X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3145f7cab016d3cf217339c443b0629bd678f0f8;hb=60541afc96ff3a4f5b79b78009922f373cbc29c3;hp=702773b6af1cf47e727f2a63bb6877513f20580c;hpb=383fd91269f510b189450fbe174e9c051103c7eb;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 702773b..3145f7c 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,6 +38,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
@@ -50,9 +51,11 @@ import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 
+import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -71,11 +74,14 @@ import java.util.Vector;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
 
 /**
  * The popup menu that is displayed on right-click on a sequence id, or in the
@@ -298,10 +304,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   {
     try
     {
-      jalview.util.BrowserLauncher.openURL(url);
+      Platform.openURL(url);
     } catch (Exception ex)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager.getString("label.web_browser_not_found_unix"),
               MessageManager.getString("label.web_browser_not_found"),
               JvOptionPane.WARNING_MESSAGE);
@@ -311,7 +317,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   }
 
   /**
-   * add a late bound groupURL item to the given linkMenu
+   * For the popup menu on the idPanel.
+   * 
+   * Add a late bound groupURL item to the given linkMenu
    * 
    * @param linkMenu
    * @param label
@@ -343,6 +351,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
           {
             try
             {
+              // Object[] { int[] { number of matches seqs },
+              // boolean[] { which matched },
+              // StringBuffer[] { segment generated from inputs },
+              // String[] { url }
+              // }
+
+              // TODO bug: urlstub is { int[], boolean[] } but constructFrom
+              // requires something else.
+
               showLink(urlgenerator.constructFrom(urlstub));
             } catch (UrlStringTooLongException e2)
             {
@@ -382,6 +399,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    *          non-positional features if in the Id panel, features at the
    *          clicked residue if in the sequence panel
    * @param groupLinks
+   *          not implemented -- empty list
    */
   public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
           List<SequenceFeature> features, List<String> groupLinks)
@@ -652,6 +670,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       // add any groupURLs to the groupURL submenu and make it visible
       if (groupLinks != null && groupLinks.size() > 0)
       {
+        // not implemented -- empty list
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
@@ -784,13 +803,38 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    */
   protected void showFeatureDetails(SequenceFeature sf)
   {
-    CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
-    // it appears Java's CSS does not support border-collaps :-(
-    cap.addStylesheetRule("table { border-collapse: collapse;}");
-    cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
-    cap.setText(sf.getDetailsReport());
-
-    Desktop.addInternalFrame(cap,
+    JInternalFrame details;
+    if (Platform.isJS())
+    {
+      details = new JInternalFrame();
+      JPanel panel = new JPanel(new BorderLayout());
+      panel.setOpaque(true);
+      panel.setBackground(Color.white);
+      // TODO JAL-3026 set style of table correctly for feature details
+      JLabel reprt = new JLabel(MessageManager
+              .formatMessage("label.html_content", new Object[]
+              { sf.getDetailsReport() }));
+      reprt.setBackground(Color.WHITE);
+      reprt.setOpaque(true);
+      panel.add(reprt, BorderLayout.CENTER);
+      details.setContentPane(panel);
+      details.pack();
+    }
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+      // it appears Java's CSS does not support border-collaps :-(
+      cap.addStylesheetRule("table { border-collapse: collapse;}");
+      cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
+      cap.setText(sf.getDetailsReport());
+      details = cap;
+    }
+    Desktop.addInternalFrame(details,
             MessageManager.getString("label.feature_details"), 500, 500);
   }
 
@@ -952,6 +996,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     showOrHideMenu.add(item);
   }
 
+  /**
+   *
+   * @param sg
+   * @param groupLinks
+   *          not implemented -- empty list
+   */
   private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
   {
 
