X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentSorterTest.java;h=090ae1ac15373d4407869680947e0a8aec8ceef9;hb=709f51ae2e2c9e2b8d798300819c7e75b282bcfc;hp=0255f666bff7a03517b57f995126a8242bcde4b0;hpb=45715055c536e1c31020b8ab7ce30b2e28f3aafd;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentSorterTest.java b/test/jalview/analysis/AlignmentSorterTest.java
index 0255f66..090ae1a 100644
--- a/test/jalview/analysis/AlignmentSorterTest.java
+++ b/test/jalview/analysis/AlignmentSorterTest.java
@@ -11,10 +11,10 @@ import jalview.datamodel.SequenceI;
 import java.util.Arrays;
 import java.util.List;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class AlignmentSorterTest
 {
   @Test(groups = "Functional")
@@ -31,7 +31,10 @@ public class AlignmentSorterTest
     /*
      * sort with no score features does nothing
      */
-    PA.setValue(AlignmentSorter.class, "lastSortByFeatureScore", null);
+    AlignmentSorter sorter = (AlignmentSorter) PA
+            .invokeMethod(AlignmentSorter.class, "getInstance()",
+                    new Object[] {});
+    PA.setValue(sorter, "sortByFeatureCriteria", null);
 
     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
             AlignmentSorter.FEATURE_SCORE);
@@ -62,9 +65,9 @@ public class AlignmentSorterTest
 
     /*
      * sort by ascending score, no filter on feature type or group
-     * NB sort order for the same feature set (none) is toggled so descending
+     * NB sort order for the same feature set (none) gets toggled, so descending
      */
-    PA.setValue(AlignmentSorter.class, "sortByFeatureScoreAscending", true);
+    PA.setValue(sorter, "sortByFeatureAscending", true);
     AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
             AlignmentSorter.FEATURE_SCORE);
     assertSame(al.getSequenceAt(3), seq3); // -0.5
@@ -114,7 +117,7 @@ public class AlignmentSorterTest
      * seq1 is now 2.0, seq3 is now -4
      */
     // fails because seq1.findPosition(4) returns 4
-    // although residue 4 is in column 5!
+    // although residue 4 is in column 5! - JAL-2544
     AlignmentSorter.sortByFeature(null, null, 0, 4, al,
             AlignmentSorter.FEATURE_SCORE);
     assertSame(al.getSequenceAt(0), seq3); // -4