X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=06be9827351abb9fa78eb8db379551f2d2f1bbbd;hp=e885733202f2907974c74f6aaa953d063bc3ec5d;hb=391467e57959e2c71a5051de06da2028dc07f2ba;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index e885733..06be982 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1,19 +1,52 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
-import jalview.util.MapList;
-
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.Iterator;
+import java.util.List;
 
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
 /**
  * Unit tests for Alignment datamodel.
  * 
@@ -22,6 +55,14 @@ import org.testng.annotations.Test;
  */
 public class AlignmentTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // @formatter:off
   private static final String TEST_DATA = 
           "# STOCKHOLM 1.0\n" +
@@ -37,21 +78,21 @@ public class AlignmentTest
           "//";
 
   private static final String AA_SEQS_1 = 
-          ">Seq1Name\n" +
+          ">Seq1Name/5-8\n" +
           "K-QY--L\n" +
-          ">Seq2Name\n" +
+          ">Seq2Name/12-15\n" +
           "-R-FP-W-\n";
 
   private static final String CDNA_SEQS_1 = 
-          ">Seq1Name\n" +
+          ">Seq1Name/100-111\n" +
           "AC-GG--CUC-CAA-CT\n" +
-          ">Seq2Name\n" +
+          ">Seq2Name/200-211\n" +
           "-CG-TTA--ACG---AAGT\n";
 
   private static final String CDNA_SEQS_2 = 
-          ">Seq1Name\n" +
+          ">Seq1Name/50-61\n" +
           "GCTCGUCGTACT\n" +
-          ">Seq2Name\n" +
+          ">Seq2Name/60-71\n" +
           "GGGTCAGGCAGT\n";
   // @formatter:on
 
@@ -66,23 +107,493 @@ public class AlignmentTest
    * @return
    * @throws IOException
    */
-  protected AlignmentI loadAlignment(final String data, String format)
+  protected AlignmentI loadAlignment(final String data, FileFormatI format)
           throws IOException
   {
-    AlignmentI a = new FormatAdapter().readFile(data,
-            AppletFormatAdapter.PASTE, format);
+    AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+            format);
     a.setDataset(null);
     return a;
   }
 
+  /**
+   * 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
+   * 
+   * @param alignment
+   *          - 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, String message)
+  {
+    if (message == null)
+    {
+      message = "";
+    }
+    if (alignment == null)
+    {
+      if (raiseAssert)
+      {
+        Assert.fail(message + "Alignment for verification was null.");
+      }
+      return false;
+    }
+    if (alignment.getDataset() != null)
+    {
+      AlignmentI dataset = alignment.getDataset();
+      // check all alignment sequences have their dataset within the dataset
+      for (SequenceI seq : alignment.getSequences())
+      {
+        SequenceI seqds = seq.getDatasetSequence();
+        if (seqds.getDatasetSequence() != null)
+        {
+          if (raiseAssert)
+          {
+            Assert.fail(message
+                    + " Alignment contained a sequence who's dataset sequence has a second dataset reference.");
+          }
+          return false;
+        }
+        if (dataset.findIndex(seqds) == -1)
+        {
+          if (raiseAssert)
+          {
+            Assert.fail(message
+                    + " Alignment contained a sequence who's dataset sequence was not in the dataset.");
+          }
+          return false;
+        }
+      }
+      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(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;
+        }
+        if (seqds.getDBRefs() != null)
+        {
+          for (DBRefEntry dbr : seqds.getDBRefs())
+          {
+            if (dbr.getMap() != null)
+            {
+              SequenceI seqdbrmapto = dbr.getMap().getTo();
+              if (seqdbrmapto != null)
+              {
+                if (seqdbrmapto.getDatasetSequence() != null)
+                {
+                  if (raiseAssert)
+                  {
+                    Assert.fail(message
+                            + " DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence");
+                  }
+                  return false;
+
+                }
+                if (alignment.findIndex(dbr.getMap().getTo()) == -1)
+                {
+                  if (raiseAssert)
+                  {
+                    Assert.fail(message + " DBRefEntry " + dbr
+                            + " for sequence " + seqds
+                            + " in alignment has map to sequence not in dataset");
+                  }
+                  return false;
+                }
+              }
+            }
+          }
+        }
+      }
+      // 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(message
+                        + " CodonFrame-SSM-FromSeq is not a dataset sequence");
+              }
+              return false;
+            }
+            if (alignment.findIndex(ssm.getFromSeq()) == -1)
+            {
+
+              if (raiseAssert)
+              {
+                Assert.fail(message
+                        + " CodonFrame-SSM-FromSeq is not contained in dataset");
+              }
+              return false;
+            }
+            if (ssm.getMapping().getTo().getDatasetSequence() != null)
+            {
+              if (raiseAssert)
+              {
+                Assert.fail(message
+                        + " CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence");
+              }
+              return false;
+            }
+            if (alignment.findIndex(ssm.getMapping().getTo()) == -1)
+            {
+
+              if (raiseAssert)
+              {
+                Assert.fail(message
+                        + " CodonFrame-SSM-Mapping-ToSeq is not contained in dataset");
+              }
+              return false;
+            }
+          }
+        }
+      }
+    }
+    return true; // all relationships verified!
