X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesTest.java;h=84a07b4ff33e210e7d78beed7805017bd3a99fe9;hb=5c10f71b18bb8a9e3320440cc1eaa95350d56120;hp=4b7609a370e54944688c8bbba6073ae377171c9a;hpb=64c1e734115c6554ef56a3e0feb7cdea40cd7f41;p=jalview.git

diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index 4b7609a..84a07b4 100644
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -70,7 +70,7 @@ public class SequenceFeaturesTest
     /*
      * get features by type
      */
-    assertTrue(store.getPositionalFeatures(null).isEmpty());
+    assertTrue(store.getPositionalFeatures((String) null).isEmpty());
     assertTrue(store.getPositionalFeatures("Cath").isEmpty());
     assertTrue(store.getPositionalFeatures("METAL").isEmpty());
 
@@ -131,7 +131,7 @@ public class SequenceFeaturesTest
     /*
      * get contact features by type
      */
-    assertTrue(store.getContactFeatures(null).isEmpty());
+    assertTrue(store.getContactFeatures((String) null).isEmpty());
     assertTrue(store.getContactFeatures("Cath").isEmpty());
     assertTrue(store.getContactFeatures("Pfam").isEmpty());
     assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
@@ -188,7 +188,7 @@ public class SequenceFeaturesTest
     /*
      * get non-positional features by type
      */
-    assertTrue(store.getNonPositionalFeatures(null).isEmpty());
+    assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
     assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
     assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
   
@@ -240,36 +240,36 @@ public class SequenceFeaturesTest
     // null type is weird but possible:
     SequenceFeature sf13 = addFeature(sf, null, 5, 12);
   
-    List<SequenceFeature> overlaps = sf.findFeatures("Pfam", 200, 200);
+    List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
     assertTrue(overlaps.isEmpty());
   
-    overlaps = sf.findFeatures("Pfam", 1, 9);
+    overlaps = sf.findFeatures( 1, 9, "Pfam");
     assertEquals(overlaps.size(), 1);
     assertTrue(overlaps.contains(sf2));
   
-    overlaps = sf.findFeatures("Pfam", 5, 18);
+    overlaps = sf.findFeatures( 5, 18, "Pfam");
     assertEquals(overlaps.size(), 2);
     assertTrue(overlaps.contains(sf1));
     assertTrue(overlaps.contains(sf2));
   
-    overlaps = sf.findFeatures("Pfam", 30, 40);
+    overlaps = sf.findFeatures(30, 40, "Pfam");
     assertEquals(overlaps.size(), 3);
     assertTrue(overlaps.contains(sf1));
     assertTrue(overlaps.contains(sf3));
     assertTrue(overlaps.contains(sf4));
   
-    overlaps = sf.findFeatures("Pfam", 80, 90);
+    overlaps = sf.findFeatures( 80, 90, "Pfam");
     assertEquals(overlaps.size(), 2);
     assertTrue(overlaps.contains(sf4));
     assertTrue(overlaps.contains(sf5));
   
-    overlaps = sf.findFeatures("Pfam", 68, 70);
+    overlaps = sf.findFeatures( 68, 70, "Pfam");
     assertEquals(overlaps.size(), 3);
     assertTrue(overlaps.contains(sf4));
     assertTrue(overlaps.contains(sf5));
     assertTrue(overlaps.contains(sf6));
 
-    overlaps = sf.findFeatures("Cath", 16, 69);
+    overlaps = sf.findFeatures(16, 69, "Cath");
     assertEquals(overlaps.size(), 4);
     assertTrue(overlaps.contains(sf7));
     assertFalse(overlaps.contains(sf8));
@@ -278,9 +278,9 @@ public class SequenceFeaturesTest
     assertTrue(overlaps.contains(sf11));
     assertFalse(overlaps.contains(sf12));
 
-    assertTrue(sf.findFeatures("Metal", 0, 1000).isEmpty());
+    assertTrue(sf.findFeatures(0, 1000, "Metal").isEmpty());
 
-    overlaps = sf.findFeatures(null, 7, 7);
+    overlaps = sf.findFeatures(7, 7, (String) null);
     assertEquals(overlaps.size(), 1);
     assertTrue(overlaps.contains(sf13));
   }