Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / test / jalview / gui / AnnotationColumnChooserTest.java

diff --git a/test/jalview/gui/AnnotationColumnChooserTest.java b/test/jalview/gui/AnnotationColumnChooserTest.java
index a9b973e..36d49dc 100644 (file)
--- a/test/jalview/gui/AnnotationColumnChooserTest.java
+++ b/test/jalview/gui/AnnotationColumnChooserTest.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import static org.testng.Assert.assertFalse;
 import static org.testng.AssertJUnit.assertEquals;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
@@ -34,7 +35,7 @@ import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.IOException;
-import java.util.List;
+import java.util.Iterator;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -75,14 +76,14 @@ public class AnnotationColumnChooserTest
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // pin down annotation sort order for test
-    Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+    Cache.setPropertyNoSave(Preferences.SORT_ANNOTATIONS,
             SequenceAnnotationOrder.NONE.name());
     final String TRUE = Boolean.TRUE.toString();
-    Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+    Cache.setPropertyNoSave(Preferences.SHOW_AUTOCALC_ABOVE,
             TRUE);
-    Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+    Cache.setPropertyNoSave("SHOW_QUALITY", TRUE);
+    Cache.setPropertyNoSave("SHOW_CONSERVATION", TRUE);
+    Cache.setPropertyNoSave("SHOW_IDENTITY", TRUE);
 
     AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
             DataSourceType.PASTE, FileFormat.Fasta);
@@ -140,17 +141,40 @@ public class AnnotationColumnChooserTest
 
     HiddenColumns currentHidden = af.getViewport().getAlignment()
             .getHiddenColumns();
-    List<int[]> regions = currentHidden.getHiddenColumnsCopy();
-    assertEquals(regions.get(0)[0], 0);
-    assertEquals(regions.get(0)[1], 3);
-    assertEquals(regions.get(1)[0], 22);
-    assertEquals(regions.get(1)[1], 25);
+    Iterator<int[]> regions = currentHidden.iterator();
+    int[] next = regions.next();
+    assertEquals(0, next[0]);
+    assertEquals(3, next[1]);
+    next = regions.next();
+    assertEquals(22, next[0]);
+    assertEquals(25, next[1]);
 
     // now reset hidden columns
     acc.reset();
     currentHidden = af.getViewport().getAlignment().getHiddenColumns();
-    regions = currentHidden.getHiddenColumnsCopy();
-    assertEquals(regions.get(0)[0], 10);
-    assertEquals(regions.get(0)[1], 20);
+    regions = currentHidden.iterator();
+    next = regions.next();
+    assertEquals(10, next[0]);
+    assertEquals(20, next[1]);
+
+    // check works with empty hidden columns as old columns
+    oldhidden = new HiddenColumns();
+    acc.setOldHiddenColumns(oldhidden);
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    assertFalse(currentHidden.hasHiddenColumns());
+
+    // check works with empty hidden columns as new columns
+    oldhidden.hideColumns(10, 20);
+    acc.setOldHiddenColumns(oldhidden);
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    assertFalse(currentHidden.hasHiddenColumns());
+
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    regions = currentHidden.iterator();
+    next = regions.next();
+    assertEquals(10, next[0]);
+    assertEquals(20, next[1]);
   }
 }