+  }
+
+  /**
+   * call verifyAlignmentDatasetRefs with and without assertion raising enabled,
+   * to check expected pass/fail actually occurs in both conditions
+   * 
+   * @param al
+   * @param expected
+   * @param msg
+   */
+  private void assertVerifyAlignment(AlignmentI al, boolean expected,
+          String msg)
+  {
+    if (expected)
+    {
+      try
+      {
+
+        Assert.assertTrue(verifyAlignmentDatasetRefs(al, true, null),
+                "Valid test alignment failed when raiseAsserts enabled:"
+                        + msg);
+      } catch (AssertionError ae)
+      {
+        ae.printStackTrace();
+        Assert.fail(
+                "Valid test alignment raised assertion errors when raiseAsserts enabled: "
+                        + msg,
+                ae);
+      }
+      // also check validation passes with asserts disabled
+      Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null),
+              "Valid test alignment tested false when raiseAsserts disabled:"
+                      + msg);
+    }
+    else
+    {
+      boolean assertRaised = false;
+      try
+      {
+        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, null),
+              "Invalid test alignment tested true when raiseAsserts disabled:"
+                      + msg);
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testVerifyAlignmentDatasetRefs()
+  {
+    SequenceI sq1 = new Sequence("sq1", "ASFDD"),
+            sq2 = new Sequence("sq2", "TTTTTT");
+
+    // construct simple valid alignment dataset
+    Alignment al = new Alignment(new SequenceI[] { sq1, sq2 });
+    // expect this to pass
+    assertVerifyAlignment(al, true, "Simple valid alignment didn't verify");
+
+    // check test for sequence->datasetSequence validity
+    sq1.setDatasetSequence(sq2);
+    assertVerifyAlignment(al, false,
+            "didn't detect dataset sequence with a dataset sequence reference.");
+
+    sq1.setDatasetSequence(null);
+    assertVerifyAlignment(al, true,
+            "didn't reinstate validity after nulling dataset sequence dataset reference");
+
+    // now create dataset and check again
+    al.createDatasetAlignment();
+    assertNotNull(al.getDataset());
+
+    assertVerifyAlignment(al, true,
+            "verify failed after createDatasetAlignment");
+
+    // create a dbref on sq1 with a sequence ref to sq2
+    DBRefEntry dbrs1tos2 = new DBRefEntry("UNIPROT", "1", "Q111111");
+    dbrs1tos2
+            .setMap(new Mapping(sq2.getDatasetSequence(), new int[]
+            { 1, 5 }, new int[] { 2, 6 }, 1, 1));
+    sq1.getDatasetSequence().addDBRef(dbrs1tos2);
+    assertVerifyAlignment(al, true,
+            "verify failed after addition of valid DBRefEntry/map");
+    // now create a dbref on a new sequence which maps to another sequence
+    // outside of the dataset
+    SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"),
+            sqnew = new Sequence("sqnew", "EEERRR");
+    DBRefEntry sqnewsqout = new DBRefEntry("ENAFOO", "1", "R000001");
+    sqnewsqout
+            .setMap(new Mapping(sqout, new int[]
+            { 1, 6 }, new int[] { 1, 18 }, 1, 3));
+    al.getDataset().addSequence(sqnew);
+
+    assertVerifyAlignment(al, true,
+            "verify failed after addition of new sequence to dataset");
+    // now start checking exception conditions
+    sqnew.addDBRef(sqnewsqout);
+    assertVerifyAlignment(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");
+    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
    * annotations.
    */
-  @BeforeMethod
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
-    al = loadAlignment(TEST_DATA, "STH");
+    al = loadAlignment(TEST_DATA, FileFormat.Stockholm);
     int i = 0;
     for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
     {
@@ -94,7 +605,7 @@ public class AlignmentTest
   /**
    * Test method that returns annotations that match on calcId.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testFindAnnotation_byCalcId()
   {
     Iterable<AlignmentAnnotation> anns = al
@@ -104,9 +615,87 @@ public class AlignmentTest
     AlignmentAnnotation ann = iter.next();
     assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
     assertFalse(iter.hasNext());
+
+    // invalid id
+    anns = al.findAnnotation("CalcIdForD.melanogaster.?");
+    assertFalse(iter.hasNext());
+    anns = al.findAnnotation(null);
+    assertFalse(iter.hasNext());
+  }
+
+  /**
+   * Test method that returns annotations that match on reference sequence,
+   * label, or calcId.
