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   private static SequenceIdMatcher getWordMatcher()
  28   {
  29     return new SequenceIdMatcher(true, Arrays.asList(someseqs));
  30   }
  31
  32   @Test(groups = { "Functional" })
  33   public void findSelfAndOthers()
  34   {
  35     for (SequenceI sq : SequenceIdMatcherTest.someseqs)
  36     {
  37       SequenceI[] idmatches = getMatcher().findAllIdMatches(sq.getName());
  38       Assert.assertTrue(
  39               idmatches.length >= 1,
  40               "Couldn't recover at least one sequence for string '"
  41                       + sq.getName() + "'");
  42       SequenceI[] seqmatches = getMatcher().findIdMatch(
  43               new SequenceI[] { sq });
  44       Assert.assertEquals(1, seqmatches.length,
  45               "Expected to recover one sequence for sequence object called '"
  46                       + sq.getName() + "'");
  47       Assert.assertEquals(sq, seqmatches[0],
  48               "Expected to recover the sequence queried with findIdMatch(SequenceI[])");
  49       // TODO: complexid and ComplexId are identical with case-insensitive
  50       // matching. This assert fails because of this.
  51       // Assert.assertTrue(seqmatches.length == idmatches.length,
  52       // "Different matches found for '" + sq.getName() + "'");
  53       for (SequenceI sid : seqmatches)
  54       {
  55         boolean found = false;
  56         for (SequenceI sobj : idmatches)
  57         {
  58           if (sid == sobj)
  59           {
  60             found = true;
  61           }
  62         }
  63         Assert.assertTrue(
  64                 found,
  65                 "Different sequences recovered for Id "
  66                         + "and SequenceI (Couldn't find match for '"
  67                         + sid.getName() + "')");
  68
  69       }
  70     }
  71   }
  72
  73   @Test(groups = { "Functional" })
  74   public void testExactMatch()
  75   {
  76     SequenceI[] matches = getMatcher().findAllIdMatches("A|ComplexId");
  77     Assert.assertTrue(matches.length == 1,
  78             "Exact match failed for 'A|ComplexId'");
  79     matches = getMatcher().findAllIdMatches("A|ComplexId|confused");
  80     Assert.assertTrue(matches.length == 1,
  81             "Exact match failed for 'A|ComplexId|confused'");
  82     matches = getMatcher().findAllIdMatches("A|ComplexId|bits_of");
  83     Assert.assertTrue(matches.length == 1,
  84             "Exact match failed for 'A|ComplexId|bits_of'");
  85     matches = getMatcher().findAllIdMatches("A ComplexId Id");
  86     Assert.assertTrue(matches.length == 1,
  87             "Exact match failed for 'A Complex Id'");
  88
  89   }
  90
  91   @Test(groups = { "Functional" })
  92   public void testCaseInsensitiveMatch()
  93   {
  94     Assert.assertNotNull(getMatcher().findIdMatch("a|complexid"),
  95             "Couldn't retrieve a single case insensitive match.");
  96   }
  97
  98   @Test(groups = { "Functional" })
  99   public void testFlankingMatch()
 100   {
 101     SequenceI[] match = getMatcher().findAllIdMatches("complexId");
 102     // should find two matches - one case exact, the other case inexact.
 103     Assert.assertNotNull(match, "Exact matches not found.");
 104     Assert.assertEquals(match.length, 2,
 105             "Expected two exact matches to be found.");
 106     SequenceI[] fmatch = getWordMatcher()
 107             .findAllIdMatches("complexId");
 108     // should find 6 distinct sequences
 109     Assert.assertNotNull(fmatch, "Flanking matches not found.");
 110     Assert.assertEquals(fmatch.length, 6,
 111             "Couldn't find all entries with IDs containing 'complexId' word match");
 112
 113   }
 114
 115 }