Merge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4805d6b..5599695 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -157,7 +157,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
 
-    annotationPanelMenuItem.setState(viewport.showAnnotation);
+    annotationPanelMenuItem.setState(viewport.isShowAnnotation());
     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
     followMouseOverFlag.setState(viewport.getFollowHighlight());
     showGroupConsensus.setState(viewport.isShowGroupConsensus());
@@ -167,7 +167,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 
-    seqLimits.setState(viewport.showJVSuffix);
+    seqLimits.setState(viewport.getShowJVSuffix());
 
     if (applet != null)
     {
@@ -498,7 +498,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     case KeyEvent.VK_PAGE_UP:
-      if (viewport.wrapAlignment)
+      if (viewport.getWrapAlignment())
       {
         alignPanel.scrollUp(true);
       }
@@ -510,7 +510,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       break;
 
     case KeyEvent.VK_PAGE_DOWN:
-      if (viewport.wrapAlignment)
+      if (viewport.getWrapAlignment())
       {
         alignPanel.scrollUp(false);
       }
@@ -1185,7 +1185,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             { e.getActionCommand() }), 600, 500);
     cap.setText(new AppletFormatAdapter().formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
-            viewport.showJVSuffix));
+            viewport.getShowJVSuffix()));
   }
 
   public void loadAnnotations()
@@ -2348,7 +2348,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   protected void displayNonconservedMenuItem_actionPerformed()
   {
-    viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+    viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
     alignPanel.paintAlignment(true);
   }