+   */
+  @Test(groups = { "Functional" })
+  public void testFindAnnotations_bySeqLabelandorCalcId()
+  {
+    // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test
+    /* Note - this is an incomplete test - need to check null or
+     * non-null [ matches, not matches ] behaviour for each of the three
+     * parameters..*/
+
+    // search for a single, unique calcId with wildcards on other params
+    Iterable<AlignmentAnnotation> anns = al.findAnnotations(null,
+            "CalcIdForD.melanogaster.2", null);
+    Iterator<AlignmentAnnotation> iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    AlignmentAnnotation ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // save reference to test sequence reference parameter
+    SequenceI rseq = ann.sequenceRef;
+
+    // search for annotation associated with a single sequence
+    anns = al.findAnnotations(rseq, null, null);
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a non-existant calcId
+    anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null);
+    iter = anns.iterator();
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a particular label - expect three
+    anns = al.findAnnotations(null, null, "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    // third found.. so
+    assertFalse(iter.hasNext());
+
+    // search for annotation on one sequence with a particular label - expect
+    // one
+    SequenceI sqfound;
+    anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+            "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    // expect reference to sequence 1 in the alignment
+    assertTrue(sqfound == iter.next().sequenceRef);
+    assertFalse(iter.hasNext());
+
+    // null on all parameters == find all annotations
+    anns = al.findAnnotations(null, null, null);
+    iter = anns.iterator();
+    int n = al.getAlignmentAnnotation().length;
+    while (iter.hasNext())
+    {
+      n--;
+      iter.next();
+    }
+    assertTrue("Found " + n + " fewer annotations from search.", n == 0);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testDeleteAllAnnotations_includingAutocalculated()
   {
     AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
@@ -120,7 +709,7 @@ public class AlignmentTest
     assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testDeleteAllAnnotations_excludingAutocalculated()
   {
     AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
@@ -144,31 +733,25 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAlignAs_dnaAsDna() throws IOException
   {
     // aligned cDNA:
-    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
+    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
     // unaligned cDNA:
-    AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA");
+    AlignmentI al2 = loadAlignment(CDNA_SEQS_2, FileFormat.Fasta);
 
     /*
      * Make mappings between sequences. The 'aligned cDNA' is playing the role
      * of what would normally be protein here.
      */
-    AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList ml = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 12 }, 1, 1);
-    acf.addMap(al2.getSequenceAt(0), al1.getSequenceAt(0), ml);
-    acf.addMap(al2.getSequenceAt(1), al1.getSequenceAt(1), ml);
-    al1.addCodonFrame(acf);
+    makeMappings(al1, al2);
 
     ((Alignment) al2).alignAs(al1, false, true);
-    assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0)
-            .getSequenceAsString());
-    assertEquals("-GG-GTC--AGG---CAGT", al2.getSequenceAt(1)
-            .getSequenceAsString());
+    assertEquals("GC-TC--GUC-GTACT",
+            al2.getSequenceAt(0).getSequenceAsString());
+    assertEquals("-GG-GTC--AGG--CAGT",
+            al2.getSequenceAt(1).getSequenceAsString());
   }
 
   /**
@@ -176,19 +759,16 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAlignAs_proteinAsCdna() throws IOException
   {
     // see also AlignmentUtilsTests
-    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
-    AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
-    AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList ml = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 4 }, 3, 1);
-    acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
-    acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
-    al2.addCodonFrame(acf);
+    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
+    makeMappings(al1, al2);
+
+    // Fudge - alignProteinAsCdna expects mappings to be on protein
+    al2.getCodonFrames().addAll(al1.getCodonFrames());
 
     ((Alignment) al2).alignAs(al1, false, true);
     assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString());
@@ -200,30 +780,112 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" }, enabled = true)
+  // TODO review / update this test after redesign of alignAs method
   public void testAlignAs_cdnaAsProtein() throws IOException
   {
     /*
      * Load alignments and add mappings for cDNA to protein
      */
-    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
-    AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
