JAL-4241 Fix non-standard residues replacement.

[jalview.git] / test / jalview / ws2 / actions / annotation / AnnotationJobTest.java

diff --git a/test/jalview/ws2/actions/annotation/AnnotationJobTest.java b/test/jalview/ws2/actions/annotation/AnnotationJobTest.java
index 4e3767f..183d6f3 100644 (file)
--- a/test/jalview/ws2/actions/annotation/AnnotationJobTest.java
+++ b/test/jalview/ws2/actions/annotation/AnnotationJobTest.java
@@ -172,7 +172,7 @@ public class AnnotationJobTest
   }
 
   @Test(groups = { "Functional"} )
-  public void testCreate_ContainsNonStandardAndNoFilterNonStandard_NonStandardToGap()
+  public void testCreate_ContainsNonStandardAndNoFilterNonStandard_NonStandardRemain()
   {
     var alignment = new Alignment(new Sequence[] {
         new Sequence("test1", "ACACAOACACAC"),
@@ -180,6 +180,20 @@ public class AnnotationJobTest
     });
     var annotJob = AnnotationJob.create(alignment, true, true, true, false, 0);
     assertThat(annotJob.getInputSequences(), contains(
+            matchesSequenceString("ACACAOACACAC"),
+            matchesSequenceString("ABAVAVAVABAV")
+    ));
+  }
+
+  @Test(groups = { "Functional"} )
+  public void testCreate_ContainsNonStandardAndFilterNonStandard_NonStandardToGap()
+  {
+    var alignment = new Alignment(new Sequence[] {
+        new Sequence("test1", "ACACAOACACAC"),
+        new Sequence("test2", "ABAVAVAVABAV")
+    });
+    var annotJob = AnnotationJob.create(alignment, true, true, true, true, 0);
+    assertThat(annotJob.getInputSequences(), contains(
             matchesSequenceString("ACACA-ACACAC"),
             matchesSequenceString("A-AVAVAVA-AV")
     ));