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 jalview.io.AppletFormatAdapter;
   7
   8 import java.io.IOException;
   9 import java.util.Iterator;
  10
  11 import org.junit.Before;
  12 import org.junit.Test;
  13
  14 /**
  15  * Unit tests for Alignment datamodel.
  16  *
  17  * @author gmcarstairs
  18  *
  19  */
  20 public class AlignmentTest
  21 {
  22   // @formatter:off
  23   private static final String TEST_DATA =
  24           "# STOCKHOLM 1.0\n" +
  25           "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
  26           "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
  27           "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
  28           "D.melanogaster.1          G.AGCC.CU...AUGAUCGA\n" +
  29           "#=GR D.melanogaster.1 SS  ................((((\n" +
  30           "D.melanogaster.2          C.AUUCAACU.UAUGAGGAU\n" +
  31           "#=GR D.melanogaster.2 SS  ................((((\n" +
  32           "D.melanogaster.3          G.UGGCGCU..UAUGACGCA\n" +
  33           "#=GR D.melanogaster.3 SS  (.(((...(....(((((((\n" +
  34           "//";
  35   // @formatter:on
  36
  37
  38   private Alignment al;
  39
  40   /*
  41    * Read in Stockholm format test data including secondary structure
  42    * annotations.
  43    */
  44   @Before
  45   public void setUp() throws IOException
  46   {
  47     al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
  48             AppletFormatAdapter.PASTE, "STH");
  49     for (int i = 0; i < al.getSequencesArray().length; ++i)
  50     {
  51       al.getSequenceAt(i).setDatasetSequence(
  52               al.getSequenceAt(i).createDatasetSequence());
  53       al.addAnnotation(al.getSequenceAt(i).getAnnotation()[0]);
  54       al.getSequenceAt(i).getAnnotation()[0].setCalcId("CalcIdFor"
  55               + al.getSequenceAt(i).getName());
  56     }
  57   }
  58
  59   /**
  60    * Test method that returns annotations that match on calcId.
  61    */
  62   @Test
  63   public void testFindAnnotation_byCalcId()
  64   {
  65     Iterable<AlignmentAnnotation> anns = al
  66             .findAnnotation("CalcIdForD.melanogaster.2");
  67     Iterator<AlignmentAnnotation> iter = anns.iterator();
  68     assertTrue(iter.hasNext());
  69     AlignmentAnnotation ann = iter.next();
  70     assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
  71     assertFalse(iter.hasNext());
  72   }
  73 }