X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f87dcef6fb4e6a198ec019e860f69c392e26cc29;hb=a94894810c6142a94239ca239ec8e800235c3b35;hp=5ff9ad9099bd3384ae2c697a41e2e3f958695473;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 5ff9ad9..f87dcef 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -63,7 +63,6 @@ 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 +76,7 @@ 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
@@ -112,9 +111,27 @@ public class PopupMenu extends JPopupMenu
             e.printStackTrace();
         }
 
-        if ((seq == null) || (seq.getPDBId() == null))
+
+        if ((seq != null)
+            && seq.getDatasetSequence().getPDBId() != null)
         {
-            pdbMenuItem.setVisible(false);
+          java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();
+          while(e.hasMoreElements())
+          {
+
+            final PDBEntry pdb = (PDBEntry)e.nextElement();
+            JMenuItem pdbMenuItem = new JMenuItem();
+            pdbMenuItem.setText("View PDB entry: "+pdb.getId());
+            pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                  new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
+                }
+            });
+            sequenceMenu.add(pdbMenuItem);
+          }
+
         }
 
         SequenceGroup sg = ap.av.getSelectionGroup();
@@ -172,7 +189,7 @@ public class PopupMenu extends JPopupMenu
                 noColourmenuItem.setSelected(true);
             }
 
-            if (sg.cs instanceof ConservationColourScheme)
+            if (sg.cs!=null && sg.cs.conservationApplied())
             {
                 conservationMenuItem.setSelected(true);
             }
@@ -195,6 +212,35 @@ public class PopupMenu extends JPopupMenu
         {
             sequenceMenu.setVisible(false);
         }
+        else
+        {
+          java.util.Vector links = Preferences.sequenceURLLinks;
+
+          JMenu linkMenu = new JMenu("Link");
+          JMenuItem item;
+          for(int i=0; i<links.size(); i++)
+          {
+            String link = links.elementAt(i).toString();
+
+            item = new JMenuItem(link.substring(0, link.indexOf("|")));
+
+            final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
+                + sequence.getName() +
+                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+
+
+            item.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    showLink(url);
+                }
+            });
+
+            linkMenu.add(item);
+          }
+          add(linkMenu);
+        }
     }
 
     /**
@@ -232,14 +278,7 @@ 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()
             {
@@ -296,7 +335,6 @@ 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);
@@ -310,6 +348,28 @@ public class PopupMenu extends JPopupMenu
         colourMenu.add(buriedColour);
         colourMenu.add(nucleotideMenuItem);
         colourMenu.add(userDefinedColour);
+
+        if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+        {
+          java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+              getUserColourSchemes().keys();
+
+          while (userColours.hasMoreElements())
+          {
+            JMenuItem item = new JMenuItem(userColours.
+                nextElement().toString());
+            item.addActionListener(new ActionListener()
+            {
+              public void actionPerformed(ActionEvent evt)
+              {
+                userDefinedColour_actionPerformed(evt);
+              }
+            });
+            colourMenu.add(item);
+          }
+        }
+
+
         colourMenu.addSeparator();
         colourMenu.add(abovePIDColour);
         colourMenu.add(conservationMenuItem);
@@ -394,7 +454,7 @@ public class PopupMenu extends JPopupMenu
                     abovePIDColour_actionPerformed(e);
                 }
             });
-        userDefinedColour.setText("User Defined");
+        userDefinedColour.setText("User Defined...");
         userDefinedColour.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -434,12 +494,17 @@ public class PopupMenu extends JPopupMenu
     void refresh()
     {
         SequenceGroup sg = getGroup();
-        SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-        if (superG != null)
+        if(sg!=null)
         {
+          SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
+
+          if (superG != null)
+          {
             superG.setSuperGroupProperties(sg);
+          }
         }
+        if (ap.overviewPanel != null)
+          ap.overviewPanel.updateOverviewImage();
 
         ap.seqPanel.repaint();
     }
@@ -553,6 +618,8 @@ public class PopupMenu extends JPopupMenu
     protected void abovePIDColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (abovePIDColour.isSelected())
         {
@@ -562,22 +629,13 @@ public class PopupMenu extends JPopupMenu
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
 
-            if (sg.cs instanceof ResidueColourScheme)
-            {
-                ((ResidueColourScheme) sg.cs).setThreshold(threshold);
-            }
-            else if (sg.cs instanceof ScoreColourScheme)
-            {
-                ((ScoreColourScheme) sg.cs).setThreshold(threshold);
-            }
+           sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
             SliderPanel.showPIDSlider();
         }
         else // remove PIDColouring
         {
-            ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-            rcs.setThreshold(0);
-            sg.cs = rcs;
+            sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
         }
 
         refresh();
@@ -590,9 +648,18 @@ public class PopupMenu extends JPopupMenu
      */
     protected void userDefinedColour_actionPerformed(ActionEvent e)
     {
-        new UserDefinedColours(ap, getGroup());
-    }
-
+       SequenceGroup sg = getGroup();
+
+       if (e.getActionCommand().equals("User Defined..."))
+         new UserDefinedColours(ap, sg);
+       else
+       {
+         UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+             getUserColourSchemes().get(e.getActionCommand());
+
+         sg.cs = udc;
+       }
+     }
     /**
      * DOCUMENT ME!
      *
@@ -643,6 +710,8 @@ public class PopupMenu extends JPopupMenu
     protected void conservationMenuItem_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (conservationMenuItem.isSelected())
         {
@@ -653,17 +722,14 @@ public class PopupMenu extends JPopupMenu
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
 
-            ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-            sg.cs = ccs;
+            sg.cs.setConservation(c);
 
-            SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+            SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
             SliderPanel.showConservationSlider();
         }
         else // remove ConservationColouring
         {
-            ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
-            sg.cs = ccs.cs;
+            sg.cs.setConservation(null);
         }
 
         refresh();
@@ -724,9 +790,9 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup getGroup()
     {
         SequenceGroup sg = ap.av.getSelectionGroup();
-
-        // this method won't add a new group if it already exists
-        ap.av.alignment.addGroup(sg);
+      // this method won't add a new group if it already exists
+        if(sg!=null)
+          ap.av.alignment.addGroup(sg);
 
         return sg;
     }
@@ -738,7 +804,7 @@ public class PopupMenu extends JPopupMenu
      */
     void sequenceName_actionPerformed(ActionEvent e)
     {
-        String id = sequence.getName();
+        String id = sequence.getDisplayId(false, false);
         String s = (String) JOptionPane.showInternalInputDialog(ap,
                 "Edit sequence name",
                 "Edit sequence name (" + sequence.getName() + ")",
@@ -773,37 +839,6 @@ 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!
@@ -856,4 +891,22 @@ public class PopupMenu extends JPopupMenu
         getGroup().setColourText(showColourText.isSelected());
         refresh();
     }
+
+    public void showLink(String url)
+    {
+      try
+      {
+        jalview.util.BrowserLauncher.openURL(url);
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            "Unixers: Couldn't find default web browser."
+           +"\nAdd the full path to your browser in Preferences.",
+           "Web browser not found", JOptionPane.WARNING_MESSAGE );
+
+
+        ex.printStackTrace();
+      }
+    }
 }