test/jalview/datamodel/AlignmentTest.java

   1 package jalview.datamodel;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.assertFalse;
   5 import static org.junit.Assert.assertTrue;
   6 import static org.junit.Assert.fail;
   7 import jalview.io.AppletFormatAdapter;
   8 import jalview.io.FormatAdapter;
   9
  10 import java.io.IOException;
  11 import java.util.Iterator;
  12
  13 import org.junit.Before;
  14 import org.junit.Test;
  15
  16 /**
  17  * Unit tests for Alignment datamodel.
  18  *
  19  * @author gmcarstairs
  20  *
  21  */
  22 public class AlignmentTest
  23 {
  24   // @formatter:off
  25   private static final String TEST_DATA =
  26           "# STOCKHOLM 1.0\n" +
  27           "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
  28           "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
  29           "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
  30           "D.melanogaster.1          G.AGCC.CU...AUGAUCGA\n" +
  31           "#=GR D.melanogaster.1 SS  ................((((\n" +
  32           "D.melanogaster.2          C.AUUCAACU.UAUGAGGAU\n" +
  33           "#=GR D.melanogaster.2 SS  ................((((\n" +
  34           "D.melanogaster.3          G.UGGCGCU..UAUGACGCA\n" +
  35           "#=GR D.melanogaster.3 SS  (.(((...(....(((((((\n" +
  36           "//";
  37
  38   private static final String TEST_DATA2 =
  39           ">TEST21 test21\n" +
  40           "AC-GG--CUC-CAA-CT\n" +
  41           ">TEST22 test22\n" +
  42           "-CG-TTA--ACG---AAGT\n";
  43
  44   private static final String TEST_DATA3 =
  45           ">TEST31 test31\n" +
  46           "K-QY--L\n" +
  47           ">TEST32 test32\n" +
  48           "-R-FP-W-\n";
  49
  50   private static final String TEST_DATA4 =
  51           ">TEST41 test41\n" +
  52           "GCTCGUCGTACT\n" +
  53           ">TEST42 test42\n" +
  54           "GGGTCAGGCAGT\n";
  55   // @formatter:on
  56
  57   private Alignment al;
  58
  59   /*
  60    * Read in Stockholm format test data including secondary structure
  61    * annotations.
  62    */
  63   @Before
  64   public void setUp() throws IOException
  65   {
  66     al = new FormatAdapter().readFile(TEST_DATA,
  67             AppletFormatAdapter.PASTE, "STH");
  68     int i = 0;
  69     for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
  70     {
  71       ann.setCalcId("CalcIdFor"
  72               + al.getSequenceAt(i).getName());
  73       i++;
  74     }
  75   }
  76
  77   /**
  78    * Test method that returns annotations that match on calcId.
  79    */
  80   @Test
  81   public void testFindAnnotation_byCalcId()
  82   {
  83     Iterable<AlignmentAnnotation> anns = al
  84             .findAnnotation("CalcIdForD.melanogaster.2");
  85     Iterator<AlignmentAnnotation> iter = anns.iterator();
  86     assertTrue(iter.hasNext());
  87     AlignmentAnnotation ann = iter.next();
  88     assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
  89     assertFalse(iter.hasNext());
  90   }
  91
  92   /**
  93    * Tests for method that checks for alignment 'mappability'.
  94    *
  95    * @throws IOException
  96    */
  97   @Test
  98   public void testIsMappableTo() throws IOException
  99   {
 100     al = new FormatAdapter().readFile(TEST_DATA2,
 101             AppletFormatAdapter.PASTE, "FASTA");
 102     al.setDataset(null);
 103
 104     // not mappable to self
 105     assertFalse(al.isMappableTo(al));
 106
 107     // dna mappable to protein and vice versa
 108     AlignmentI alp = new FormatAdapter().readFile(TEST_DATA3,
 109             AppletFormatAdapter.PASTE, "FASTA");
 110     alp.setDataset(null);
 111     assertTrue(al.isMappableTo(alp));
 112     assertTrue(alp.isMappableTo(al));
 113     assertFalse(alp.isMappableTo(alp));
 114
 115     // not mappable if any sequence length mismatch
 116     alp.getSequenceAt(1).setSequence("-R--FP-");
 117     alp.getSequenceAt(1).setDatasetSequence(new Sequence("", "RFP"));
 118     assertFalse(alp.isMappableTo(al));
 119     assertFalse(al.isMappableTo(alp));
 120
 121     // not mappable if number of sequences differs
 122     alp.deleteSequence(1);
 123     assertFalse(alp.isMappableTo(al));
 124     assertFalse(al.isMappableTo(alp));
 125   }
 126
 127   /**
 128    * Tests for realigning as per a supplied alignment.
 129    *
 130    * @throws IOException
 131    */
 132   @Test
 133   public void testAlignAs_dnaAsDna() throws IOException
 134   {
 135     // aligned cDNA:
 136     Alignment al1 = new FormatAdapter().readFile(TEST_DATA2,
 137             AppletFormatAdapter.PASTE, "FASTA");
 138     al1.setDataset(null);
 139     // unaligned cDNA:
 140     Alignment al2 = new FormatAdapter().readFile(TEST_DATA4,
 141             AppletFormatAdapter.PASTE, "FASTA");
 142     al2.setDataset(null);
 143
 144     al2.alignAs(al1);
 145     assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0)
 146             .getSequenceAsString());
 147     assertEquals("-GG-GTC--AGG---CAGT", al2.getSequenceAt(1)
 148             .getSequenceAsString());
 149   }
 150
 151   /**
 152    * Aligning protein from cDNA yet to be implemented.
 153    *
 154    * @throws IOException
 155    */
 156   @Test
 157   public void testAlignAs_proteinAsCdna() throws IOException
 158   {
 159     // aligned cDNA:
 160     Alignment al1 = new FormatAdapter().readFile(TEST_DATA2,
 161             AppletFormatAdapter.PASTE, "FASTA");
 162     al1.setDataset(null);
 163     // unaligned cDNA:
 164     Alignment al2 = new FormatAdapter().readFile(TEST_DATA3,
 165             AppletFormatAdapter.PASTE, "FASTA");
 166     al2.setDataset(null);
 167
 168     try
 169     {
 170       al2.alignAs(al1);
 171       fail("No exception thrown");
 172     } catch (UnsupportedOperationException e)
 173     {
 174       // expected;
 175     }
 176   }
 177
 178   /**
 179    * Test aligning cdna as per protein alignment.
 180    *
 181    * @throws IOException
 182    */
 183   @Test
 184   public void testAlignAs_cdnaAsProtein() throws IOException
 185   {
 186     // aligned cDNA:
 187     Alignment al1 = new FormatAdapter().readFile(TEST_DATA2,
 188             AppletFormatAdapter.PASTE, "FASTA");
 189     al1.setDataset(null);
 190     // unaligned cDNA:
 191     Alignment al2 = new FormatAdapter().readFile(TEST_DATA3,
 192             AppletFormatAdapter.PASTE, "FASTA");
 193     al2.setDataset(null);
 194
 195     al1.alignAs(al2);
 196     assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
 197             .getSequenceAsString());
 198     assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
 199             .getSequenceAsString());
 200   }
 201 }