test/jalview/analysis/SequenceIdMatcherTest.java

   1 package jalview.analysis;
   2
   3 import jalview.datamodel.Sequence;
   4 import jalview.datamodel.SequenceI;
   5
   6 import java.util.Arrays;
   7
   8 import org.testng.Assert;
   9 import org.testng.annotations.Test;
  10
  11 public class SequenceIdMatcherTest
  12 {
  13   private static SequenceI[] someseqs = {
  14       new Sequence("A|ComplexId", "dummy"),
  15       new Sequence("A|ComplexId|confused", "dummy"),
  16       new Sequence("A|ComplexId|bits_of", "dummy"),
  17       new Sequence("ComplexId", "dummy"),
  18       new Sequence("A|ComplexIdNot", "dummy"),
  19       new Sequence("A ComplexId Id", "dummy"),
  20       new Sequence("complexid", "dummy") };
  21
  22   private static SequenceIdMatcher getMatcher()
  23   {
  24     return new SequenceIdMatcher(Arrays.asList(someseqs));
  25   }
  26
  27   @Test(groups = { "Functional" })
  28   public void findSelfAndOthers()
  29   {
  30     for (SequenceI sq : SequenceIdMatcherTest.someseqs)
  31     {
  32       SequenceI[] idmatches = getMatcher().findAllIdMatches(sq.getName());
  33       Assert.assertTrue(
  34               idmatches.length >= 1,
  35               "Couldn't recover at least one sequence for string '"
  36                       + sq.getName() + "'");
  37       SequenceI[] seqmatches = getMatcher().findIdMatch(
  38               new SequenceI[] { sq });
  39       Assert.assertTrue(seqmatches.length >= 1,
  40               "Couldn't recover at least one sequence for sequence object called '"
  41                       + sq.getName() + "'");
  42       Assert.assertTrue(seqmatches.length == idmatches.length,
  43               "Different matches found for '" + sq.getName() + "'");
  44       for (SequenceI sid : idmatches)
  45       {
  46         boolean found = false;
  47         for (SequenceI sobj : seqmatches)
  48         {
  49           if (sid == sobj)
  50           {
  51             found = true;
  52           }
  53         }
  54         Assert.assertTrue(
  55                 found,
  56                 "Different sequences recovered for Id "
  57                         + "and SequenceI (Couldn't find match for '"
  58                         + sid.getName() + "')");
  59
  60       }
  61     }
  62   }
  63
  64   @Test(groups = { "Functional" })
  65   public void testExactMatch()
  66   {
  67     SequenceI[] matches = getMatcher().findAllIdMatches("A|ComplexId");
  68     Assert.assertTrue(matches.length == 1,
  69             "Exact match failed for 'A|ComplexId'");
  70     matches = getMatcher().findAllIdMatches("A|ComplexId|confused");
  71     Assert.assertTrue(matches.length == 1,
  72             "Exact match failed for 'A|ComplexId|confused'");
  73     matches = getMatcher().findAllIdMatches("A|ComplexId|bits_of");
  74     Assert.assertTrue(matches.length == 1,
  75             "Exact match failed for 'A|ComplexId|bits_of'");
  76     matches = getMatcher().findAllIdMatches("A ComplexId Id");
  77     Assert.assertTrue(matches.length == 1,
  78             "Exact match failed for 'A Complex Id'");
  79
  80   }
  81
  82   public void testContainedMatch()
  83   {
  84
  85   }
  86 }