Updates checkboxes on load

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e787b48..addba63 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -626,16 +626,24 @@ public class Jalview2XML
     af.viewport.showQuality = view.getShowQuality();\r
     af.viewport.showIdentity = view.getShowIdentity();\r
     af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
+    af.abovePIDThreshold.setSelected(view.getPidSelected());\r
     af.viewport.setColourText(view.getShowColourText());\r
+    af.colourTextMenuItem.setSelected(view.getShowColourText());\r
     af.viewport.setConservationSelected(view.getConservationSelected());\r
+    af.conservationMenuItem.setSelected(view.getConservationSelected());\r
+\r
     af.viewport.setShowFullId(view.getShowFullId());\r
+    af.fullSeqId.setSelected(view.getShowFullId());\r
+\r
     af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
                                           view.getFontStyle(), view.getFontSize()));\r
     af.alignPanel.fontChanged();\r
 \r
     af.viewport.setRenderGaps(view.getRenderGaps());\r
+    af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 \r
     af.viewport.setWrapAlignment(view.getWrapAlignment());\r
+    af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 \r
     if (view.getWrapAlignment())\r
     {\r
@@ -648,7 +656,9 @@ public class Jalview2XML
     }\r
 \r
     af.viewport.setShowBoxes(view.getShowBoxes());\r
+    af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
     af.viewport.setShowText(view.getShowText());\r
+    af.viewTextMenuItem.setSelected(view.getShowText());\r
 \r
     ColourSchemeI cs = null;\r
 \r
@@ -687,8 +697,8 @@ public class Jalview2XML
     if (view.getShowSequenceFeatures())\r
     {\r
       af.viewport.showSequenceFeatures = true;\r
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,\r
-          af.alignPanel);\r
+      af.sequenceFeatures.setSelected(true);\r
+      new SequenceFeatureFetcher(al, af.alignPanel);\r
        al.featuresAdded = true;\r
     }\r
 \r