-    AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList ml = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 4 }, 3, 1);
-    acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
-    acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
-    al2.addCodonFrame(acf);
+    AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
+    makeMappings(al1, al2);
 
     /*
      * Realign DNA; currently keeping existing gaps in introns only
      */
     ((Alignment) al1).alignAs(al2, false, true);
-    assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
-            .getSequenceAsString());
-    assertEquals("---CGT---TAACGA---AGT", al1.getSequenceAt(1)
-            .getSequenceAsString());
+    assertEquals("ACG---GCUCCA------ACT---",
+            al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals("---CGT---TAACGA---AGT---",
+            al1.getSequenceAt(1).getSequenceAsString());
+  }
+
+  /**
+   * Test aligning cdna as per protein - single sequences
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  // TODO review / update this test after redesign of alignAs method
+  public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException
+  {
+    /*
+     * simple case insert one gap
+     */
+    verifyAlignAs(">dna\nCAAaaa\n", ">protein\nQ-K\n", "CAA---aaa");
+
+    /*
+     * simple case but with sequence offsets
+     */
+    verifyAlignAs(">dna/5-10\nCAAaaa\n", ">protein/20-21\nQ-K\n",
+            "CAA---aaa");
+
+    /*
+     * insert gaps as per protein, drop gaps within codons
+     */
+    verifyAlignAs(">dna/10-18\nCA-Aa-aa--AGA\n", ">aa/6-8\n-Q-K--R\n",
+            "---CAA---aaa------AGA");
+  }
+
+  /**
+   * Helper method that makes mappings and then aligns the first alignment as
+   * the second
+   * 
+   * @param fromSeqs
+   * @param toSeqs
+   * @param expected
+   * @throws IOException
+   */
+  public void verifyAlignAs(String fromSeqs, String toSeqs, String expected)
+          throws IOException
+  {
+    /*
+     * Load alignments and add mappings from nucleotide to protein (or from
+     * first to second if both the same type)
+     */
+    AlignmentI al1 = loadAlignment(fromSeqs, FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(toSeqs, FileFormat.Fasta);
+    makeMappings(al1, al2);
+
+    /*
+     * Realign DNA; currently keeping existing gaps in introns only
+     */
+    ((Alignment) al1).alignAs(al2, false, true);
+    assertEquals(expected, al1.getSequenceAt(0).getSequenceAsString());
+  }
+
+  /**
+   * Helper method to make mappings between sequences, and add the mappings to
+   * the 'mapped from' alignment
+   * 
+   * @param alFrom
+   * @param alTo
+   */
+  public void makeMappings(AlignmentI alFrom, AlignmentI alTo)
+  {
+    int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3);
+
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+
+    for (int i = 0; i < alFrom.getHeight(); i++)
+    {
+      SequenceI seqFrom = alFrom.getSequenceAt(i);
+      SequenceI seqTo = alTo.getSequenceAt(i);
+      MapList ml = new MapList(
+              new int[]
+              { seqFrom.getStart(), seqFrom.getEnd() },
+              new int[]
+              { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
+      acf.addMap(seqFrom, seqTo, ml);
+    }
+
+    /*
+     * not sure whether mappings 'belong' or protein or nucleotide
+     * alignment, so adding to both ;~)
+     */
+    alFrom.addCodonFrame(acf);
+    alTo.addCodonFrame(acf);
   }
 
   /**
@@ -232,7 +894,8 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" }, enabled = false)
+  // TODO review / update this test after redesign of alignAs method
   public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
   {
     /*
@@ -240,20 +903,21 @@ public class AlignmentTest
      */
     String dna1 = "A-Aa-gG-GCC-cT-TT";
     String dna2 = "c--CCGgg-TT--T-AA-A";
-    AlignmentI al1 = loadAlignment(">Seq1\n" + dna1 + "\n>Seq2\n" + dna2
-            + "\n", "FASTA");
-    AlignmentI al2 = loadAlignment(">Seq1\n-P--YK\n>Seq2\nG-T--F\n",
-            "FASTA");
+    AlignmentI al1 = loadAlignment(
+            ">Dna1/6-17\n" + dna1 + "\n>Dna2/20-31\n" + dna2 + "\n",
+            FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(
+            ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", FileFormat.Fasta);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
     // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
-    MapList ml1 = new MapList(new int[]
-    { 1, 2, 5, 8, 10, 12 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 },
+            new int[]
+            { 7, 9 }, 3, 1);
     acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
-    MapList ml2 = new MapList(new int[]
-    { 2, 4, 7, 12 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 },
+            new int[]
+            { 11, 13 }, 3, 1);
     acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
     al2.addCodonFrame(acf);
 
@@ -261,11 +925,11 @@ public class AlignmentTest
      * Align ignoring gaps in dna introns and exons
      */
     ((Alignment) al1).alignAs(al2, false, false);
-    assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
-            .getSequenceAsString());
