+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel.features;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
-import jalview.datamodel.SequenceFeature;
-import jalview.util.MessageManager;
-import jalview.util.matcher.Condition;
-
import java.util.Locale;
import org.testng.annotations.Test;
+import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
+import jalview.util.matcher.Condition;
+import jalview.util.matcher.Matcher;
+import jalview.util.matcher.MatcherI;
+import junit.extensions.PA;
+
public class FeatureMatcherTest
{
@Test(groups = "Functional")
/*
* a numeric matcher - MatcherTest covers more conditions
*/
- FeatureMatcherI fm = FeatureMatcher
- .byAttribute(Condition.GE, "-2", "AF");
+ FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2",
+ "AF");
SequenceFeature sf = new SequenceFeature("Cath", "desc", 11, 12, "grp");
assertFalse(fm.matches(sf));
sf.setValue("AF", "foobar");
}
@Test(groups = "Functional")
+ public void testIsByAttribute()
+ {
+ assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "foo")
+ .isByAttribute());
+ assertFalse(FeatureMatcher.byScore(Condition.LE, "-1").isByAttribute());
+ assertTrue(FeatureMatcher.byAttribute(Condition.LE, "-1", "AC")
+ .isByAttribute());
+ }
+
+ @Test(groups = "Functional")
public void testIsByLabel()
{
assertTrue(FeatureMatcher.byLabel(Condition.NotContains, "foo")
FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2f",
"AF");
assertEquals(fm.getMatcher().getCondition(), Condition.GE);
- assertEquals(fm.getMatcher().getFloatValue(), -2F);
+ assertEquals(PA.getValue(fm.getMatcher(), "floatValue"), -2F);
assertEquals(fm.getMatcher().getPattern(), "-2.0");
}
assertFalse(fm.isByLabel());
assertFalse(fm.isByScore());
assertEquals(fm.getAttribute(), new String[] { "AF" });
- assertSame(Condition.LT, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getFloatValue(), 1.2f);
- assertEquals(fm.getMatcher().getPattern(), "1.2");
+ MatcherI matcher = fm.getMatcher();
+ assertSame(Condition.LT, matcher.getCondition());
+ assertEquals(PA.getValue(matcher, "floatValue"), 1.2f);
+ assertSame(PA.getValue(matcher, "patternType"),
+ Matcher.PatternType.Float);
+ assertEquals(matcher.getPattern(), "1.2");
// quotes are optional, condition is not case sensitive
fm = FeatureMatcher.fromString("AF lt '1.2'");
+ matcher = fm.getMatcher();
assertFalse(fm.isByLabel());
assertFalse(fm.isByScore());
assertEquals(fm.getAttribute(), new String[] { "AF" });
- assertSame(Condition.LT, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getFloatValue(), 1.2f);
- assertEquals(fm.getMatcher().getPattern(), "1.2");
+ assertSame(Condition.LT, matcher.getCondition());
+ assertEquals(PA.getValue(matcher, "floatValue"), 1.2F);
+ assertEquals(matcher.getPattern(), "1.2");
fm = FeatureMatcher.fromString("'AF' Present");
+ matcher = fm.getMatcher();
assertFalse(fm.isByLabel());
assertFalse(fm.isByScore());
assertEquals(fm.getAttribute(), new String[] { "AF" });
- assertSame(Condition.Present, fm.getMatcher().getCondition());
+ assertSame(Condition.Present, matcher.getCondition());
+ assertSame(PA.getValue(matcher, "patternType"),
+ Matcher.PatternType.String);
fm = FeatureMatcher.fromString("CSQ:Consequence contains damaging");
+ matcher = fm.getMatcher();
assertFalse(fm.isByLabel());
assertFalse(fm.isByScore());
assertEquals(fm.getAttribute(), new String[] { "CSQ", "Consequence" });
- assertSame(Condition.Contains, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getPattern(), "damaging");
+ assertSame(Condition.Contains, matcher.getCondition());
+ assertEquals(matcher.getPattern(), "damaging");
// keyword Label is not case sensitive
fm = FeatureMatcher.fromString("LABEL Matches 'foobar'");
+ matcher = fm.getMatcher();
assertTrue(fm.isByLabel());
assertFalse(fm.isByScore());
assertNull(fm.getAttribute());
- assertSame(Condition.Matches, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getPattern(), "foobar");
+ assertSame(Condition.Matches, matcher.getCondition());
+ assertEquals(matcher.getPattern(), "foobar");
fm = FeatureMatcher.fromString("'Label' matches 'foo bar'");
+ matcher = fm.getMatcher();
assertTrue(fm.isByLabel());
assertFalse(fm.isByScore());
assertNull(fm.getAttribute());
- assertSame(Condition.Matches, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getPattern(), "foo bar");
+ assertSame(Condition.Matches, matcher.getCondition());
+ assertEquals(matcher.getPattern(), "foo bar");
// quotes optional on pattern
fm = FeatureMatcher.fromString("'Label' matches foo bar");
+ matcher = fm.getMatcher();
assertTrue(fm.isByLabel());
assertFalse(fm.isByScore());
assertNull(fm.getAttribute());
- assertSame(Condition.Matches, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getPattern(), "foo bar");
+ assertSame(Condition.Matches, matcher.getCondition());
+ assertEquals(matcher.getPattern(), "foo bar");
- fm = FeatureMatcher.fromString("Score GE 12.2");
+ // integer condition
+ fm = FeatureMatcher.fromString("Score GE 12");
+ matcher = fm.getMatcher();
assertFalse(fm.isByLabel());
assertTrue(fm.isByScore());
assertNull(fm.getAttribute());
- assertSame(Condition.GE, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getPattern(), "12.2");
- assertEquals(fm.getMatcher().getFloatValue(), 12.2f);
+ assertSame(Condition.GE, matcher.getCondition());
+ assertEquals(matcher.getPattern(), "12");
+ assertEquals(PA.getValue(matcher, "floatValue"), 0f);
+ assertEquals(PA.getValue(matcher, "longValue"), 12L);
+ assertSame(PA.getValue(matcher, "patternType"),
+ Matcher.PatternType.Integer);
// keyword Score is not case sensitive
fm = FeatureMatcher.fromString("'SCORE' ge '12.2'");
+ matcher = fm.getMatcher();
assertFalse(fm.isByLabel());
assertTrue(fm.isByScore());
assertNull(fm.getAttribute());
- assertSame(Condition.GE, fm.getMatcher().getCondition());
- assertEquals(fm.getMatcher().getPattern(), "12.2");
- assertEquals(fm.getMatcher().getFloatValue(), 12.2f);
+ assertSame(Condition.GE, matcher.getCondition());
+ assertEquals(matcher.getPattern(), "12.2");
+ assertEquals(PA.getValue(matcher, "floatValue"), 12.2F);
// invalid numeric pattern
assertNull(FeatureMatcher.fromString("Score eq twelve"));
git://source.jalview.org / jalview.git / blobdiff