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JAL-2843 read/write feature filters from/to Jalview features file
[jalview.git]
/
test
/
jalview
/
datamodel
/
features
/
SequenceFeaturesTest.java
diff --git
a/test/jalview/datamodel/features/SequenceFeaturesTest.java
b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index
b7b52a7
..
39d6dce
100644
(file)
--- a/
test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/
test/jalview/datamodel/features/SequenceFeaturesTest.java
@@
-10,8
+10,11
@@
import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import java.util.Set;
+import junit.extensions.PA;
+
import org.testng.annotations.Test;
public class SequenceFeaturesTest
import org.testng.annotations.Test;
public class SequenceFeaturesTest
@@
-886,12
+889,15
@@
public class SequenceFeaturesTest
* no type specified - get all types stored
* they are returned in keyset (alphabetical) order
*/
* no type specified - get all types stored
* they are returned in keyset (alphabetical) order
*/
- Iterable<String> types = sf.varargToTypes();
- Iterator<String> iterator = types.iterator();
+ Map<String, FeatureStore> featureStores = (Map<String, FeatureStore>) PA
+ .getValue(sf, "featureStore");
+
+ Iterable<FeatureStore> types = sf.varargToTypes();
+ Iterator<FeatureStore> iterator = types.iterator();
assertTrue(iterator.hasNext());
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Cath");
+ assertSame(iterator.next(), featureStores.get("Cath"));
assertTrue(iterator.hasNext());
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
+ assertSame(iterator.next(), featureStores.get("Metal"));
assertFalse(iterator.hasNext());
/*
assertFalse(iterator.hasNext());
/*
@@
-901,9
+907,9
@@
public class SequenceFeaturesTest
types = sf.varargToTypes(new String[] {});
iterator = types.iterator();
assertTrue(iterator.hasNext());
types = sf.varargToTypes(new String[] {});
iterator = types.iterator();
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Cath");
+ assertSame(iterator.next(), featureStores.get("Cath"));
assertTrue(iterator.hasNext());
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
+ assertSame(iterator.next(), featureStores.get("Metal"));
assertFalse(iterator.hasNext());
/*
assertFalse(iterator.hasNext());
/*
@@
-919,9
+925,9
@@
public class SequenceFeaturesTest
types = sf.varargToTypes((String[]) null);
iterator = types.iterator();
assertTrue(iterator.hasNext());
types = sf.varargToTypes((String[]) null);
iterator = types.iterator();
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Cath");
+ assertSame(iterator.next(), featureStores.get("Cath"));
assertTrue(iterator.hasNext());
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
+ assertSame(iterator.next(), featureStores.get("Metal"));
assertFalse(iterator.hasNext());
/*
assertFalse(iterator.hasNext());
/*
@@
-930,29
+936,27
@@
public class SequenceFeaturesTest
types = sf.varargToTypes("Metal");
iterator = types.iterator();
assertTrue(iterator.hasNext());
types = sf.varargToTypes("Metal");
iterator = types.iterator();
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
+ assertSame(iterator.next(), featureStores.get("Metal"));
assertFalse(iterator.hasNext());
/*
* two types specified - get sorted alphabetically
*/
assertFalse(iterator.hasNext());
/*
* two types specified - get sorted alphabetically
*/
- types = sf.varargToTypes("Metal", "Helix");
+ types = sf.varargToTypes("Metal", "Cath");
iterator = types.iterator();
assertTrue(iterator.hasNext());
iterator = types.iterator();
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Helix");
+ assertSame(iterator.next(), featureStores.get("Cath"));
assertTrue(iterator.hasNext());
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
+ assertSame(iterator.next(), featureStores.get("Metal"));
assertFalse(iterator.hasNext());
/*
assertFalse(iterator.hasNext());
/*
- * null type included - should get removed
+ * null type included - should be ignored
*/
types = sf.varargToTypes("Metal", null, "Helix");
iterator = types.iterator();
assertTrue(iterator.hasNext());
*/
types = sf.varargToTypes("Metal", null, "Helix");
iterator = types.iterator();
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Helix");
- assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
+ assertSame(iterator.next(), featureStores.get("Metal"));
assertFalse(iterator.hasNext());
}
assertFalse(iterator.hasNext());
}
@@
-1028,6
+1032,9
@@
public class SequenceFeaturesTest
assertEquals(features.size(), 2);
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
assertEquals(features.size(), 2);
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf3));
+
+ features = store.getFeaturesByOntology("sequence_variant");
+ assertTrue(features.isEmpty());
}
@Test(groups = "Functional")
}
@Test(groups = "Functional")