JAL-1641 updated applet version

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5c8135d..1b1a5b8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -103,6 +103,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
@@ -197,7 +198,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.updateConsensus(alignPanel);
 
     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
-    followMouseOverFlag.setState(viewport.getFollowHighlight());
+    followMouseOverFlag.setState(viewport.isFollowHighlight());
     showGroupConsensus.setState(viewport.isShowGroupConsensus());
     showGroupConservation.setState(viewport.isShowGroupConservation());
     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
@@ -926,7 +927,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   private void mouseOverFlag_stateChanged()
   {
-    viewport.followHighlight = followMouseOverFlag.getState();
+    viewport.setFollowHighlight(followMouseOverFlag.getState());
     // TODO: could kick the scrollTo mechanism to reset view for current
     // searchresults.
   }
@@ -1312,7 +1313,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(
+
+    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+    viewport.setFeatureRenderer(fr);
+    viewport.setIncludeHiddenRegion(false);
+    cap.setText(new AppletFormatAdapter(viewport).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
@@ -1594,7 +1599,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.addToRedoList(command);
     command.undoCommand(null);
 
-    AlignViewport originalSource = getOriginatingSource(command);
+    AlignmentViewport originalSource = getOriginatingSource(command);
     // JBPNote Test
     if (originalSource != viewport)
     {
@@ -1626,7 +1631,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.addToHistoryList(command);
     command.doCommand(null);
 
-    AlignViewport originalSource = getOriginatingSource(command);
+    AlignmentViewport originalSource = getOriginatingSource(command);
     // JBPNote Test
     if (originalSource != viewport)
     {
@@ -1642,9 +1647,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getAlignment().getSequences());
   }
 
-  AlignViewport getOriginatingSource(CommandI command)
+  AlignmentViewport getOriginatingSource(CommandI command)
   {
-    AlignViewport originalSource = null;
+    AlignmentViewport originalSource = null;
     // For sequence removal and addition, we need to fire
     // the property change event FROM the viewport where the
     // original alignment was altered
@@ -2541,7 +2546,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
-  void changeColour(ColourSchemeI cs)
+  public void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;
 
@@ -4177,4 +4182,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     this.splitFrame = sf;
   }
+
+  @Override
+  public void setShowSeqFeatures(boolean b)
+  {
+    this.sequenceFeatures.setState(b);
+    viewport.setShowSequenceFeatures(b);
+  }
+
+  @Override
+  public void setMenusForViewport()
+  {
+    // setMenusFromViewport(viewport);
+
+  }
+
+  @Override
+  public void hideColumns(List<int[]> colsToHide)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void syncHiddenSequences()
+  {
+    // TODO Auto-generated method stub
+
+  }
 }