X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=7ad9436c858f8ef2fed092007d4d26a6550a73d8;hb=6c43dd36929855a7907380ffb36b4df249d4a557;hp=dbecc20b2743c1bb25beca3984a1183b628bc6dd;hpb=f11011db0fddcb60941d20e4ee9d63a87fda2a23;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index dbecc20..7ad9436 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -178,9 +178,11 @@ public class AlignmentTest
     }
     else
     {
+      int dsp = -1;
       // verify all dataset sequences
       for (SequenceI seqds : alignment.getSequences())
       {
+        dsp++;
         if (seqds.getDatasetSequence() != null)
         {
           if (raiseAssert)
@@ -189,6 +191,18 @@ public class AlignmentTest
           }
           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;
+        }
         if (seqds.getDBRefs() != null)
         {
           for (DBRefEntry dbr : seqds.getDBRefs())
@@ -405,7 +419,143 @@ public class AlignmentTest
     al.getDataset().addSequence(sqanotherout);
     assertVerifyAlignment(al, false,
             "verify should have failed when a sequence was added twice to the dataset");
+    al.getDataset().deleteSequence(sqanotherout);
+    assertVerifyAlignment(al, true,
+            "verify should have passed after duplicate entry for sequence was removed");
+  }
+
+  /**
+   * checks that the sequence data for an alignment's dataset is non-redundant.
+   * Fails if there are sequences with same id, sequence, start, and.
+   */
+
+  public static void assertDatasetIsNormalised(AlignmentI al)
+  {
+    assertDatasetIsNormalised(al, null);
+  }
+
+  /**
+   * checks that the sequence data for an alignment's dataset is non-redundant.
+   * Fails if there are sequences with same id, sequence, start, and.
+   * 
+   * @param al
+   *          - alignment to verify
+   * @param message
+   *          - null or message prepended to exception message.
+   */
+  public static void assertDatasetIsNormalised(AlignmentI al, String message)
+  {
+    if (al.getDataset()!=null)
+    {
+      assertDatasetIsNormalised(al.getDataset(), message);
+      return;
+    }
+    /*
+     * look for pairs of sequences with same ID, start, end, and sequence
+     */
+    List<SequenceI> seqSet = al.getSequences();
+    for (int p=0;p<seqSet.size(); p++)
+    {
+      SequenceI pSeq = seqSet.get(p);
+      for (int q=p+1; q<seqSet.size(); q++)
+      {
+        SequenceI qSeq = seqSet.get(q);
+        if (pSeq.getStart()!=qSeq.getStart())
+        {
+          continue;
+        }
+        if (pSeq.getEnd()!=qSeq.getEnd())
+        {
+          continue;
+        }
+        if (!pSeq.getName().equals(qSeq.getName()))
+        {
+          continue;
+        }
+        if (!Arrays.equals(pSeq.getSequence(), qSeq.getSequence()))
+        {
+          continue;
+        }
+        Assert.fail((message == null ? "" : message + " :")
+                + "Found similar sequences at position " + p + " and " + q
+                + "\n" + pSeq.toString());
+      }
+    }
+  }
+  
+  @Test(groups = { "Functional", "Asserts" })
+  public void testAssertDatasetIsNormalised()
+  {
+    Sequence sq1 = new Sequence("s1/1-4", "asdf");
+    Sequence sq1shift = new Sequence("s1/2-5", "asdf");
+    Sequence sq1seqd = new Sequence("s1/1-4", "asdt");
+    Sequence sq2 = new Sequence("s2/1-4", "asdf");
+    Sequence sq1dup = new Sequence("s1/1-4", "asdf");
+
+    Alignment al = new Alignment(new SequenceI[] { sq1 });
+    al.setDataset(null);
+
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("Single sequence should be valid normalised dataset.");
+    }
+    al.addSequence(sq2);
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("Two different sequences should be valid normalised dataset.");
+    }
+    /*
+     * now change sq2's name in the alignment. should still be valid
+     */
+    al.findName(sq2.getName()).setName("sq1");
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("Two different sequences in dataset, but same name in alignment, should be valid normalised dataset.");
+    }
+
+    al.addSequence(sq1seqd);
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("sq1 and sq1 with different sequence should be distinct.");
+    }
+
+    al.addSequence(sq1shift);
+    try
+    {
+      assertDatasetIsNormalised(al);
+    } catch (AssertionError ae)
+    {
+      Assert.fail("sq1 and sq1 with different start/end should be distinct.");
+    }
+    /*
+     * finally, the failure case
+     */
+    al.addSequence(sq1dup);
+    boolean ssertRaised = false;
+    try
+    {
+      assertDatasetIsNormalised(al);
 
+    } catch (AssertionError ae)
+    {
+      ssertRaised = true;
+    }
+    if (!ssertRaised)
+    {
+      Assert.fail("Expected identical sequence to raise exception.");
+    }
   }
   /*
    * Read in Stockholm format test data including secondary structure
@@ -843,6 +993,27 @@ public class AlignmentTest
   }
 
   @Test(groups = "Functional")
+  public void testAddSequencePreserveDatasetIntegrity()
+  {
+    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    Alignment align = new Alignment(new SequenceI[] { seq });
+    align.createDatasetAlignment();
+    AlignmentI ds = align.getDataset();
+    SequenceI copy = new Sequence(seq);
+    copy.insertCharAt(3, 5, '-');
+    align.addSequence(copy);
+    Assert.assertEquals(align.getDataset().getHeight(), 1,
+            "Dataset shouldn't have more than one sequence.");
+
+    Sequence seq2 = new Sequence("newtestSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    align.addSequence(seq2);
+    Assert.assertEquals(align.getDataset().getHeight(), 2,
+            "Dataset should now have two sequences.");
+
+    assertAlignmentDatasetRefs(align,
+            "addSequence broke dataset reference integrity");
+  }
+  @Test(groups = "Functional")
   public void getVisibleStartAndEndIndexTest()
   {
     Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
@@ -870,4 +1041,5 @@ public class AlignmentTest
     assertEquals(1, startEnd[0]);
     assertEquals(23, startEnd[1]);
   }
+
 }