        }catch(java.io.IOException ex)
-        {
-          ex.printStackTrace();
-        }
+        pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+      } catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
     }
     else
     {
@@ -80,61 +94,49 @@ public class PDBViewer extends JInternalFrame implements Runnable
       worker.start();
     }
 
-
-
-    setContentPane(pdbcanvas);
-    StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
-    if(pdb.getProperty()!=null)
+    if (pdbentry.getProperty() != null)
     {
-      if (pdb.getProperty().get("method")!=null)
+      if (pdbentry.getProperty().get("method") != null)
       {
         title.append(" Method: ");
-        title.append(pdb.getProperty().get("method"));
+        title.append(pdbentry.getProperty().get("method"));
       }
-      if (pdb.getProperty().get("chains") != null)
+      if (pdbentry.getProperty().get("chains") != null)
       {
         title.append(" Chain:");
-        title.append(pdb.getProperty().get("chains"));
+        title.append(pdbentry.getProperty().get("chains"));
       }
     }
-     Desktop.addInternalFrame(this,title.toString(),400, 400);
+    Desktop.addInternalFrame(this, title.toString(), 400, 400);
   }
 
   public void run()
   {
     try
     {
-        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)
+      EBIFetchClient ebi = new EBIFetchClient();
+      String query = "pdb:" + pdbentry.getId();
+      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+              .getAbsolutePath());
+
+      if (pdbentry.getFile() != null)
+        pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+    } catch (Exception ex)
     {
+      pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
       ex.printStackTrace();
-      showErrorMessage("Failed to retrieve PDB structure.");
-//      this.dispose();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.addKeyListener(new KeyAdapter()
-        {
-            public void keyPressed(KeyEvent evt)
-            {
-              pdbcanvas.keyPressed(evt);
-            }
-        });
+    {
+      public void keyPressed(KeyEvent evt)
+      {
+        pdbcanvas.keyPressed(evt);
+      }
+    });
 
     this.setJMenuBar(jMenuBar1);
     fileMenu.setText("File");
@@ -339,45 +341,49 @@ public class PDBViewer extends JInternalFrame implements Runnable
     bg.add(buried);
     bg.add(user);
 
-
-    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
-            nextElement().toString());
+        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))
             {
-              public void mousePressed(MouseEvent evt)
-              {
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
-                {
-                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+              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)
+              if (option == JOptionPane.YES_OPTION)
+              {
+                jalview.gui.UserDefinedColours
+                        .removeColourFromDefaults(radioItem.getText());
+                coloursMenu.remove(radioItem);
+              }
+              else
+              {
+                radioItem.addActionListener(new ActionListener()
+                {
+                  public void actionPerformed(ActionEvent evt)
                   {
-                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
-                    coloursMenu.remove(radioItem);
+                    user_actionPerformed(evt);
                   }
-                  else
-                    radioItem.addActionListener(new ActionListener()
-                    {
-                      public void actionPerformed(ActionEvent evt)
-                      {
-                        user_actionPerformed(evt);
-                      }
-                    });
-                }
+                });
               }
-            });
+            }
+          }
+        });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -397,36 +403,60 @@ public class PDBViewer extends JInternalFrame implements Runnable
   }
 
   JMenuBar jMenuBar1 = new JMenuBar();
+
   JMenu fileMenu = new JMenu();
+
   JMenu coloursMenu = new JMenu();
+
   JMenu saveMenu = new JMenu();
+
   JMenuItem png = new JMenuItem();
+
   JMenuItem eps = new JMenuItem();
+
   JMenuItem mapping = new JMenuItem();
+
   JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 
   JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
-  JRadioButtonMenuItem zappo = 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!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
    */
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -435,12 +465,13 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
    */
   public void png_actionPerformed(ActionEvent e)
   {
-     makePDBImage(jalview.util.ImageMaker.PNG);
+    makePDBImage(jalview.util.ImageMaker.PNG);
   }
 
   void makePDBImage(int type)
@@ -451,17 +482,16 @@ public class PDBViewer extends JInternalFrame implements Runnable
     jalview.util.ImageMaker im;
 
     if (type == jalview.util.ImageMaker.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.PNG,
+              "Make PNG image from view", width, height, null, null);
+    }
     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.EPS,
+              "Make EPS file from view", width, height, null,
+              this.getTitle());
+    }
 
     if (im.getGraphics() != null)
     {
@@ -469,11 +499,12 @@ public class PDBViewer extends JInternalFrame implements Runnable
       im.writeImage();
     }
   }
+
   public void charge_actionPerformed(ActionEvent e)
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setChargeColours();
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -481,7 +512,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -489,35 +520,35 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setChainColours();
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void zbuffer_actionPerformed(ActionEvent e)
   {
-    pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void molecule_actionPerformed(ActionEvent e)
   {
-    pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void depth_actionPerformed(ActionEvent e)
   {
-  pdbcanvas.depthcue = ! pdbcanvas.depthcue;
-  pdbcanvas.redrawneeded=true;
+    pdbcanvas.depthcue = !pdbcanvas.depthcue;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
   public void wire_actionPerformed(ActionEvent e)
   {
-    pdbcanvas.wire = ! pdbcanvas.wire;
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.wire = !pdbcanvas.wire;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -527,30 +558,30 @@ public class PDBViewer extends JInternalFrame implements Runnable
     pdbcanvas.updateSeqColours();
   }
 
-
   public void mapping_actionPerformed(ActionEvent e)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
-    cap.setText(pdbcanvas.mappingDetails.toString());
+    try
+    {
+      cap.setText(pdbcanvas.mappingDetails.toString());
+      Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Opening sequence to structure mapping report", oom);
+      cap.dispose();
+    }
   }
 
   public void allchains_itemStateChanged(ItemEvent e)
   {
     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.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -558,7 +589,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new TaylorColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -566,7 +597,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new HelixColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -574,7 +605,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new StrandColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -582,7 +613,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new TurnColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -590,7 +621,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     pdbcanvas.bysequence = false;
     pdbcanvas.pdb.setColours(new BuriedColourScheme());
-    pdbcanvas.redrawneeded=true;
+    pdbcanvas.redrawneeded = true;
     pdbcanvas.repaint();
   }
 
@@ -598,37 +629,36 @@ public class PDBViewer extends JInternalFrame implements Runnable
   {
     if (e.getActionCommand().equals("User Defined..."))
     {
-      new UserDefinedColours(pdbcanvas, null);
+      // new UserDefinedColours(pdbcanvas, null);
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
-          getUserColourSchemes().get(e.getActionCommand());
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+              .getUserColourSchemes().get(e.getActionCommand());
 
       pdbcanvas.pdb.setColours(udc);
-      pdbcanvas.redrawneeded=true;
+      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();
-       }
+    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"));
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save PDB File");
@@ -638,26 +668,26 @@ public class PDBViewer extends JInternalFrame implements Runnable
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        try
-        {
-          BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
-          File outFile = chooser.getSelectedFile();
+      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)
+        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+        String data;
+        while ((data = in.readLine()) != null)
+        {
+          if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
           {
-            if (
-                !( data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
-                )
-              out.println(data);
+            out.println(data);
           }
-          out.close();
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
         }
+        out.close();
+        in.close();
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
       }
+    }
   }
 }