JAL-2326 updated references of JOptionPane to JvOptionPane

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 672f7ac..7b751bf 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -71,6 +71,7 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
+import jalview.io.StructureFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.Blosum62ColourScheme;
@@ -108,6 +109,7 @@ import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.DataFlavor;
 import java.awt.datatransfer.StringSelection;
 import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
 import java.awt.dnd.DropTargetDragEvent;
 import java.awt.dnd.DropTargetDropEvent;
 import java.awt.dnd.DropTargetEvent;
@@ -668,6 +670,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           toggleHiddenRegions(toggleSeqs, toggleCols);
           break;
         }
+        case KeyEvent.VK_B:
+        {
+          boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
+          boolean modifyExisting = true; // always modify, don't clear
+                                         // evt.isShiftDown();
+          boolean invertHighlighted = evt.isAltDown();
+          avc.markHighlightedColumns(invertHighlighted, modifyExisting,
+                  toggleSel);
+          break;
+        }
         case KeyEvent.VK_PAGE_UP:
           if (viewport.getWrapAlignment())
           {
@@ -1116,14 +1128,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       currentFileFormat = chooser.getSelectedFormat();
       while (currentFileFormat == null)
       {
-        JOptionPane
+        JvOptionPane
                 .showInternalMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.select_file_format_before_saving"),
                         MessageManager
                                 .getString("label.file_format_not_specified"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         currentFileFormat = chooser.getSelectedFormat();
         value = chooser.showSaveDialog(this);
         if (value != JalviewFileChooser.APPROVE_OPTION)
@@ -1224,11 +1236,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!success)
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager
+      JvOptionPane.showInternalMessageDialog(this, MessageManager
               .formatMessage("label.couldnt_save_file",
                       new Object[] { fileName }), MessageManager
               .getString("label.error_saving_file"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
     }
 
     return success;
@@ -1243,8 +1255,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      JOptionPane.showInternalMessageDialog(this, warning, title,
-              JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showInternalMessageDialog(this, warning, title,
+              JvOptionPane.WARNING_MESSAGE);
     }
     return;
   }
@@ -1339,14 +1351,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HtmlSvgOutput(null, alignPanel);
+    HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
+    htmlSVG.exportHTML(null);
   }
 
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
-    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
-    bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+    bjs.exportHTML(null);
   }
 
   public void createImageMap(File file, String image)
@@ -2355,13 +2368,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .getAlignment().getWidth()) ? true : false;
       if (isEntireAlignWidth)
       {
-        int confirm = JOptionPane.showConfirmDialog(this,
+        int confirm = JvOptionPane.showConfirmDialog(this,
                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
-                JOptionPane.OK_CANCEL_OPTION);
+                JvOptionPane.OK_CANCEL_OPTION);
 
-        if (confirm == JOptionPane.CANCEL_OPTION
-                || confirm == JOptionPane.CLOSED_OPTION)
+        if (confirm == JvOptionPane.CANCEL_OPTION
+                || confirm == JvOptionPane.CLOSED_OPTION)
         {
           return;
         }
@@ -2906,8 +2919,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(
-              alignPanel.getSeqPanel().seqCanvas.searchResults, false);
+      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
     }
   }
 
@@ -3639,13 +3651,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-            int option = JOptionPane.showInternalConfirmDialog(
+            int option = JvOptionPane.showInternalConfirmDialog(
                     jalview.gui.Desktop.desktop, MessageManager
                             .getString("label.remove_from_default_list"),
                     MessageManager
                             .getString("label.remove_user_defined_colour"),
-                    JOptionPane.YES_NO_OPTION);
-            if (option == JOptionPane.YES_OPTION)
+                    JvOptionPane.YES_NO_OPTION);
+            if (option == JvOptionPane.YES_OPTION)
             {
               jalview.gui.UserDefinedColours
                       .removeColourFromDefaults(radioItem.getText());
@@ -3793,10 +3805,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if ((viewport.getSelectionGroup() == null)
             || (viewport.getSelectionGroup().getSize() < 2))
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager
+      JvOptionPane.showInternalMessageDialog(this, MessageManager
               .getString("label.you_must_select_least_two_sequences"),
               MessageManager.getString("label.invalid_selection"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -3822,14 +3834,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getSelectionGroup().getSize() > 0))
             || (viewport.getAlignment().getHeight() < 4))
     {
-      JOptionPane
+      JvOptionPane
               .showInternalMessageDialog(
                       this,
                       MessageManager
                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
                       MessageManager
                               .getString("label.sequence_selection_insufficient"),
-                      JOptionPane.WARNING_MESSAGE);
+                      JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -3927,14 +3939,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
                         MessageManager
                                 .getString("label.not_enough_sequences"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         return;
       }
 
