X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=6a637e301cb412c66d05e19401969e891e325fa7;hb=cb826506dcdac81d5299be92bc81f67118cfdf9f;hp=e8b865b03ae70d21df6d48054f94c70359367202;hpb=f269ceeb37293f592c4916dd91cff9c4fdd3f874;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e8b865b..6a637e3 100644
--- 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;
@@ -669,6 +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())
           {
@@ -1340,14 +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(null);
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+    bjs.exportHTML(null);
   }
 
   public void createImageMap(File file, String image)
@@ -2907,8 +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);
     }
   }
 
@@ -4885,8 +4896,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (type != null)
               {
-                if (type.equalsIgnoreCase("PDB")
-                        || type.equalsIgnoreCase("mmCIF"))
+                if (StructureFile.isStructureFile(type))
                 {
                   filesmatched.add(new Object[] { file, protocol, mtch });
                   continue;
@@ -5931,6 +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