@@ -983,12 +1033,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       {
         sqi = sqi.getDatasetSequence();
       }
-      DBRefEntry[] dbr = sqi.getDBRefs();
-      if (dbr != null && dbr.length > 0)
+      List<DBRefEntry> dbr = sqi.getDBRefs();
+      int nd;
+      if (dbr != null && (nd = dbr.size()) > 0)
       {
-        for (int d = 0; d < dbr.length; d++)
+        for (int d = 0; d < nd; d++)
         {
-          String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          DBRefEntry e = dbr.get(d);
+          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
           Object[] sarray = commonDbrefs.get(src);
           if (sarray == null)
           {
@@ -1001,19 +1053,25 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
           if (((String[]) sarray[1])[sq] == null)
           {
-            if (!dbr[d].hasMap() || (dbr[d].getMap()
+            if (!e.hasMap() || (e.getMap()
                     .locateMappedRange(start, end) != null))
             {
-              ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+              ((String[]) sarray[1])[sq] = e.getAccessionId();
               ((int[]) sarray[0])[0]++;
             }
           }
         }
       }
     }
+    if (groupLinks.size() == 0)
+    {
+      return;
+    }
     // now create group links for all distinct ID/sequence sets.
     boolean addMenu = false; // indicates if there are any group links to give
                              // to user
+
+    // not implmeented -- empty list
     for (String link : groupLinks)
     {
       GroupUrlLink urlLink = null;
@@ -1066,6 +1124,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       {
         urlset = urlLink.makeUrlStubs(ids, seqstr,
                 "FromJalview" + System.currentTimeMillis(), false);
+        // { int[], boolean[] } only here
       } catch (UrlStringTooLongException e)
       {
       }
@@ -1094,7 +1153,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
           groupLinksMenu.add(linkMenus[m]);
         }
       }
-
       groupMenu.add(groupLinksMenu);
     }
   }
@@ -1323,7 +1381,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        editSequence_actionPerformed(actionEvent);
+        editSequence_actionPerformed();
       }
     });
     makeReferenceSeq.setText(
@@ -1671,8 +1729,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   public void createSequenceDetailsReport(SequenceI[] sequences)
   {
-    CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
     StringBuilder contents = new StringBuilder(128);
+    contents.append("<html><body>");
     for (SequenceI seq : sequences)
     {
       contents.append("<p><h2>" + MessageManager.formatMessage(
@@ -1683,9 +1741,35 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
       contents.append("</p>");
     }
-    cap.setText("<html>" + contents.toString() + "</html>");
+    contents.append("</body></html>");
+    String report = contents.toString();
+
+    JInternalFrame frame;
+    if (Platform.isJS())
+    {
+      JLabel textLabel = new JLabel();
+      textLabel.setText(report);
+      textLabel.setBackground(Color.WHITE);
+      JPanel pane = new JPanel(new BorderLayout());
+      pane.setOpaque(true);
+      pane.setBackground(Color.WHITE);
+      pane.add(textLabel, BorderLayout.NORTH);
+      frame = new JInternalFrame();
+      frame.getContentPane().add(new JScrollPane(pane));
+    }
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+      cap.setText(report);
+      frame = cap;
+    }
 
-    Desktop.addInternalFrame(cap,
+    Desktop.addInternalFrame(frame,
             MessageManager.formatMessage("label.sequence_details_for",
                     (sequences.length == 1 ? new Object[]
                     { sequences[0].getDisplayId(true) }
@@ -1693,7 +1777,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                             { MessageManager
                                     .getString("label.selection") })),
             500, 400);
-
   }
 
   protected void showNonconserved_actionPerformed()
@@ -1812,30 +1895,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Shows a dialog where group name and description may be edited
    */
   protected void groupName_actionPerformed()
   {
-
     SequenceGroup sg = getGroup();
     EditNameDialog dialog = new EditNameDialog(sg.getName(),
             sg.getDescription(),
-            "       " + MessageManager.getString("label.group_name") + " ",
-            MessageManager.getString("label.group_description") + " ",
+            MessageManager.getString("label.group_name"),
+            MessageManager.getString("label.group_description"));
+    dialog.showDialog(ap.alignFrame,
             MessageManager.getString("label.edit_group_name_description"),
-            ap.alignFrame);
-
-    if (!dialog.accept)
-    {
-      return;
-    }
-
-    sg.setName(dialog.getName());
-    sg.setDescription(dialog.getDescription());
-    refresh();
+            new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                sg.setName(dialog.getName());
+                sg.setDescription(dialog.getDescription());
+                refresh();
+              }
+            });
   }
 