@@ -3945,14 +3957,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (_s.getLength() < sg.getEndRes())
         {
-          JOptionPane
+          JvOptionPane
                   .showMessageDialog(
                           Desktop.desktop,
                           MessageManager
                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
                           MessageManager
                                   .getString("label.sequences_selection_not_aligned"),
-                          JOptionPane.WARNING_MESSAGE);
+                          JvOptionPane.WARNING_MESSAGE);
 
           return;
         }
@@ -3966,14 +3978,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // are the visible sequences aligned?
       if (!viewport.getAlignment().isAligned(false))
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
                         MessageManager
                                 .getString("label.sequences_not_aligned"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
 
         return;
       }
@@ -4238,11 +4250,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() == 1)
     {
-      int option = JOptionPane.showConfirmDialog(this,
+      int option = JvOptionPane.showConfirmDialog(this,
               MessageManager.getString("warn.oneseq_msainput_selection"),
               MessageManager.getString("label.invalid_selection"),
-              JOptionPane.OK_CANCEL_OPTION);
-      if (option == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION);
+      if (option == JvOptionPane.OK_OPTION)
       {
         msa = viewport.getAlignmentView(false);
       }
@@ -4318,21 +4330,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       } catch (Exception ex)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         ex.getMessage(),
                         MessageManager
                                 .getString("label.problem_reading_tree_file"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
       if (fin != null && fin.hasWarningMessage())
       {
-        JOptionPane.showMessageDialog(Desktop.desktop, fin
+        JvOptionPane.showMessageDialog(Desktop.desktop, fin
                 .getWarningMessage(), MessageManager
                 .getString("label.possible_problem_with_tree_file"),
-                JOptionPane.WARNING_MESSAGE);
+                JvOptionPane.WARNING_MESSAGE);
       }
     }
   }
@@ -4717,8 +4729,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("label.translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
-              JOptionPane.ERROR_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+              JvOptionPane.ERROR_MESSAGE);
       return;
     }
     if (al == null || al.getHeight() == 0)
@@ -4727,8 +4739,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
       final String errorTitle = MessageManager
               .getString("label.translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
-              JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+              JvOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -4814,6 +4826,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void drop(DropTargetDropEvent evt)
   {
+    // JAL-1552 - acceptDrop required before getTransferable call for
+    // Java's Transferable for native dnd
+    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
 
@@ -4881,7 +4896,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (type != null)
               {
-                if (type.equalsIgnoreCase("PDB"))
+                if (StructureFile.isStructureFile(type))
                 {
                   filesmatched.add(new Object[] { file, protocol, mtch });
                   continue;
@@ -4896,20 +4911,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (filesmatched.size() > 0)
         {
           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                  || JOptionPane
+                  || JvOptionPane
                           .showConfirmDialog(
                                   this,
                                   MessageManager
                                           .formatMessage(
-                                                  "label.automatically_associate_pdb_files_with_sequences_same_name",
+                                                  "label.automatically_associate_structure_files_with_sequences_same_name",
                                                   new Object[] { Integer
                                                           .valueOf(
                                                                   filesmatched
                                                                           .size())
                                                           .toString() }),
                                   MessageManager
-                                          .getString("label.automatically_associate_pdb_files_by_name"),
-                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+                                          .getString("label.automatically_associate_structure_files_by_name"),
+                                  JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
 
           {
             for (Object[] fm : filesmatched)
@@ -4939,7 +4954,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           if (assocfiles > 0
                   && (Cache.getDefault(
-                          "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+                          "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
                           .showConfirmDialog(
                                   this,
                                   "<html>"
@@ -4954,7 +4969,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                           + "</html>",
                                   MessageManager
                                           .getString("label.ignore_unmatched_dropped_files"),
-                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+                                  JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
           {
             return;
           }
@@ -5019,7 +5034,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               // some problem - if no warning its probable that the ID matching
               // process didn't work
-              JOptionPane
+              JvOptionPane
                       .showMessageDialog(
                               Desktop.desktop,
                               tcf.getWarningMessage() == null ? MessageManager
@@ -5027,7 +5042,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                       : tcf.getWarningMessage(),
                               MessageManager
                                       .getString("label.problem_reading_tcoffee_score_file"),
-                              JOptionPane.WARNING_MESSAGE);
+                              JvOptionPane.WARNING_MESSAGE);
             }
           }
           else
@@ -5148,8 +5163,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (e.isPopupTrigger())
     {
       String msg = MessageManager.getString("label.enter_view_name");
-      String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
-              JOptionPane.QUESTION_MESSAGE);
+      String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
+              JvOptionPane.QUESTION_MESSAGE);
 
       if (reply != null)
       {
@@ -5888,12 +5903,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       } catch (Exception ex)
       {
         System.err.println((ex.toString()));
-        JOptionPane
+        JvOptionPane
                 .showInternalMessageDialog(Desktop.desktop, MessageManager
                         .getString("label.couldnt_run_groovy_script"),
                         MessageManager
                                 .getString("label.groovy_support_failed"),
-                        JOptionPane.ERROR_MESSAGE);
+                        JvOptionPane.ERROR_MESSAGE);
       }
     }
     else
@@ -5926,6 +5941,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return false;
   }
+
+  @Override
+  protected void selectHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // include key modifier check in case user selects from menu
+    avc.markHighlightedColumns(
+            (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
+            true,
+            (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
+  }
 }
 
 class PrintThread extends Thread