+    assertEquals("---AAagG------GCCcTTT",
+            al1.getSequenceAt(0).getSequenceAsString());
     // note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
-    assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1)
-            .getSequenceAsString());
+    assertEquals("cCCGgg-TTT------AAA",
+            al1.getSequenceAt(1).getSequenceAsString());
 
     /*
      * Reset and realign, preserving gaps in dna introns and exons
@@ -276,9 +940,655 @@ public class AlignmentTest
     // String dna1 = "A-Aa-gG-GCC-cT-TT";
     // String dna2 = "c--CCGgg-TT--T-AA-A";
     // assumption: we include 'the greater of' protein/dna gap lengths, not both
-    assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
-            .getSequenceAsString());
-    assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
-            .getSequenceAsString());
+    assertEquals("---A-Aa-gG------GCC-cT-TT",
+            al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals("c--CCGgg-TT--T------AA-A",
+            al1.getSequenceAt(1).getSequenceAsString());
+  }
+
+  @Test(groups = "Functional")
+  public void testCopyConstructor() throws IOException
+  {
+    AlignmentI protein = loadAlignment(AA_SEQS_1, FileFormat.Fasta);
+    // create sequence and alignment datasets
+    protein.setDataset(null);
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    List<AlignedCodonFrame> acfList = Arrays
+            .asList(new AlignedCodonFrame[]
+            { acf });
+    protein.getDataset().setCodonFrames(acfList);
+    AlignmentI copy = new Alignment(protein);
+
+    /*
+     * copy has different aligned sequences but the same dataset sequences
+     */
+    assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
+    assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
+    assertSame(copy.getSequenceAt(0).getDatasetSequence(),
+            protein.getSequenceAt(0).getDatasetSequence());
+    assertSame(copy.getSequenceAt(1).getDatasetSequence(),
+            protein.getSequenceAt(1).getDatasetSequence());
+
+    // TODO should the copy constructor copy the dataset?
+    // or make a new one referring to the same dataset sequences??
+    assertNull(copy.getDataset());
+    // TODO test metadata is copied when AlignmentI is a dataset
+
+    // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
+    // .getDataset().getSequencesArray());
+  }
+
+  /**
+   * Test behaviour of createDataset
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testCreateDatasetAlignment() throws IOException
+  {
+    AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
+            DataSourceType.PASTE, FileFormat.Fasta);
+    /*
+     * create a dataset sequence on first sequence
+     * leave the second without one
+     */
+    protein.getSequenceAt(0).createDatasetSequence();
+    assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
+    assertNull(protein.getSequenceAt(1).getDatasetSequence());
+
+    /*
+     * add a mapping to the alignment
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    protein.addCodonFrame(acf);
+    assertNull(protein.getDataset());
+    assertTrue(protein.getCodonFrames().contains(acf));
+
+    /*
+     * create the alignment dataset
+     * note this creates sequence datasets where missing
+     * as a side-effect (in this case, on seq2
+     */
+    // TODO promote this method to AlignmentI
+    ((Alignment) protein).createDatasetAlignment();
+
+    AlignmentI ds = protein.getDataset();
+
+    // side-effect: dataset created on second sequence
+    assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
+    // dataset alignment has references to dataset sequences
+    assertEquals(ds.getSequenceAt(0),
+            protein.getSequenceAt(0).getDatasetSequence());
+    assertEquals(ds.getSequenceAt(1),
+            protein.getSequenceAt(1).getDatasetSequence());
+
+    // codon frames should have been moved to the dataset
+    // getCodonFrames() should delegate to the dataset:
+    assertTrue(protein.getCodonFrames().contains(acf));
+    // prove the codon frames are indeed on the dataset:
+    assertTrue(ds.getCodonFrames().contains(acf));
+  }
+
+  /**
+   * tests the addition of *all* sequences referred to by a sequence being added
+   * to the dataset
+   */
+  @Test(groups = "Functional")
+  public void testCreateDatasetAlignmentWithMappedToSeqs()
+  {
+    // Alignment with two sequences, gapped.
+    SequenceI sq1 = new Sequence("sq1", "A--SDF");
+    SequenceI sq2 = new Sequence("sq2", "G--TRQ");
+
+    // cross-references to two more sequences.
+    DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3");
+    SequenceI sq3 = new Sequence("sq3", "VWANG");
+    dbr.setMap(
+            new Mapping(sq3, new MapList(new int[]
+            { 1, 4 }, new int[] { 2, 5 }, 1, 1)));
+    sq1.addDBRef(dbr);
+
+    SequenceI sq4 = new Sequence("sq4", "ERKWI");
+    DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4");
+    dbr2.setMap(
+            new Mapping(sq4, new MapList(new int[]
+            { 1, 4 }, new int[] { 2, 5 }, 1, 1)));
+    sq2.addDBRef(dbr2);
+    // and a 1:1 codonframe mapping between them.
