X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=68440725fc6bee2235f7b226fbc83550d14166f4;hb=817741c8e9b1258fc0e5cad8f2ccdddec401d8cf;hp=d1f42909826d3031c0abaaf1115df2f957184f0a;hpb=bba9e58f08fc55c0f789f8354d1444e5c5e1b0e6;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index d1f4290..6844072 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1343,23 +1343,25 @@ public class SequenceTest
             null);
     sq.addSequenceFeature(sf0);
     // add feature on BCD
-    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 9, 11, 2f,
+    SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
             null);
-    sq.addSequenceFeature(sf1);
+    sq.addSequenceFeature(sfBCD);
     // add feature on DE
-    SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 11, 12, 2f,
+    SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
             null);
-    sq.addSequenceFeature(sf2);
+    sq.addSequenceFeature(sfDE);
     // add contact feature at [B, H]
-    SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 9,
-            15, 2f,
-            null);
-    sq.addSequenceFeature(sf3);
+    SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
+            "desc", 9, 15, 2f, null);
+    sq.addSequenceFeature(sfContactBH);
     // add contact feature at [F, G]
-    SequenceFeature sf4 = new SequenceFeature("Disulfide Bond", "desc", 13,
-            14, 2f,
-            null);
-    sq.addSequenceFeature(sf4);
+    SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
+            "desc", 13, 14, 2f, null);
+    sq.addSequenceFeature(sfContactFG);
+    // add single position feature at [I]
+    SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
+            "desc", 16, 16, null);
+    sq.addSequenceFeature(sfI);
 
     // no features in columns 1-2 (-A)
     List<SequenceFeature> found = sq.findFeatures(1, 2);
@@ -1368,20 +1370,29 @@ public class SequenceTest
     // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
     found = sq.findFeatures(1, 6);
     assertEquals(2, found.size());
-    assertTrue(found.contains(sf1));
-    assertTrue(found.contains(sf3));
+    assertTrue(found.contains(sfBCD));
+    assertTrue(found.contains(sfContactBH));
 
     // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
     found = sq.findFeatures(5, 6);
     assertEquals(1, found.size());
-    assertTrue(found.contains(sf1));
+    assertTrue(found.contains(sfBCD));
 
     // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
     found = sq.findFeatures(7, 10);
     assertEquals(3, found.size());
-    assertTrue(found.contains(sf1));
-    assertTrue(found.contains(sf2));
-    assertTrue(found.contains(sf4));
+    assertTrue(found.contains(sfBCD));
+    assertTrue(found.contains(sfDE));
+    assertTrue(found.contains(sfContactFG));
+
+    // columns 10-11 (--) should find nothing
+    found = sq.findFeatures(10, 11);
+    assertEquals(0, found.size());
+
+    // columns 14-14 (I) should find variant feature
+    found = sq.findFeatures(14, 14);
+    assertEquals(1, found.size());
+    assertTrue(found.contains(sfI));
   }
 
   @Test(groups = { "Functional" })