merge commit

[jalview.git] / test / jalview / analysis / AlignmentAnnotationUtilsTest.java

diff --git a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
index 1da1939..19a5163 100644 (file)
--- a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
+++ b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
@@ -36,7 +36,7 @@ public class AlignmentAnnotationUtilsTest
           "TIETHKEEELTA-" + EOL;
   // @formatter:on
 
-  private static final int SEQ_ANN_COUNT = 10;
+  private static final int SEQ_ANN_COUNT = 12;
 
   private AlignmentI alignment;
 
@@ -212,6 +212,7 @@ public class AlignmentAnnotationUtilsTest
   @Test
   public void testGetShownHiddenTypes_withGraphGroups()
   {
+    final int GROUP_3 = 3;
     final int GROUP_4 = 4;
     final int GROUP_5 = 5;
     final int GROUP_6 = 6;
@@ -222,10 +223,10 @@ public class AlignmentAnnotationUtilsTest
     SequenceI[] seqs = alignment.getSequencesArray();
   
     /*
-     * Configure annotation properties for test
+     * Annotations for selection group and graph group
+     * 
+     * Hidden annotations Label2, Label3, in (hidden) group 5
      */
-    // annotations for selection group and graph group
-    // hidden annotations Label2, Label3, in (hidden) group 5
     anns[2].sequenceRef = seqs[3];
     anns[2].visible = false;
     anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
@@ -236,6 +237,19 @@ public class AlignmentAnnotationUtilsTest
     anns[3].graphGroup = GROUP_5;
     // need to ensure annotations have the same calcId as well
     anns[3].setCalcId("CalcId2");
+    // annotations for a different hidden group generating the same group label
+    anns[10].sequenceRef = seqs[0];
+    anns[10].visible = false;
+    anns[10].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[10].graphGroup = GROUP_3;
+    anns[10].label = "Label3";
+    anns[10].setCalcId("CalcId2");
+    anns[11].sequenceRef = seqs[3];
+    anns[11].visible = false;
+    anns[11].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[11].graphGroup = GROUP_3;
+    anns[11].label = "Label2";
+    anns[11].setCalcId("CalcId2");
   
     // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
     anns[1].sequenceRef = seqs[3];
@@ -248,9 +262,29 @@ public class AlignmentAnnotationUtilsTest
     anns[5].graph = AlignmentAnnotation.LINE_GRAPH;
     anns[5].graphGroup = GROUP_6;
     anns[5].setCalcId("CalcId1");
+    /*
+     * Annotations 0 and 4 are visible, for a different CalcId and graph group.
+     * They produce the same label as annotations 1 and 5, which should not be
+     * duplicated in the results. This case corresponds to (e.g.) many
+     * occurrences of an IUPred Short/Long annotation group, one per sequence.
+     */
+    anns[4].sequenceRef = seqs[0];
+    anns[4].visible = false;
+    anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[4].graphGroup = GROUP_4;
+    anns[4].label = "Label1";
+    anns[4].setCalcId("CalcId1");
+    anns[0].sequenceRef = seqs[0];
+    anns[0].visible = true;
+    anns[0].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[0].graphGroup = GROUP_4;
+    anns[0].label = "Label5";
+    anns[0].setCalcId("CalcId1");
   
-    // annotations outwith selection group - should be ignored
-    // hidden grouped annotations
+    /*
+     * Annotations outwith selection group - should be ignored.
+     */
+    // Hidden grouped annotations
     anns[6].sequenceRef = seqs[2];
     anns[6].visible = false;
     anns[6].graph = AlignmentAnnotation.LINE_GRAPH;
@@ -259,6 +293,7 @@ public class AlignmentAnnotationUtilsTest
     anns[8].visible = false;
     anns[8].graph = AlignmentAnnotation.LINE_GRAPH;
     anns[8].graphGroup = GROUP_4;
+
     // visible grouped annotations Label7, Label9
     anns[7].sequenceRef = seqs[2];
     anns[7].visible = true;
@@ -276,13 +311,16 @@ public class AlignmentAnnotationUtilsTest
   
     consoleDebug(shownTypes, hiddenTypes);
   
-    // CalcId1 / Label1, Label5 (only) should be 'shown', as a compound type
+    // CalcId1 / Label1, Label5 (only) should be 'shown', once, as a compound
+    // type
+    assertEquals(1, shownTypes.size());
     assertEquals(1, shownTypes.get("CalcId1").size());
     assertEquals(2, shownTypes.get("CalcId1").get(0).size());
     assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
     assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));
   
     // CalcId2 / Label2, Label3 (only) should be 'hidden'
+    assertEquals(1, hiddenTypes.size());
     assertEquals(1, hiddenTypes.get("CalcId2").size());
     assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
     assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));