JAL-2154 verify sequenceI/dataset refs for codonmappings

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 09645fd..9434569 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
 import jalview.util.MapList;
@@ -115,6 +116,14 @@ public class AlignmentTest
   public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment,
           boolean raiseAssert)
   {
+    if (alignment == null)
+    {
+      if (raiseAssert)
+      {
+        Assert.fail("Alignment for verification was null.");
+      }
+      return false;
+    }
     if (alignment.getDataset() != null)
     {
       AlignmentI dataset = alignment.getDataset();
@@ -185,6 +194,50 @@ public class AlignmentTest
           }
         }
       }
+      // finally, verify codonmappings involve only dataset sequences.
+      if (alignment.getCodonFrames() != null)
+      {
+        for (AlignedCodonFrame alc : alignment.getCodonFrames())
+        {
+          for (SequenceToSequenceMapping ssm : alc.getMappings())
+          {
+            if (ssm.getFromSeq().getDatasetSequence() != null)
+            {
+              if (raiseAssert)
+              {
+                Assert.fail("CodonFrame-SSM-FromSeq is not a dataset sequence");
+              }
+              return false;
+            }
+            if (alignment.findIndex(ssm.getFromSeq()) == -1)
+            {
+
+              if (raiseAssert)
+              {
+                Assert.fail("CodonFrame-SSM-FromSeq is not contained in dataset");
+              }
+              return false;
+            }
+            if (ssm.getMapping().getTo().getDatasetSequence() != null)
+            {
+              if (raiseAssert)
+              {
+                Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+              }
+              return false;
+            }
+            if (alignment.findIndex(ssm.getMapping().getTo()) == -1)
+            {
+
+              if (raiseAssert)
+              {
+                Assert.fail("CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+              }
+              return false;
+            }
+          }
+        }
+      }
     }
     return true; // all relationships verified!
   }
@@ -293,6 +346,32 @@ public class AlignmentTest
             al,
             false,
             "verify passed when a dbref with map to sequence outside of dataset was added");
+    // make the verify pass by adding the outsider back in
+    al.getDataset().addSequence(sqout);
+    assertVerifyAlignment(al, true,
+            "verify should have passed after adding dbref->to sequence in to dataset");
+    // and now the same for a codon mapping...
+    SequenceI sqanotherout = new Sequence("sqanotherout",
+            "aggtutaggcagcagcag");
+
+    AlignedCodonFrame alc = new AlignedCodonFrame();
+    alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 },
+            new int[] { 1, 18 }, 3, 1));
+
+    al.addCodonFrame(alc);
+    Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1);
+
+    assertVerifyAlignment(
+            al,
+            false,
+            "verify passed when alCodonFrame mapping to sequence outside of dataset was added");
+    // make the verify pass by adding the outsider back in
+    al.getDataset().addSequence(sqanotherout);
+    assertVerifyAlignment(
+            al,
+            true,
+            "verify should have passed once all sequences involved in alCodonFrame were added to dataset");
+
   }
   /*
    * Read in Stockholm format test data including secondary structure