+    AlignedCodonFrame alc = new AlignedCodonFrame();
+    alc.addMap(sq1, sq2,
+            new MapList(new int[]
+            { 1, 4 }, new int[] { 1, 4 }, 1, 1));
+
+    AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 });
+
+    /*
+     * create the alignment dataset
+     * note this creates sequence datasets where missing
+     * as a side-effect (in this case, on seq2
+     */
+
+    // TODO promote this method to AlignmentI
+    ((Alignment) protein).createDatasetAlignment();
+
+    AlignmentI ds = protein.getDataset();
+
+    // should be 4 sequences in dataset - two materialised, and two propagated
+    // from dbref
+    assertEquals(4, ds.getHeight());
+    assertTrue(ds.getSequences().contains(sq1.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(sq2.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(sq3));
+    assertTrue(ds.getSequences().contains(sq4));
+    // Should have one codon frame mapping between sq1 and sq2 via dataset
+    // sequences
+    assertEquals(ds.getCodonFrame(sq1.getDatasetSequence()),
+            ds.getCodonFrame(sq2.getDatasetSequence()));
+  }
+
+  @Test(groups = "Functional")
+  public void testAddCodonFrame()
+  {
+    AlignmentI align = new Alignment(new SequenceI[] {});
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    align.addCodonFrame(acf);
+    assertEquals(1, align.getCodonFrames().size());
+    assertTrue(align.getCodonFrames().contains(acf));
+    // can't add the same object twice:
+    align.addCodonFrame(acf);
+    assertEquals(1, align.getCodonFrames().size());
+
+    // create dataset alignment - mappings move to dataset
+    ((Alignment) align).createDatasetAlignment();
+    assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
+    assertEquals(1, align.getCodonFrames().size());
+
+    AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    align.addCodonFrame(acf2);
+    assertTrue(align.getDataset().getCodonFrames().contains(acf));
+  }
+
+  @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");
+  }
+
+  /**
+   * Tests that dbrefs with mappings to sequence get updated if the sequence
+   * acquires a dataset sequence
+   */
+  @Test(groups = "Functional")
+  public void testCreateDataset_updateDbrefMappings()
+  {
+    SequenceI pep = new Sequence("pep", "ASD");
+    SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg");
+    SequenceI cds = new Sequence("cds", "GCCTCGGAT");
+
+    // add dbref from dna to peptide
+    DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
+    dbr.setMap(
+            new Mapping(pep, new MapList(new int[]
+            { 4, 15 }, new int[] { 1, 4 }, 3, 1)));
+    dna.addDBRef(dbr);
+
+    // add dbref from dna to peptide
+    DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep");
+    dbr2.setMap(
+            new Mapping(pep, new MapList(new int[]
+            { 1, 12 }, new int[] { 1, 4 }, 3, 1)));
+    cds.addDBRef(dbr2);
+
+    // add dbref from peptide to dna
+    DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna");
+    dbr3.setMap(
+            new Mapping(dna, new MapList(new int[]
+            { 1, 4 }, new int[] { 4, 15 }, 1, 3)));
+    pep.addDBRef(dbr3);
+
+    // add dbref from peptide to cds
+    DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds");
+    dbr4.setMap(
+            new Mapping(cds, new MapList(new int[]
+            { 1, 4 }, new int[] { 1, 12 }, 1, 3)));
+    pep.addDBRef(dbr4);
+
+    AlignmentI protein = new Alignment(new SequenceI[] { pep });
+
+    /*
+     * create the alignment dataset
+     */
+    ((Alignment) protein).createDatasetAlignment();
+
+    AlignmentI ds = protein.getDataset();
+
+    // should be 3 sequences in dataset
+    assertEquals(3, ds.getHeight());
+    assertTrue(ds.getSequences().contains(pep.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(dna));
+    assertTrue(ds.getSequences().contains(cds));
+
+    /*
+     * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
+     */
+    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" })
+  public void testFindGroup()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+    SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+
+    assertNull(a.findGroup(null, 0));
+    assertNull(a.findGroup(seq1, 1));
+    assertNull(a.findGroup(seq1, -1));
+
+    /*
+     * add a group consisting of just "DEF"
+     */
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(seq1, false);
+    sg1.setStartRes(3);
+    sg1.setEndRes(5);
+    a.addGroup(sg1);
+
+    assertNull(a.findGroup(seq1, 2)); // position not in group
+    assertNull(a.findGroup(seq1, 6)); // position not in group
+    assertNull(a.findGroup(seq2, 5)); // sequence not in group
+    assertSame(a.findGroup(seq1, 3), sg1); // yes
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * add a group consisting of 
+     * EF--
+     * KLMN
+     */
+    SequenceGroup sg2 = new SequenceGroup();
+    sg2.addSequence(seq1, false);
+    sg2.addSequence(seq2, false);
