JAL-2322 Refactored unified architecture for data + html exporting for SVG & BioJS...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1848595..1372749 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;
@@ -1339,14 +1341,15 @@ 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)
@@ -2977,9 +2980,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.getColumnSelection() != null
-              && viewport.getColumnSelection().getSelected() != null && viewport
-              .getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns()
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -3007,8 +3008,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         hideSelSequences_actionPerformed(null);
         hide = true;
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
-              .size() > 0))
+      else if (!(toggleCols && viewport.hasSelectedColumns()))
       {
         showAllSeqs_actionPerformed(null);
       }
@@ -3016,7 +3016,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (toggleCols)
     {
-      if (viewport.getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns())
       {
         hideSelColumns_actionPerformed(null);
         if (!toggleSeqs)
@@ -3643,8 +3643,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
             int option = JOptionPane.showInternalConfirmDialog(
-                    jalview.gui.Desktop.desktop,
-                    MessageManager
+                    jalview.gui.Desktop.desktop, MessageManager
                             .getString("label.remove_from_default_list"),
                     MessageManager
                             .getString("label.remove_user_defined_colour"),
@@ -4818,6 +4817,9 @@ 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>();
 
@@ -4885,7 +4887,7 @@ 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;
@@ -4905,14 +4907,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   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"),
+                                          .getString("label.automatically_associate_structure_files_by_name"),
                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
 
           {