+/*
+ * 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.assertFalse;
+import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
import jalview.datamodel.SequenceFeature;
public void testFindFeatures_nonNested()
{
FeatureStore fs = new FeatureStore();
- fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN,
- null));
+ fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN, null));
// same range different description
fs.addFeature(new SequenceFeature("", "desc", 10, 20, Float.NaN, null));
fs.addFeature(new SequenceFeature("", "", 15, 25, Float.NaN, null));
assertTrue(overlaps.contains(sf));
}
- /**
- * Tests for the method that returns false for an attempt to add a feature
- * that would enclose, or be enclosed by, another feature
- */
- @Test(groups = "Functional")
- public void testAddNonNestedFeature()
- {
- FeatureStore fs = new FeatureStore();
-
- String type = "Domain";
- SequenceFeature sf1 = new SequenceFeature(type, type, 10, 20,
- Float.NaN, null);
- assertTrue(fs.addNonNestedFeature(sf1));
-
- // co-located feature is ok
- SequenceFeature sf2 = new SequenceFeature(type, type, 10, 20,
- Float.NaN, null);
- assertTrue(fs.addNonNestedFeature(sf2));
-
- // overlap left is ok
- SequenceFeature sf3 = new SequenceFeature(type, type, 5, 15, Float.NaN,
- null);
- assertTrue(fs.addNonNestedFeature(sf3));
-
- // overlap right is ok
- SequenceFeature sf4 = new SequenceFeature(type, type, 15, 25,
- Float.NaN, null);
- assertTrue(fs.addNonNestedFeature(sf4));
-
- // add enclosing feature is not ok
- SequenceFeature sf5 = new SequenceFeature(type, type, 10, 21,
- Float.NaN, null);
- assertFalse(fs.addNonNestedFeature(sf5));
- SequenceFeature sf6 = new SequenceFeature(type, type, 4, 15, Float.NaN,
- null);
- assertFalse(fs.addNonNestedFeature(sf6));
- SequenceFeature sf7 = new SequenceFeature(type, type, 1, 50, Float.NaN,
- null);
- assertFalse(fs.addNonNestedFeature(sf7));
-
- // add enclosed feature is not ok
- SequenceFeature sf8 = new SequenceFeature(type, type, 10, 19,
- Float.NaN, null);
- assertFalse(fs.addNonNestedFeature(sf8));
- SequenceFeature sf9 = new SequenceFeature(type, type, 16, 25,
- Float.NaN, null);
- assertFalse(fs.addNonNestedFeature(sf9));
- SequenceFeature sf10 = new SequenceFeature(type, type, 7, 7, Float.NaN,
- null);
- assertFalse(fs.addNonNestedFeature(sf10));
- }
-
@Test(groups = "Functional")
public void testGetPositionalFeatures()
{
Float.NaN, null);
store.addFeature(sf6);
// contact feature
- SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
- 18, 45, Float.NaN, null);
+ SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", 18,
+ 45, Float.NaN, null);
store.addFeature(sf7);
List<SequenceFeature> features = store.getPositionalFeatures();
/*
* contact feature deletion
*/
- SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11,
- 23, Float.NaN, null);
+ SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11, 23,
+ Float.NaN, null);
store.addFeature(sf3);
assertEquals(store.getPositionalFeatures().size(), 1);
assertTrue(store.getPositionalFeatures().contains(sf3));
{
FeatureStore fs = new FeatureStore();
- SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, null);
- SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, null);
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ null);
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ null);
assertTrue(fs.addFeature(sf1));
assertEquals(fs.getFeatureCount(true), 1); // positional
/*
* non-nested feature
*/
- SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, null);
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ null);
fs.addFeature(sf1);
assertFalse(fs.isEmpty());
assertEquals(fs.getFeatureCount(true), 1);
/*
* contact feature
*/
- sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN, null);
+ sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN,
+ null);
fs.addFeature(sf1);
assertFalse(fs.isEmpty());
assertEquals(fs.getFeatureCount(true), 1);
* sf2, sf3 added as nested features
*/
sf1 = new SequenceFeature("Cath", "", 19, 49, Float.NaN, null);
- SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40,
- Float.NaN, null);
- SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35,
- Float.NaN, null);
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40, Float.NaN,
+ null);
+ SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35, Float.NaN,
+ null);
fs.addFeature(sf1);
