SequenceFeature display added

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4ad7090..2bdaf37 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -5,7 +5,8 @@ import jalview.analysis.*;
 import jalview.schemes.*;\r
 import javax.swing.*;\r
 import java.awt.event.*;\r
-\r
+import jalview.io.*;\r
+import MCview.*;\r
 \r
 public class PopupMenu extends JPopupMenu\r
 {\r
@@ -39,10 +40,11 @@ public class PopupMenu extends JPopupMenu
   JMenu residueMenu = new JMenu();\r
   JMenuItem annotateResidue = new JMenuItem();\r
 \r
-  SequenceI sequence;\r
+  Sequence sequence;\r
   JMenuItem unGroupMenuItem = new JMenuItem();\r
+  JMenuItem pdbMenuItem = new JMenuItem();\r
 \r
-  public PopupMenu(AlignmentPanel ap, SequenceI seq)\r
+  public PopupMenu(AlignmentPanel ap, Sequence seq)\r
   {\r
     ///////////////////////////////////////////////////////////\r
     // If this is activated from the sequence panel, the user may want to\r
@@ -189,6 +191,14 @@ public class PopupMenu extends JPopupMenu
         unGroupMenuItem_actionPerformed(e);\r
       }\r
     });\r
+    pdbMenuItem.setText("View PDB structure");\r
+    pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        pdbMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
     add(groupMenu);\r
     this.add(sequenceMenu);\r
     this.add(residueMenu);\r
@@ -220,6 +230,7 @@ public class PopupMenu extends JPopupMenu
     defineMenu.add(conservationMenuItem);\r
 \r
     sequenceMenu.add(sequenceName);\r
+    sequenceMenu.add(pdbMenuItem);\r
     residueMenu.add(annotateResidue);\r
 \r
     noColourmenuItem.setText("None");\r
@@ -597,4 +608,33 @@ public class PopupMenu extends JPopupMenu
      ap.av.setRubberbandGroup(null);\r
      ap.RefreshPanels();\r
   }\r
+\r
+  void pdbMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    if(sequence.getPDBId()==null)\r
+      return;\r
+\r
+    try\r
+    {\r
+      EBIFetchClient ebi = new EBIFetchClient();\r
+      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
+\r
+      PDBfile pdb = new PDBfile(result);\r
+      sequence.setPDBfile(pdb);\r
+\r
+      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;\r
+      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;\r
+    //  ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();\r
+\r
+      rotCanvas rc = new rotCanvas(pdb);\r
+      JInternalFrame frame = new JInternalFrame();\r
+      frame.setContentPane(rc);\r
+      Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+  }\r
+\r
 }\r