X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FDBRefEntryTest.java;fp=test%2Fjalview%2Fdatamodel%2FDBRefEntryTest.java;h=476e0bb5d65fda00ca5e13c19a4b8c6930916f20;hb=9949854f4c2dc75980f15acdee69594ca6b22631;hp=c8f998b247bc57a9f17d7f4d2e0e94f6d178b684;hpb=cfba86992cd64bb0df6105bbf5dfc076ba8a93b2;p=jalview.git

diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index c8f998b..476e0bb 100644
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -62,12 +62,14 @@ public class DBRefEntryTest
     assertFalse(ref1.equalRef(new DBRefEntry("UNIPROT", "1", "V71632")));
 
     // presence of or differences in mappings are ignored
-    ref1.setMap(new Mapping(new MapList(new int[] { 1, 3 }, new int[] { 1,
-        1 }, 3, 1)));
+    ref1.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 3 }, new int[] { 1, 1 }, 3, 1)));
     assertTrue(ref1.equalRef(ref2));
     assertTrue(ref2.equalRef(ref1));
-    ref1.setMap(new Mapping(new MapList(new int[] { 1, 6 }, new int[] { 1,
-        2 }, 3, 1)));
+    ref1.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 6 }, new int[] { 1, 2 }, 3, 1)));
     assertTrue(ref1.equalRef(ref2));
     assertTrue(ref2.equalRef(ref1));
   }
@@ -94,8 +96,9 @@ public class DBRefEntryTest
     /*
      * ref1 has no mapping, acquires mapping from ref2
      */
-    Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
-        1, 1 }, 3, 1));
+    Mapping map = new Mapping(
+            new MapList(new int[]
+            { 1, 3 }, new int[] { 1, 1 }, 3, 1));
     ref2.setMap(map);
     assertTrue(ref1.updateFrom(ref2));
     assertSame(map, ref1.getMap()); // null mapping updated
@@ -134,6 +137,21 @@ public class DBRefEntryTest
     assertEquals("3", ref1.getVersion());
 
     /*
+     * canonical == false superseded by canonical == true
+     */
+    ref1.setCanonical(false);
+    ref2.setCanonical(true);
+    assertTrue(ref1.updateFrom(ref2));
+    assertTrue(ref1.isCanonical());
+
+    /*
+     * canonical == true NOT superseded by canonical == false
+     */
+    ref1.setCanonical(true);
+    ref2.setCanonical(false);
+    assertFalse(ref1.updateFrom(ref2));
+
+    /*
      * version "source:n" with n>0 is not superseded
      */
     ref1.setVersion("UNIPROT:1");
@@ -157,29 +175,33 @@ public class DBRefEntryTest
     /*
      *  1:1 mapping - ok
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
-            1));
+    dbr.setMap(
+            new Mapping(null, new int[]
+            { 1, 3 }, new int[] { 1, 3 }, 1, 1));
     assertTrue(dbr.isPrimaryCandidate());
 
     /*
      *  1:1 mapping of identical split ranges - not ok
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3, 6, 9 }, new int[] { 1,
-        3, 6, 9 }, 1, 1));
+    dbr.setMap(
+            new Mapping(null, new int[]
+            { 1, 3, 6, 9 }, new int[] { 1, 3, 6, 9 }, 1, 1));
     assertFalse(dbr.isPrimaryCandidate());
 
     /*
      *  1:1 mapping of different ranges - not ok
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 2, 5 }, 1,
-            1));
+    dbr.setMap(
+            new Mapping(null, new int[]
+            { 1, 4 }, new int[] { 2, 5 }, 1, 1));
     assertFalse(dbr.isPrimaryCandidate());
 
     /*
      *  1:1 mapping of 'isoform' ranges - not ok
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 2, 6, 9 }, new int[] { 1,
-        3, 7, 9 }, 1, 1));
+    dbr.setMap(
+            new Mapping(null, new int[]
+            { 1, 2, 6, 9 }, new int[] { 1, 3, 7, 9 }, 1, 1));
     assertFalse(dbr.isPrimaryCandidate());
     dbr.setMap(null);
     assertTrue(dbr.isPrimaryCandidate());
@@ -207,22 +229,25 @@ public class DBRefEntryTest
     /*
      *  1:1 mapping and sequenceRef (fail)
      */
-    dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 },
-            new int[] { 1, 3 }, 1, 1));
+    dbr.setMap(
+            new Mapping(new Sequence("foo", "ASDF"), new int[]
+            { 1, 3 }, new int[] { 1, 3 }, 1, 1));
     assertFalse(dbr.isPrimaryCandidate());
 
     /*
      * 1:3 mapping (fail)
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
-            3));
+    dbr.setMap(
+            new Mapping(null, new int[]
+            { 1, 3 }, new int[] { 1, 3 }, 1, 3));
     assertFalse(dbr.isPrimaryCandidate());
 
     /*
      * 2:2 mapping with shift (expected fail, but maybe use case for a pass)
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 1, 4 }, 2,
-            2));
+    dbr.setMap(
+            new Mapping(null, new int[]
+            { 1, 4 }, new int[] { 1, 4 }, 2, 2));
     assertFalse(dbr.isPrimaryCandidate());
   }
 }