+    sg2.setStartRes(4);
+    sg2.setEndRes(7);
+    a.addGroup(sg2);
+
+    assertNull(a.findGroup(seq1, 2)); // unchanged
+    assertSame(a.findGroup(seq1, 3), sg1); // unchanged
+    /*
+     * if a residue is in more than one group, method returns
+     * the first found (in order groups were added)
+     */
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * seq2 only belongs to the second group
+     */
+    assertSame(a.findGroup(seq2, 4), sg2);
+    assertSame(a.findGroup(seq2, 5), sg2);
+    assertSame(a.findGroup(seq2, 6), sg2);
+    assertSame(a.findGroup(seq2, 7), sg2);
+    assertNull(a.findGroup(seq2, 3));
+    assertNull(a.findGroup(seq2, 8));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceByIndex()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete -ve index, nothing happens
+    a.deleteSequence(-1);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete beyond end of alignment, nothing happens
+    a.deleteSequence(14);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceBySeq()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(10);
+    a.deleteSequence(seq);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete non-existent sequence, nothing happens
+    seq = new Sequence("cds", "GCCTCGGAT");
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteHiddenSequence()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete a sequence which is hidden, check it is NOT removed from hidden
+    // sequences
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(2);
+    a.getHiddenSequences().hideSequence(seq);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+    a.deleteSequence(2);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+
+    // delete a sequence which is not hidden, check hiddenSequences are not
+    // affected
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 2);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+  }
+
+  @Test(
+    groups = "Functional",
+    expectedExceptions =
+    { IllegalArgumentException.class })
+  public void testSetDataset_selfReference()
+  {
+    SequenceI seq = new Sequence("a", "a");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+    alignment.setDataset(alignment);
+  }
+
+  @Test(groups = "Functional")
+  public void testAppend()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+    alignment.setGapCharacter('-');
+    SequenceI seq2 = new Sequence("seq1", "KP..L.FQII.");
+    AlignmentI alignment2 = new Alignment(new SequenceI[] { seq2 });
+    alignment2.setGapCharacter('.');
+
+    alignment.append(alignment2);
+
+    assertEquals('-', alignment.getGapCharacter());
+    assertSame(seq, alignment.getSequenceAt(0));
+    assertEquals("KP--L-FQII-",
+            alignment.getSequenceAt(1).getSequenceAsString());
+
+    // todo test coverage for annotations, mappings, groups,
+    // hidden sequences, properties
+  }
+
+  /**
+   * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+   * an annotation with a null calcId
+   * 
+   */
+  @Test(groups = "Functional")
+  public void testFindOrCreateForNullCalcId()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+    AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+            "Temperature Factor", null, false, seq, null);
+    assertNotNull(ala);
+    assertEquals(seq, ala.sequenceRef);
+    assertEquals("", ala.calcId);
+  }
+
+  @Test(groups = "Functional")
+  public void testPropagateInsertions()
+  {
+    // create an alignment with no gaps - this will be the profile seq and other
+    // JPRED seqs
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
+
+    // get the profileseq
+    SequenceI profileseq = al.getSequenceAt(0);
+    SequenceI gappedseq = new Sequence(profileseq);
+    gappedseq.insertCharAt(5, al.getGapCharacter());
+    gappedseq.insertCharAt(6, al.getGapCharacter());
+    gappedseq.insertCharAt(7, al.getGapCharacter());
+    gappedseq.insertCharAt(8, al.getGapCharacter());
+
+    // force different kinds of padding
+    al.getSequenceAt(3).deleteChars(2, 23);
+    al.getSequenceAt(4).deleteChars(2, 27);
+    al.getSequenceAt(5).deleteChars(10, 27);
+
+    // create an alignment view with the gapped sequence
+    SequenceI[] seqs = new SequenceI[1];
+    seqs[0] = gappedseq;
+    AlignmentI newal = new Alignment(seqs);
+    HiddenColumns hidden = new HiddenColumns();
+    hidden.hideColumns(15, 17);
+
+    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+            false);
+
+    // confirm that original contigs are as expected
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
+    int[] region = visible.next();
+    assertEquals("[0, 14]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[18, 24]", Arrays.toString(region));
+
+    // propagate insertions
+    HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+    // confirm that the contigs have changed to account for the gaps
+    visible = result.getVisContigsIterator(0, 25, false);
+    region = visible.next();
