JAL-3383 tests and fixes for overloaded SequenceFeatures.findFeatures

[jalview.git] / test / jalview / datamodel / AlignmentTest.java

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index dd19eb6..cdcc219 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -243,7 +243,24 @@ public class AlignmentTest
                   return false;
 
                 }
-                if (alignment.findIndex(dbr.getMap().getTo()) == -1)
+
+                SequenceI x = dbr.getMap().getTo();
+//                System.out.println(alignment.toString());
+//                System.out.println(dbr);
+//                System.out.println("map " + dbr.getMap());
+//                System.out.println("to " + dbr.getMap().getTo());
+//                if (x.toString().indexOf("ENSP00000395337") >= 0)
+//                {
+//                  // The TO name here is "ENSP00000395337"
+//                  // But the name in the table is "LDAH_HUMAN"
+//                  System.out.println(x.getSequenceAsString());
+//                  SequenceI y = alignment.getSequenceAt(0);
+//                  System.out.println(y.getSequenceAsString());
+//                  System.out.println(x.getSequenceAsString()
+//                          .equals(y.getSequenceAsString()));
+//
+//                }
+                if (alignment.findIndex(x) == -1)
                 {
                   if (raiseAssert)
                   {
@@ -1173,14 +1190,14 @@ public class AlignmentTest
     /*
      * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
      */
-    DBRefEntry[] dbRefs = pep.getDBRefs();
-    assertEquals(2, dbRefs.length);
-    assertSame(dna, dbRefs[0].map.to);
-    assertSame(cds, dbRefs[1].map.to);
-    assertEquals(1, dna.getDBRefs().length);
-    assertSame(pep.getDatasetSequence(), dna.getDBRefs()[0].map.to);
-    assertEquals(1, cds.getDBRefs().length);
-    assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
+    List<DBRefEntry> dbRefs = pep.getDBRefs();
+    assertEquals(2, dbRefs.size());
+    assertSame(dna, dbRefs.get(0).map.to);
+    assertSame(cds, dbRefs.get(1).map.to);
+    assertEquals(1, dna.getDBRefs().size());
+    assertSame(pep.getDatasetSequence(), dna.getDBRefs().get(0).map.to);
+    assertEquals(1, cds.getDBRefs().size());
+    assertSame(pep.getDatasetSequence(), cds.getDBRefs().get(0).map.to);
   }
 
   @Test(groups = { "Functional" })