JAL-3026 Java bug associated with File/String mods

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..81816aa 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -52,7 +52,6 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
@@ -1450,9 +1449,10 @@ public class Jalview2XML
         }
         else
         {
-          ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
-          for (int[] region : hiddenRegions)
+          Iterator<int[]> hiddenRegions = hidden.iterator();
+          while (hiddenRegions.hasNext())
           {
+            int[] region = hiddenRegions.next();
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -2677,6 +2677,7 @@ public class Jalview2XML
     if (errorMessage != null)
     {
       final String finalErrorMessage = errorMessage;
+      errorMessage = null;
       if (raiseGUI)
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
@@ -2694,10 +2695,10 @@ public class Jalview2XML
       }
       else
       {
-        System.err.println("Problem loading Jalview file: " + errorMessage);
+        System.err.println(
+                "Problem loading Jalview file: " + finalErrorMessage);
       }
     }
-    errorMessage = null;
   }
 
   Map<String, String> alreadyLoadedPDB = new HashMap<>();