JAL-1976 Added progress indicators for HTML_SVG and BioJS export operations

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d20d62e..a616dc0 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1369,7 +1369,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
-    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
   }
 
@@ -2547,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
-    if (colSel.size() > 0)
+    if (!colSel.isEmpty())
     {
       if (trimLeft)
       {
@@ -2966,6 +2966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.showAllHiddenColumns();
     repaint();
+    viewport.sendSelection();
   }
 
   @Override
@@ -3056,6 +3057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
     toggleHiddenRegions(false, false);
+    viewport.sendSelection();
   }
 
   /*
@@ -3073,6 +3075,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   /*
@@ -3088,6 +3091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.showAllHiddenColumns();
     viewport.showAllHiddenSeqs();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
@@ -3095,6 +3099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
@@ -5531,8 +5536,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           @Override
           public void run()
           {
+            boolean isNuclueotide = alignPanel.alignFrame
+                    .getViewport().getAlignment()
+                    .isNucleotide();
             new jalview.ws.DBRefFetcher(alignPanel.av
-                    .getSequenceSelection(), alignPanel.alignFrame)
+                    .getSequenceSelection(),
+                    alignPanel.alignFrame, null,
+                    alignPanel.alignFrame.featureSettings,
+                    isNuclueotide)
                     .fetchDBRefs(false);
           }
         }).start();
@@ -5601,9 +5612,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
+                        boolean isNuclueotide = alignPanel.alignFrame
+                                .getViewport().getAlignment()
+                                .isNucleotide();
                         new jalview.ws.DBRefFetcher(alignPanel.av
                                 .getSequenceSelection(),
-                                alignPanel.alignFrame, dassource)
+                                alignPanel.alignFrame, dassource,
+                                alignPanel.alignFrame.featureSettings,
+                                isNuclueotide)
                                 .fetchDBRefs(false);
                       }
                     }).start();
@@ -5637,9 +5653,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
+                        boolean isNuclueotide = alignPanel.alignFrame
+                                .getViewport().getAlignment()
+                                .isNucleotide();
                         new jalview.ws.DBRefFetcher(alignPanel.av
                                 .getSequenceSelection(),
-                                alignPanel.alignFrame, dassource)
+                                alignPanel.alignFrame, dassource,
+                                alignPanel.alignFrame.featureSettings,
+                                isNuclueotide)
                                 .fetchDBRefs(false);
                       }
                     }).start();
@@ -5688,9 +5709,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         @Override
                         public void run()
                         {
+                          boolean isNuclueotide = alignPanel.alignFrame
+                                  .getViewport().getAlignment()
+                                  .isNucleotide();
                           new jalview.ws.DBRefFetcher(alignPanel.av
                                   .getSequenceSelection(),
-                                  alignPanel.alignFrame, dassrc)
+                                  alignPanel.alignFrame, dassrc,
+                                  alignPanel.alignFrame.featureSettings,
+                                  isNuclueotide)
                                   .fetchDBRefs(false);
                         }
                       }).start();