JAL-2154 patch verifyAlignment so it fails for duplicate entries for same SequenceI...

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 9434569..379a9c5 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -104,6 +104,29 @@ public class AlignmentTest
   }
 
   /**
+   * assert wrapper: tests all references in the given alignment are consistent
+   * 
+   * @param alignment
+   */
+  public static void assertAlignmentDatasetRefs(AlignmentI alignment)
+  {
+    verifyAlignmentDatasetRefs(alignment, true, null);
+  }
+
+  /**
+   * assert wrapper: tests all references in the given alignment are consistent
+   * 
+   * @param alignment
+   * @param message
+   *          - prefixed to any assert failed messages
+   */
+  public static void assertAlignmentDatasetRefs(AlignmentI alignment,
+          String message)
+  {
+    verifyAlignmentDatasetRefs(alignment, true, message);
+  }
+
+  /**
    * verify sequence and dataset references are properly contained within
    * dataset
    * 
@@ -111,16 +134,19 @@ public class AlignmentTest
    *          - the alignmentI object to verify (either alignment or dataset)
    * @param raiseAssert
    *          - when set, testng assertions are raised.
+   *          @param message
+   *          - null or a string message to prepend to the assert failed messages.
    * @return true if alignment references were in order, otherwise false.
    */
   public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
-          boolean raiseAssert)
+          boolean raiseAssert, String message)
   {
+    if (message==null) { message = ""; }
     if (alignment == null)
     {
       if (raiseAssert)
       {
-        Assert.fail("Alignment for verification was null.");
+        Assert.fail(message+"Alignment for verification was null.");
       }
       return false;
     }
@@ -135,7 +161,7 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail("Alignment contained a sequence who's dataset sequence has a second dataset reference.");
+            Assert.fail(message+" Alignment contained a sequence who's dataset sequence has a second dataset reference.");
           }
           return false;
         }
@@ -143,23 +169,37 @@ public class AlignmentTest
         {
           if (raiseAssert)
           {
-            Assert.fail("Alignment contained a sequence who's dataset sequence was not in the dataset.");
+            Assert.fail(message+" Alignment contained a sequence who's dataset sequence was not in the dataset.");
           }
           return false;
         }
       }
-      return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert);
+      return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert, message);
     }
     else
     {
+      int dsp = -1;
       // verify all dataset sequences
       for (SequenceI seqds : alignment.getSequences())
       {
+        dsp++;
         if (seqds.getDatasetSequence() != null)
         {
           if (raiseAssert)
           {
-            Assert.fail("Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
+            Assert.fail(message+" Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)");
+          }
+          return false;
+        }
+        int foundp = alignment.findIndex(seqds);
+        if (foundp != dsp)
+        {
+          if (raiseAssert)
+          {
+            Assert.fail(message
+                    + " Dataset sequence array contains a reference at "
+                    + dsp + " to a sequence first seen at " + foundp + " ("
+                    + seqds.toString() + ")");
           }
           return false;
         }
@@ -176,7 +216,7 @@ public class AlignmentTest
                 {
                   if (raiseAssert)
                   {
-                    Assert.fail("DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
+                    Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
                   }
                   return false;
 
@@ -185,7 +225,7 @@ public class AlignmentTest
                 {
                   if (raiseAssert)
                   {
-                    Assert.fail("DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                    Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence not in dataset");
                   }
                   return false;
                 }
@@ -205,7 +245,7 @@ public class AlignmentTest
             {
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-FromSeq is not a dataset sequence");
+                Assert.fail(message+" CodonFrame-SSM-FromSeq is not a dataset sequence");
               }
               return false;
             }
@@ -214,7 +254,7 @@ public class AlignmentTest
 
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-FromSeq is not contained in dataset");
+                Assert.fail(message+" CodonFrame-SSM-FromSeq is not contained in dataset");
               }
               return false;
             }
@@ -222,7 +262,7 @@ public class AlignmentTest
             {
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+                Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
               }
               return false;
             }
@@ -231,7 +271,7 @@ public class AlignmentTest
 
               if (raiseAssert)
               {
-                Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+                Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
               }
               return false;
             }
@@ -258,7 +298,7 @@ public class AlignmentTest
       try
       {
 
-        Assert.assertTrue(verifyAlignmentDatasetRefs(al, true),
+        Assert.assertTrue(verifyAlignmentDatasetRefs(al, true, null),
                 "Valid test alignment failed when raiseAsserts enabled:"
                         + msg);
       } catch (AssertionError ae)
@@ -269,24 +309,29 @@ public class AlignmentTest
                         + msg, ae);
       }
       // also check validation passes with asserts disabled
-      Assert.assertTrue(verifyAlignmentDatasetRefs(al, false),
-              "Valid test alignment failed when raiseAsserts disabled:"
+      Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null),
+              "Valid test alignment tested false when raiseAsserts disabled:"
                       + msg);
     }
     else
     {
+      boolean assertRaised = false;
       try
       {
-        Assert.assertFalse(verifyAlignmentDatasetRefs(al, true));
-        Assert.fail("Invalid test alignment passed but no assertion raised when raiseAsserts enabled:"
-                + msg);
+        verifyAlignmentDatasetRefs(al, true, null);
       } catch (AssertionError ae)
       {
         // expected behaviour
+        assertRaised = true;
+      }
+      if (!assertRaised)
+      {
+        Assert.fail("Invalid test alignment passed when raiseAsserts enabled:"
+                + msg);
       }
       // also check validation passes with asserts disabled
-      Assert.assertFalse(verifyAlignmentDatasetRefs(al, false),
-              "Invalid test alignment passed when raiseAsserts disabled:"
+      Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null),
+              "Invalid test alignment tested true when raiseAsserts disabled:"
                       + msg);
     }
   }
@@ -371,6 +416,9 @@ public class AlignmentTest
             al,
             true,
             "verify should have passed once all sequences involved in alCodonFrame were added to dataset");
+    al.getDataset().addSequence(sqanotherout);
+    assertVerifyAlignment(al, false,
+            "verify should have failed when a sequence was added twice to the dataset");
 
   }
   /*