X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=d778125ad4c104d4950a81e4cd58b69fbed782ce;hb=7c28880430765f06ccd5ec8ad3caf17871336e97;hp=94d22ef0a0029bffe49a9cdfe34fd0f917295cfb;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
old mode 100755
new mode 100644
index 94d22ef..d778125
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -21,6 +21,7 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
 import MCview.*;
@@ -37,7 +38,7 @@ import jalview.util.UrlLink;
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.118 $
  */
 public class PopupMenu extends JPopupMenu
 {
@@ -207,11 +208,11 @@ public class PopupMenu extends JPopupMenu
       e.printStackTrace();
     }
 
+    JMenuItem menuItem;
     if (seq != null)
     {
       sequenceMenu.setText(sequence.getName());
 
-      JMenuItem menuItem;
       if (seq.getDatasetSequence().getPDBId() != null
               && seq.getDatasetSequence().getPDBId().size() > 0)
       {
@@ -228,33 +229,11 @@ public class PopupMenu extends JPopupMenu
           {
             public void actionPerformed(ActionEvent e)
             {
-              Vector seqs = new Vector();
-              for (int i = 0; i < ap.av.alignment.getHeight(); i++)
-              {
-                Vector pdbs = ap.av.alignment.getSequenceAt(i)
-                        .getDatasetSequence().getPDBId();
-                if (pdbs == null)
-                  continue;
-
-                for (int p = 0; p < pdbs.size(); p++)
-                {
-                  PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
-                  if (p1.getId().equals(pdb.getId()))
-                  {
-                    if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
-                      seqs.addElement(ap.av.alignment.getSequenceAt(i));
-
-                    continue;
-                  }
-                }
-              }
-
-              SequenceI[] seqs2 = new SequenceI[seqs.size()];
-              seqs.toArray(seqs2);
-
-              new AppJmol(pdb, seqs2, null, ap);
+            	// TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
+              new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
             }
+
           });
           viewStructureMenu.add(menuItem);
 
@@ -318,7 +297,11 @@ public class PopupMenu extends JPopupMenu
           });
           add(menuItem);
         }
-
+      }
+    }
+    // for the case when no sequences are even visible
+    if (ap.av.hasHiddenRows) {
+      {
         menuItem = new JMenuItem("Reveal All");
         menuItem.addActionListener(new ActionListener()
         {
@@ -339,9 +322,10 @@ public class PopupMenu extends JPopupMenu
 
     SequenceGroup sg = ap.av.getSelectionGroup();
 
-    if (sg != null)
+    if (sg != null&& sg.getSize()>0)
     {
-      groupName.setText(sg.getName());
+      groupName.setText("Name: "+sg.getName());
+      groupName.setText("Edit name and description of current group.");
 
       if (sg.cs instanceof ZappoColourScheme)
       {
@@ -405,6 +389,44 @@ public class PopupMenu extends JPopupMenu
       {
         buildGroupURLMenu(sg, groupLinks);
       }
+      // Add a 'show all structures' for the current selection
+      Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
+      SequenceI sqass=null;
+      for (SequenceI sq: ap.av.getSequenceSelection())
+      {
+        Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
+        if (pes!=null) {
+          for (PDBEntry pe: pes)
+          {
+            pdbe.put(pe.getId(),  pe);
+            if (sqass==null)
+            {
+              sqass = sq;
+            }
+          }
+        }
+      }
+      if (pdbe.size()>0)
+      {
+        final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
+        final JMenuItem gpdbview;
+        if (pdbe.size()==1)
+        {
+          structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
+        } else {
+          structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures."));
+        }
+        gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
+        gpdbview.addActionListener(new ActionListener()
+        {
+          
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+          }
+        });
+      }
     }
     else
     {
@@ -423,7 +445,7 @@ public class PopupMenu extends JPopupMenu
       structureMenu.setVisible(false);
     }
 
-    if (links != null && links.size() > 0)
+    if (seq !=null && links != null && links.size() > 0)
     {
 
       JMenu linkMenu = new JMenu("Link");
@@ -1730,47 +1752,16 @@ public class PopupMenu extends JPopupMenu
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Select a PDB file");
-    chooser.setToolTipText("Load a PDB file");
+    chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
+    chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
 
     int value = chooser.showOpenDialog(null);
 
     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
     {
-      PDBEntry entry = new PDBEntry();
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      try
-      {
-        MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-                jalview.io.AppletFormatAdapter.FILE);
-
-        if (pdbfile.id == null)
-        {
-          String reply = JOptionPane
-                  .showInternalInputDialog(
-                          Desktop.desktop,
-                          "Couldn't find a PDB id in the file supplied."
-                                  + "Please enter an Id to identify this structure.",
-                          "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
-          if (reply == null)
-          {
-            return;
-          }
-
-          entry.setId(reply);
-        }
-        else
-        {
-          entry.setId(pdbfile.id);
-        }
-      } catch (java.io.IOException ex)
-      {
-        ex.printStackTrace();
-      }
-
-      entry.setFile(choice);
-      sequence.getDatasetSequence().addPDBId(entry);
+      new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
     }
 
   }
@@ -1856,8 +1847,7 @@ public class PopupMenu extends JPopupMenu
 
   public void colourByStructure(String pdbid)
   {
-    Annotation[] anots = jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().colourSequenceFromStructure(
+    Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
                     sequence, pdbid);
 
     AlignmentAnnotation an = new AlignmentAnnotation("Structure",