test/jalview/datamodel/features/FeatureMatcherTest.java

   1 package jalview.datamodel.features;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertFalse;
   5 import static org.testng.Assert.assertTrue;
   6
   7 import jalview.datamodel.SequenceFeature;
   8 import jalview.util.matcher.Condition;
   9
  10 import org.testng.annotations.Test;
  11
  12 public class FeatureMatcherTest
  13 {
  14   @Test
  15   public void testMatches_byLabel()
  16   {
  17     SequenceFeature sf = new SequenceFeature("Cath", "this is my label", 11,
  18             12, "grp");
  19
  20     /*
  21      * contains - not case sensitive
  22      */
  23     assertTrue(
  24             FeatureMatcher.byLabel(Condition.Contains, "IS").matches(sf));
  25     assertTrue(FeatureMatcher.byLabel(Condition.Contains, "").matches(sf));
  26     assertFalse(
  27             FeatureMatcher.byLabel(Condition.Contains, "ISNT").matches(sf));
  28
  29     /*
  30      * does not contain
  31      */
  32     assertTrue(FeatureMatcher.byLabel(Condition.NotContains, "isnt")
  33             .matches(sf));
  34     assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "is")
  35             .matches(sf));
  36
  37     /*
  38      * matches
  39      */
  40     assertTrue(FeatureMatcher.byLabel(Condition.Matches, "THIS is MY label")
  41             .matches(sf));
  42     assertFalse(FeatureMatcher.byLabel(Condition.Matches, "THIS is MY")
  43             .matches(sf));
  44
  45     /*
  46      * does not match
  47      */
  48     assertFalse(FeatureMatcher
  49             .byLabel(Condition.NotMatches, "THIS is MY label").matches(sf));
  50     assertTrue(FeatureMatcher.byLabel(Condition.NotMatches, "THIS is MY")
  51             .matches(sf));
  52
  53     /*
  54      * is present / not present
  55      */
  56     assertTrue(FeatureMatcher.byLabel(Condition.Present, "").matches(sf));
  57     assertFalse(
  58             FeatureMatcher.byLabel(Condition.NotPresent, "").matches(sf));
  59   }
  60
  61   @Test
  62   public void testMatches_byScore()
  63   {
  64     SequenceFeature sf = new SequenceFeature("Cath", "this is my label", 11,
  65             12, 3.2f, "grp");
  66
  67     assertTrue(FeatureMatcher.byScore(Condition.LT, "3.3").matches(sf));
  68     assertFalse(FeatureMatcher.byScore(Condition.LT, "3.2").matches(sf));
  69     assertFalse(FeatureMatcher.byScore(Condition.LT, "2.2").matches(sf));
  70
  71     assertTrue(FeatureMatcher.byScore(Condition.LE, "3.3").matches(sf));
  72     assertTrue(FeatureMatcher.byScore(Condition.LE, "3.2").matches(sf));
  73     assertFalse(FeatureMatcher.byScore(Condition.LE, "2.2").matches(sf));
  74
  75     assertFalse(FeatureMatcher.byScore(Condition.EQ, "3.3").matches(sf));
  76     assertTrue(FeatureMatcher.byScore(Condition.EQ, "3.2").matches(sf));
  77
  78     assertFalse(FeatureMatcher.byScore(Condition.GE, "3.3").matches(sf));
  79     assertTrue(FeatureMatcher.byScore(Condition.GE, "3.2").matches(sf));
  80     assertTrue(FeatureMatcher.byScore(Condition.GE, "2.2").matches(sf));
  81
  82     assertFalse(FeatureMatcher.byScore(Condition.GT, "3.3").matches(sf));
  83     assertFalse(FeatureMatcher.byScore(Condition.GT, "3.2").matches(sf));
  84     assertTrue(FeatureMatcher.byScore(Condition.GT, "2.2").matches(sf));
  85   }
  86   @Test
  87   public void testMatches_byAttribute()
  88   {
  89     /*
  90      * a numeric matcher - MatcherTest covers more conditions
  91      */
  92     FeatureMatcherI fm = FeatureMatcher
  93             .byAttribute(Condition.GE, "-2", "AF");
  94     SequenceFeature sf = new SequenceFeature("Cath", "desc", 11, 12, "grp");
  95     assertFalse(fm.matches(sf));
  96     sf.setValue("AF", "foobar");
  97     assertFalse(fm.matches(sf));
  98     sf.setValue("AF", "-2");
  99     assertTrue(fm.matches(sf));
 100     sf.setValue("AF", "-1");
 101     assertTrue(fm.matches(sf));
 102     sf.setValue("AF", "-3");
 103     assertFalse(fm.matches(sf));
 104     sf.setValue("AF", "");
 105     assertFalse(fm.matches(sf));
 106
 107     /*
 108      * a string pattern matcher
 109      */
 110     fm = FeatureMatcher.byAttribute(Condition.Contains, "Cat", "AF");
 111     assertFalse(fm.matches(sf));
 112     sf.setValue("AF", "raining cats and dogs");
 113     assertTrue(fm.matches(sf));
 114
 115     fm = FeatureMatcher.byAttribute(Condition.Present, "", "AC");
 116     assertFalse(fm.matches(sf));
 117     sf.setValue("AC", "21");
 118     assertTrue(fm.matches(sf));
 119
 120     fm = FeatureMatcher.byAttribute(Condition.NotPresent, "", "AC_Females");
 121     assertTrue(fm.matches(sf));
 122     sf.setValue("AC_Females", "21");
 123     assertFalse(fm.matches(sf));
 124   }
 125
 126   @Test
 127   public void testToString()
 128   {
 129     /*
 130      * toString uses the i18n translation of the enum conditions
 131      */
 132     FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.LT, "1.2",
 133             "AF");
 134     assertEquals(fm.toString(), "AF < 1.2");
 135
 136     /*
 137      * Present / NotPresent omit the value pattern
 138      */
 139     fm = FeatureMatcher.byAttribute(Condition.Present, "", "AF");
 140     assertEquals(fm.toString(), "AF Is present");
 141     fm = FeatureMatcher.byAttribute(Condition.NotPresent, "", "AF");
 142     assertEquals(fm.toString(), "AF Is not present");
 143   }
 144
 145   @Test
 146   public void testGetKey()
 147   {
 148     FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2",
 149             "AF");
 150     assertEquals(fm.getKey(), new String[] { "AF" });
 151
 152     /*
 153      * compound key (attribute / subattribute)
 154      */
 155     fm = FeatureMatcher.byAttribute(Condition.GE, "-2F", "CSQ",
 156             "Consequence");
 157     assertEquals(fm.getKey(), new String[] { "CSQ", "Consequence" });
 158   }
 159
 160   @Test
 161   public void testGetMatcher()
 162   {
 163     FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2f",
 164             "AF");
 165     assertEquals(fm.getMatcher().getCondition(), Condition.GE);
 166     assertEquals(fm.getMatcher().getFloatValue(), -2F);
 167     assertEquals(fm.getMatcher().getPattern(), "-2.0");
 168   }
 169 }