X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=14363e187f0c55eca1a5535e6ce0ba8d0245e1e1;hb=c77ccc33971183dba9cb66b40886a6b61fe8eaa0;hp=1377de2b1fef0fab631c3e63a3efced38ca90076;hpb=3dc211ddfada6bd9036697ec8236c188f131b84f;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1377de2..14363e1 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -24,7 +24,6 @@ import jalview.analysis.*;
 
 import jalview.datamodel.*;
 
-import jalview.io.*;
 
 import jalview.schemes.*;
 
@@ -63,7 +62,6 @@ public class PopupMenu extends JPopupMenu
     JMenuItem sequenceName = new JMenuItem();
     Sequence sequence;
     JMenuItem unGroupMenuItem = new JMenuItem();
-    JMenuItem pdbMenuItem = new JMenuItem();
     JMenuItem outline = new JMenuItem();
     JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
     JMenu colourMenu = new JMenu();
@@ -77,7 +75,7 @@ public class PopupMenu extends JPopupMenu
      * @param ap DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public PopupMenu(AlignmentPanel ap, Sequence seq)
+    public PopupMenu(final AlignmentPanel ap, Sequence seq)
     {
         ///////////////////////////////////////////////////////////
         // If this is activated from the sequence panel, the user may want to
@@ -112,11 +110,59 @@ public class PopupMenu extends JPopupMenu
             e.printStackTrace();
         }
 
-        if ((seq == null) || (seq.getPDBId() == null))
+
+        if (seq != null)
         {
-            pdbMenuItem.setVisible(false);
+          JMenuItem menuItem;
+          if( seq.getDatasetSequence().getPDBId() != null)
+          {
+            java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+                elements();
+            while (e.hasMoreElements())
+            {
+              final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+              menuItem = new JMenuItem();
+              menuItem.setText("View PDB entry: " + pdb.getId());
+              menuItem.addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(ActionEvent e)
+                {
+                  new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
+                }
+              });
+              sequenceMenu.add(menuItem);
+            }
+          }
+
+          menuItem = new JMenuItem("Hide Sequences");
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(ActionEvent e)
+                {
+                  hideSequences(false);
+                }
+              });
+          sequenceMenu.add(menuItem);
+
+          if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)
+          {
+            menuItem = new JMenuItem("Represent Group with " + seq.getName());
+            menuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                hideSequences(true);
+              }
+            });
+            sequenceMenu.add(menuItem);
+          }
+
+
         }
 
+
+
         SequenceGroup sg = ap.av.getSelectionGroup();
 
         if (sg != null)
@@ -206,9 +252,12 @@ public class PopupMenu extends JPopupMenu
             String link = links.elementAt(i).toString();
 
             item = new JMenuItem(link.substring(0, link.indexOf("|")));
+            String id = sequence.getName();
+            if(id.indexOf("|")>-1)
+              id = id.substring(id.lastIndexOf("|")+1);
 
             final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-                + sequence.getName() +
+                + id +
                 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
 
 
@@ -226,6 +275,7 @@ public class PopupMenu extends JPopupMenu
         }
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -244,7 +294,7 @@ public class PopupMenu extends JPopupMenu
                 }
             });
         sequenceMenu.setText("Sequence");
-        sequenceName.setText("Edit name");
+        sequenceName.setText("Edit Name/Description");
         sequenceName.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -261,14 +311,7 @@ public class PopupMenu extends JPopupMenu
                     unGroupMenuItem_actionPerformed(e);
                 }
             });
-        pdbMenuItem.setText("View PDB structure");
-        pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    pdbMenuItem_actionPerformed(e);
-                }
-            });
+
         outline.setText("Border colour");
         outline.addActionListener(new java.awt.event.ActionListener()
             {
@@ -325,7 +368,6 @@ public class PopupMenu extends JPopupMenu
         groupMenu.addSeparator();
         groupMenu.add(outline);
         sequenceMenu.add(sequenceName);
-        sequenceMenu.add(pdbMenuItem);
         colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
@@ -484,16 +526,6 @@ public class PopupMenu extends JPopupMenu
      */
     void refresh()
     {
-        SequenceGroup sg = getGroup();
-        if(sg!=null)
-        {
-          SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-          if (superG != null)
-          {
-            superG.setSuperGroupProperties(sg);
-          }
-        }
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
@@ -795,11 +827,34 @@ public class PopupMenu extends JPopupMenu
      */
     void sequenceName_actionPerformed(ActionEvent e)
     {
-        String id = sequence.getName();
-        String s = (String) JOptionPane.showInternalInputDialog(ap,
-                "Edit sequence name",
-                "Edit sequence name (" + sequence.getName() + ")",
-                JOptionPane.PLAIN_MESSAGE, null, null, id);
+      JLabel idlabel = new JLabel(  "       Sequence Name ");
+      JLabel desclabel = new JLabel("Sequence Description ");
+      idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
+      desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
+      JTextField id = new JTextField(sequence.getName(), 40);
+      JTextField description = new JTextField(sequence.getDescription(), 40);
+      JPanel panel = new JPanel(new BorderLayout());
+      JPanel panel2 = new JPanel(new BorderLayout());
+      panel2.add(idlabel, BorderLayout.WEST);
+      panel2.add(id, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.NORTH);
+      panel2 = new JPanel(new BorderLayout());
+      panel2.add(desclabel, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.SOUTH);
+
+
+       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          panel, "Edit Sequence Name/Description",
+          JOptionPane.OK_CANCEL_OPTION );
+
+
+        if (reply != JOptionPane.OK_OPTION )
+        {
+            return;
+        }
+
+        String s = id.getText();
 
         if (s != null)
         {
@@ -812,9 +867,13 @@ public class PopupMenu extends JPopupMenu
             }
 
             s = s.replace(' ', '_');
+            sequence.getDatasetSequence().setName(s);
             sequence.setName(s);
             ap.repaint();
         }
+
+        sequence.getDatasetSequence().setDescription(description.getText());
+        sequence.setDescription(description.getText());
     }
 
     /**
@@ -830,37 +889,6 @@ public class PopupMenu extends JPopupMenu
         refresh();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    void pdbMenuItem_actionPerformed(ActionEvent e)
-    {
-        if (sequence.getPDBId() == null)
-        {
-            return;
-        }
-
-        try
-        {
-            EBIFetchClient ebi = new EBIFetchClient();
-            String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
-                    null);
-
-            PDBfile pdb = new PDBfile(result);
-
-            rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
-            JInternalFrame frame = new JInternalFrame();
-            frame.setContentPane(rc);
-            Desktop.addInternalFrame(frame,
-                sequence.getName() + " " + sequence.getPDBId(), 400, 400);
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
-    }
 
     /**
      * DOCUMENT ME!
@@ -931,4 +959,33 @@ public class PopupMenu extends JPopupMenu
         ex.printStackTrace();
       }
     }
+
+    void hideSequences(boolean representGroup)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if(sg==null || sg.getSize()<1)
+      {
+        ap.av.hideSequence(sequence);
+        return;
+      }
+
+        int index = 0;
+        while(index < sg.sequences.size())
+        {
+          if(representGroup && sg.getSequenceAt(index)!=sequence)
+          {
+            sequence.addHiddenSequence(sg.getSequenceAt(index));
+            ap.av.hideSequence(sg.getSequenceAt(index));
+          }
+          else if(!representGroup)
+          {
+            ap.av.hideSequence(sg.getSequenceAt(index));
+          }
+          index ++;
+        }
+
+        ap.av.setSelectionGroup(null);
+        refresh();
+    }
+
 }