+    assertEquals("[0, 10]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[14, 24]", Arrays.toString(region));
+
+    // confirm the alignment has been changed so that the other sequences have
+    // gaps inserted where the columns are hidden
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
+
+  }
+
+  @Test(groups = "Functional")
+  public void testPropagateInsertionsOverlap()
+  {
+    // test propagateInsertions where gaps and hiddenColumns overlap
+
+    // create an alignment with no gaps - this will be the profile seq and other
+    // JPRED seqs
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+    // get the profileseq
+    SequenceI profileseq = al.getSequenceAt(0);
+    SequenceI gappedseq = new Sequence(profileseq);
+    gappedseq.insertCharAt(5, al.getGapCharacter());
+    gappedseq.insertCharAt(6, al.getGapCharacter());
+    gappedseq.insertCharAt(7, al.getGapCharacter());
+    gappedseq.insertCharAt(8, al.getGapCharacter());
+
+    // create an alignment view with the gapped sequence
+    SequenceI[] seqs = new SequenceI[1];
+    seqs[0] = gappedseq;
+    AlignmentI newal = new Alignment(seqs);
+
+    // hide columns so that some overlap with the gaps
+    HiddenColumns hidden = new HiddenColumns();
+    hidden.hideColumns(7, 10);
+
+    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+            false);
+
+    // confirm that original contigs are as expected
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
+    int[] region = visible.next();
+    assertEquals("[0, 6]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[11, 19]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // propagate insertions
+    HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+    // confirm that the contigs have changed to account for the gaps
+    visible = result.getVisContigsIterator(0, 20, false);
+    region = visible.next();
+    assertEquals("[0, 4]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[7, 19]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // confirm the alignment has been changed so that the other sequences have
+    // gaps inserted where the columns are hidden
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testPadGaps()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    a.setGapCharacter('.'); // this replaces existing gaps
+    assertEquals("ABCDEF..", seq1.getSequenceAsString());
+    a.padGaps();
+    // trailing gaps are pruned, short sequences padded with gap character
+    assertEquals("ABCDEF.", seq1.getSequenceAsString());
+    assertEquals(".JKLMNO", seq2.getSequenceAsString());
+    assertEquals(".PQR...", seq3.getSequenceAsString());
+  }
+
+  /**
+   * Test for setHiddenColumns, to check it returns true if the hidden columns
+   * have changed, else false
+   */
+  @Test(groups = { "Functional" })
+  public void testSetHiddenColumns()
+  {
+    AlignmentI al = new Alignment(new SequenceI[] {});
+    assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+    HiddenColumns hc = new HiddenColumns();
+    assertFalse(al.setHiddenColumns(hc)); // no change
+    assertSame(hc, al.getHiddenColumns());
+
+    hc.hideColumns(2, 4);
+    assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+    /*
+     * set a different object but with the same columns hidden
+     */
+    HiddenColumns hc2 = new HiddenColumns();
+    hc2.hideColumns(2, 4);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+    assertSame(hc2, al.getHiddenColumns());
+
+    assertTrue(al.setHiddenColumns(null));
+    assertNull(al.getHiddenColumns());
+    assertTrue(al.setHiddenColumns(hc));
+    assertSame(hc, al.getHiddenColumns());
+
+    al.getHiddenColumns().hideColumns(10, 12);
+    hc2.hideColumns(10, 12);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+
+    /*
+     * hide columns 15-16 then 17-18 in hc
+     * hide columns 15-18 in hc2
+     * these are not now 'equal' objects even though they
+     * represent the same set of columns
+     */
+    assertSame(hc2, al.getHiddenColumns());
+    hc.hideColumns(15, 16);
+    hc.hideColumns(17, 18);
+    hc2.hideColumns(15, 18);
+    assertFalse(hc.equals(hc2));
+    assertTrue(al.setHiddenColumns(hc)); // 'changed'
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getWidth());
+
+    // width includes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(9, a.getWidth());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getVisibleWidth());
+
+    // width excludes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(5, a.getVisibleWidth());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetContactMap()
+  {
+    // TODO
+    // 1. test adding/removing/manipulating contact maps with/without associated
+    // sequence(s) or groups
+    // 2. For sequence associated - ensure that inserting a gap in sequence
+    // results in the contact map being relocated accordingly
+    // 3. RENDERER QUESTION - should contact maps reflect gaps in the alignment
+    // ?
+
   }
 }