X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FPDBViewer.java;h=082ce6e1f0b9d7cddc0d1a373e441f55896d3305;hb=fbd79f8f62abc6337af57ab87ff07311eff1c74e;hp=95d4b35f788148487bf470394c9b55b01753884c;hpb=6ba4f96a2593b209c3fde5fb65556fd368d791d4;p=jalview.git

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 95d4b35..082ce6e 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -19,9 +19,13 @@ public class PDBViewer extends JInternalFrame implements Runnable
                    Sequence seq,
                    SeqCanvas seqcanvas)
   {
+
     pdb = entry;
     sequence = seq;
 
+    Thread worker = new Thread(this);
+    worker.start();
+
     try
     {
       jbInit();
@@ -42,10 +46,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
       title.append( " Chain:" );
       title.append( pdb.getProperty().get("chains"));
     }
-    Desktop.addInternalFrame(this,title.toString(),400, 400);
 
-     Thread worker = new Thread(this);
-     worker.start();
+     Desktop.addInternalFrame(this,title.toString(),400, 400);
   }
 
   public void run()
@@ -53,8 +55,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     try
     {
       EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,
-                                      null);
+      String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");
 
       PDBfile pdbfile = new PDBfile(result);
 
@@ -174,6 +175,15 @@ public class PDBViewer extends JInternalFrame implements Runnable
         molecule_actionPerformed(e);
       }
     });
+    allchains.setSelected(true);
+    allchains.setText("Show All Chains");
+    allchains.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        allchains_itemStateChanged(e);
+      }
+    });
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(coloursMenu);
     fileMenu.add(saveMenu);
@@ -189,6 +199,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     coloursMenu.add(depth);
     coloursMenu.add(zbuffer);
     coloursMenu.add(molecule);
+    coloursMenu.add(allchains);
     ButtonGroup bg = new ButtonGroup();
     bg.add(seqButton);
     bg.add(chain);
@@ -211,6 +222,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
   JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 
   /**
    * DOCUMENT ME!
@@ -326,7 +338,12 @@ public class PDBViewer extends JInternalFrame implements Runnable
   public void mapping_actionPerformed(ActionEvent e)
   {
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);
+    Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
     cap.setText(pdbcanvas.mappingDetails.toString());
   }
+
+  public void allchains_itemStateChanged(ItemEvent e)
+  {
+    pdbcanvas.setAllchainsVisible(allchains.getState());
+  }
 }