X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=480b1959d49250a5db6c3130ba530e43a1fd7b64;hb=c5aa740f1fff4c8caee4ccf0c0e0de517ca4dcb8;hp=705d4078ca133e7f3ab73e8a7ec60796521ed0be;hpb=5fbe7c141f482121b3f7f04570ab84bf6203ebf6;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 705d407..480b195 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.*;
 
@@ -33,6 +32,8 @@ import java.awt.event.*;
 
 import javax.swing.*;
 
+import java.util.Vector;
+
 
 /**
  * DOCUMENT ME!
@@ -63,21 +64,26 @@ 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();
     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
-    /**
+  JMenu editMenu = new JMenu();
+  JMenuItem cut = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem upperCase = new JMenuItem();
+  JMenuItem lowerCase = new JMenuItem();
+  JMenuItem toggle = new JMenuItem();
+
+  /**
      * Creates a new PopupMenu object.
      *
      * @param ap DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public PopupMenu(AlignmentPanel ap, Sequence seq)
+    public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
     {
         ///////////////////////////////////////////////////////////
         // If this is activated from the sequence panel, the user may want to
@@ -112,11 +118,59 @@ 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)
@@ -172,7 +226,7 @@ public class PopupMenu extends JPopupMenu
                 noColourmenuItem.setSelected(true);
             }
 
-            if (sg.cs instanceof ConservationColourScheme)
+            if (sg.cs!=null && sg.cs.conservationApplied())
             {
                 conservationMenuItem.setSelected(true);
             }
@@ -181,6 +235,11 @@ public class PopupMenu extends JPopupMenu
             showColourText.setSelected(sg.getColourText());
             showBoxes.setSelected(sg.getDisplayBoxes());
         }
+        else
+        {
+          groupMenu.setVisible(false);
+          editMenu.setVisible(false);
+        }
 
         if (!ap.av.alignment.getGroups().contains(sg))
         {
@@ -195,8 +254,48 @@ public class PopupMenu extends JPopupMenu
         {
             sequenceMenu.setVisible(false);
         }
+
+        if(links != null && links.size()>0)
+        {
+          JMenu linkMenu = new JMenu("Link");
+          JMenuItem item;
+          for(int i=0; i<links.size(); i++)
+          {
+            String link = links.elementAt(i).toString();
+            final String label = link.substring(0, link.indexOf("|"));
+            item = new JMenuItem(label);
+            final String url;
+
+            if (link.indexOf("$SEQUENCE_ID$") > -1)
+            {
+              String id = seq.getName();
+              if (id.indexOf("|") > -1)
+                id = id.substring(id.lastIndexOf("|") + 1);
+
+              url = link.substring(link.indexOf("|") + 1,
+                                   link.indexOf("$SEQUENCE_ID$"))
+                  + id +
+                  link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            }
+            else
+              url = link.substring(link.lastIndexOf("|")+1);
+
+
+            item.addActionListener(new java.awt.event.ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    showLink(url);
+                }
+            });
+
+            linkMenu.add(item);
+          }
+          add(linkMenu);
+        }
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -205,7 +304,7 @@ public class PopupMenu extends JPopupMenu
     private void jbInit() throws Exception
     {
         groupMenu.setText("Group");
-        groupMenu.setText("Define");
+        groupMenu.setText("Group");
         groupName.setText("Name");
         groupName.addActionListener(new java.awt.event.ActionListener()
             {
@@ -215,7 +314,7 @@ 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)
@@ -232,14 +331,7 @@ 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()
             {
@@ -283,9 +375,51 @@ public class PopupMenu extends JPopupMenu
                     showColourText_actionPerformed(e);
                 }
             });
-        add(groupMenu);
+    editMenu.setText("Edit");
+    cut.setText("Cut");
+    cut.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    upperCase.setText("To Upper Case");
+    upperCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        upperCase_actionPerformed(e);
+      }
+    });
+    copy.setText("Copy");
+    copy.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+    lowerCase.setText("To Lower Case");
+    lowerCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        lowerCase_actionPerformed(e);
+      }
+    });
+    toggle.setText("Toggle Case");
+    toggle.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        toggle_actionPerformed(e);
+      }
+    });
+    add(groupMenu);
         add(sequenceMenu);
-        groupMenu.add(groupName);
+    this.add(editMenu);
+    groupMenu.add(groupName);
         groupMenu.addSeparator();
         groupMenu.add(unGroupMenuItem);
         groupMenu.add(colourMenu);
@@ -296,7 +430,6 @@ 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);
@@ -310,10 +443,37 @@ 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);
-        noColourmenuItem.setText("None");
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
+    noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -394,7 +554,7 @@ 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)
@@ -433,16 +593,9 @@ public class PopupMenu extends JPopupMenu
      */
     void refresh()
     {
-        SequenceGroup sg = getGroup();
-        if(sg!=null)
-        {
-          SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
+        if (ap.overviewPanel != null)
+          ap.overviewPanel.updateOverviewImage();
 
-          if (superG != null)
-          {
-            superG.setSuperGroupProperties(sg);
-          }
-        }
         ap.seqPanel.repaint();
     }
 
@@ -555,6 +708,8 @@ public class PopupMenu extends JPopupMenu
     protected void abovePIDColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (abovePIDColour.isSelected())
         {
@@ -564,22 +719,13 @@ 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();
@@ -592,9 +738,18 @@ 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!
      *
@@ -645,6 +800,8 @@ public class PopupMenu extends JPopupMenu
     protected void conservationMenuItem_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (conservationMenuItem.isSelected())
         {
@@ -655,17 +812,14 @@ 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();
@@ -740,11 +894,34 @@ 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)
         {
@@ -757,9 +934,13 @@ 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());
     }
 
     /**
@@ -775,37 +956,6 @@ 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!
@@ -858,4 +1008,101 @@ 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();
+      }
+    }
+
+    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();
+    }
+
+  public void copy_actionPerformed(ActionEvent e)
+  {
+    ap.alignFrame.copy_actionPerformed(null);
+  }
+
+  public void cut_actionPerformed(ActionEvent e)
+  {
+    ap.alignFrame.cut_actionPerformed(null);
+  }
+
+  public void upperCase_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    for(int g=0; g<sg.getSize(); g++)
+    {
+      sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
+    }
+    ap.repaint();
+  }
+
+  public void lowerCase_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    for(int g=0; g<sg.getSize(); g++)
+    {
+      sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
+    }
+    ap.repaint();
+  }
+
+  public void toggle_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null)
+      return;
+
+    for (int g = 0; g < sg.getSize(); g++)
+    {
+      sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
+    }
+
+    ap.repaint();
+  }
+
 }