JAL-2571 Corrected alignment width/height checks to visible only

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5f1fe73..dee921e 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1415,16 +1415,16 @@ public class Jalview2XML
       {
         jalview.datamodel.HiddenColumns hidden = av.getAlignment()
                 .getHiddenColumns();
-        if (hidden == null || hidden.getListOfCols() == null)
+        if (hidden == null || hidden.getHiddenRegions() == null)
         {
           warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
         }
         else
         {
-          for (int c = 0; c < hidden.getListOfCols()
+          for (int c = 0; c < hidden.getHiddenRegions()
                   .size(); c++)
           {
-            int[] region = hidden.getListOfCols()
+            int[] region = hidden.getHiddenRegions()
                     .get(c);
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
@@ -4464,7 +4464,7 @@ public class Jalview2XML
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
     af.viewport.getRanges().setStartRes(view.getStartRes());
-    af.viewport.getRanges().setStartSeq(view.getStartSeq());
+    // startSeq set in af.alignPanel.updateLayout below
     af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
     // apply colourschemes