   /**
@@ -1856,48 +1936,41 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Shows a dialog where sequence name and description may be edited
    */
   void sequenceName_actionPerformed()
   {
     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
             sequence.getDescription(),
-            "       " + MessageManager.getString("label.sequence_name")
-                    + " ",
-            MessageManager.getString("label.sequence_description") + " ",
+            MessageManager.getString("label.sequence_name"),
+            MessageManager.getString("label.sequence_description"));
+    dialog.showDialog(ap.alignFrame,
             MessageManager.getString(
                     "label.edit_sequence_name_description"),
-            ap.alignFrame);
-
-    if (!dialog.accept)
-    {
-      return;
-    }
-
-    if (dialog.getName() != null)
-    {
-      if (dialog.getName().indexOf(" ") > -1)
-      {
-        JvOptionPane.showMessageDialog(ap,
-                MessageManager
-                        .getString("label.spaces_converted_to_backslashes"),
-                MessageManager
-                        .getString("label.no_spaces_allowed_sequence_name"),
-                JvOptionPane.WARNING_MESSAGE);
-      }
-
-      sequence.setName(dialog.getName().replace(' ', '_'));
-      ap.paintAlignment(false, false);
-    }
-
-    sequence.setDescription(dialog.getDescription());
-
-    ap.av.firePropertyChange("alignment", null,
-            ap.av.getAlignment().getSequences());
-
+            new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                if (dialog.getName() != null)
+                {
+                  if (dialog.getName().indexOf(" ") > -1)
+                  {
+                    JvOptionPane.showMessageDialog(ap,
+                            MessageManager.getString(
+                                    "label.spaces_converted_to_underscores"),
+                            MessageManager.getString(
+                                    "label.no_spaces_allowed_sequence_name"),
+                            JvOptionPane.WARNING_MESSAGE);
+                  }
+                  sequence.setName(dialog.getName().replace(' ', '_'));
+                  ap.paintAlignment(false, false);
+                }
+                sequence.setDescription(dialog.getDescription());
+                ap.av.firePropertyChange("alignment", null,
+                        ap.av.getAlignment().getSequences());
+              }
+            });
   }
 
   /**
@@ -1922,24 +1995,23 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Offers a colour chooser and sets the selected colour as the group outline
    */
   protected void outline_actionPerformed()
   {
-    SequenceGroup sg = getGroup();
-    Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_outline_colour"),
-            Color.BLUE);
-
-    if (col != null)
+    String title = MessageManager
+            .getString("label.select_outline_colour");
+    ColourChooserListener listener = new ColourChooserListener()
     {
-      sg.setOutlineColour(col);
-    }
-
-    refresh();
+      @Override
+      public void colourSelected(Color c)
+      {
+        getGroup().setOutlineColour(c);
+        refresh();
+      };
+    };
+    JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
+            title, Color.BLUE, listener);
   }
 
   /**
@@ -1985,12 +2057,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   public void copy_actionPerformed()
   {
-    ap.alignFrame.copy_actionPerformed(null);
+    ap.alignFrame.copy_actionPerformed();
   }
 
   public void cut_actionPerformed()
   {
-    ap.alignFrame.cut_actionPerformed(null);
+    ap.alignFrame.cut_actionPerformed();
   }
 
   void changeCase(ActionEvent e)
@@ -2086,13 +2158,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      */
     if (!seqs.isEmpty())
     {
-      if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-              .amendFeatures(seqs, features, true, ap))
-      {
-        ap.alignFrame.setShowSeqFeatures(true);
-        ap.av.setSearchResults(null); // clear highlighting
-        ap.repaint(); // draw new/amended features
-      }
+      new FeatureEditor(ap, seqs, features, true).showDialog();
     }
   }
 
@@ -2124,7 +2190,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   }
 
-  public void editSequence_actionPerformed(ActionEvent actionEvent)
+  /**
+   * Shows a dialog where sequence characters may be edited. Any changes are
+   * applied, and added as an available 'Undo' item in the edit commands
+   * history.
+   */
+  public void editSequence_actionPerformed()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
 
@@ -2138,24 +2209,28 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       EditNameDialog dialog = new EditNameDialog(
               sequence.getSequenceAsString(sg.getStartRes(),
                       sg.getEndRes() + 1),
-              null, MessageManager.getString("label.edit_sequence"), null,
+              null, MessageManager.getString("label.edit_sequence"), null);
+      dialog.showDialog(ap.alignFrame,
               MessageManager.getString("label.edit_sequence"),
-              ap.alignFrame);
-
-      if (dialog.accept)
-      {
-        EditCommand editCommand = new EditCommand(
-                MessageManager.getString("label.edit_sequences"),
-                Action.REPLACE,
-                dialog.getName().replace(' ', ap.av.getGapCharacter()),
-                sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
-                sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
-
-        ap.alignFrame.addHistoryItem(editCommand);
-
-        ap.av.firePropertyChange("alignment", null,
-                ap.av.getAlignment().getSequences());
-      }
+              new Runnable()
+              {
+                @Override
+                public void run()
+                {
+                  EditCommand editCommand = new EditCommand(
+                          MessageManager.getString("label.edit_sequences"),
+                          Action.REPLACE,
+                          dialog.getName().replace(' ',
+                                  ap.av.getGapCharacter()),
+                          sg.getSequencesAsArray(
+                                  ap.av.getHiddenRepSequences()),
+                          sg.getStartRes(), sg.getEndRes() + 1,
+                          ap.av.getAlignment());
+                  ap.alignFrame.addHistoryItem(editCommand);
+                  ap.av.firePropertyChange("alignment", null,
+                          ap.av.getAlignment().getSequences());
+                }
+              });
     }
   }