fs.addFeature(sf2);
fs.addFeature(sf3);
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
- // FeatureStore should now only contain features in the NCList
- assertTrue(fs.nonNestedFeatures.isEmpty());
- assertEquals(fs.nestedFeatures.size(), 2);
+ assertEquals(fs.features.size(), 2);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
assertTrue(fs.getFeatureGroups(true).isEmpty());
assertTrue(fs.getFeatureGroups(false).isEmpty());
- SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f,
+ "group1");
fs.addFeature(sf1);
Set<String> groups = fs.getFeatureGroups(true);
assertEquals(groups.size(), 1);
/*
* add another feature of the same group, delete one, delete both
*/
- SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group1");
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ "group1");
fs.addFeature(sf2);
groups = fs.getFeatureGroups(true);
assertEquals(groups.size(), 1);
groups = fs.getFeatureGroups(true);
assertTrue(fs.getFeatureGroups(true).isEmpty());
- SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group2");
+ SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ "group2");
fs.addFeature(sf3);
- SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "Group2");
+ SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ "Group2");
fs.addFeature(sf4);
- SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f, null);
+ SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ null);
fs.addFeature(sf5);
groups = fs.getFeatureGroups(true);
assertEquals(groups.size(), 3);
assertEquals(fs.getTotalFeatureLength(), 93);
// contact features count 1
- SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc",
- 15, 35, 1f, "group1");
+ SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc", 15,
+ 35, 1f, "group1");
fs.addFeature(sf3);
assertEquals(fs.getTotalFeatureLength(), 94);
/*
* positional feature
*/
- SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f,
+ "group1");
assertEquals(FeatureStore.getFeatureLength(sf1), 11);
-
+
/*
* non-positional feature
*/
/*
* contact feature counts 1
*/
- SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc",
- 14, 28, 1f, "AGroup");
+ SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc", 14,
+ 28, 1f, "AGroup");
assertEquals(FeatureStore.getFeatureLength(sf3), 1);
}
public void testListContains()
{
assertFalse(FeatureStore.listContains(null, null));
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> features = new ArrayList<>();
assertFalse(FeatureStore.listContains(features, null));
SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
public void testShiftFeatures()
{
FeatureStore fs = new FeatureStore();
- assertFalse(fs.shiftFeatures(1));
+ assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
fs.addFeature(sf1);
fs.addFeature(sf4);
/*
- * shift features right by 5
+ * shift all features right by 5
*/
- assertTrue(fs.shiftFeatures(5));
+ assertTrue(fs.shiftFeatures(0, 5));
// non-positional features untouched:
List<SequenceFeature> nonPos = fs.getNonPositionalFeatures();
* feature at [7-10] should be removed
* feature at [13-19] should become [1-4]
*/
- assertTrue(fs.shiftFeatures(-15));
+ assertTrue(fs.shiftFeatures(0, -15));
pos = fs.getPositionalFeatures();
assertEquals(pos.size(), 2);
SequenceFeatures.sortFeatures(pos, true);
assertEquals(pos.get(0).getEnd(), 4);
assertEquals(pos.get(1).getBegin(), 13);
assertEquals(pos.get(1).getEnd(), 22);
+
+ /*
+ * shift right by 4 from position 2 onwards
+ * feature at [1-4] unchanged, feature at [13-22] shifts
+ */
+ assertTrue(fs.shiftFeatures(2, 4));
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertEquals(pos.get(0).getBegin(), 1);
+ assertEquals(pos.get(0).getEnd(), 4);
+ assertEquals(pos.get(1).getBegin(), 17);
+ assertEquals(pos.get(1).getEnd(), 26);
+
+ /*
+ * shift right by 4 from position 18 onwards
+ * should be no change
+ */
+ SequenceFeature f1 = pos.get(0);
+ SequenceFeature f2 = pos.get(1);
+ assertFalse(fs.shiftFeatures(18, 4)); // no update
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertSame(pos.get(0), f1);
+ assertSame(pos.get(1), f2);
}
@Test(groups = "Functional")
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
- assertTrue(store.nonNestedFeatures.contains(sf1));
- assertTrue(store.nestedFeatures.contains(sf2));
-
+ assertTrue(store.features.contains(sf1));
+ assertTrue(store.features.contains(sf2));
+
/*
* delete the first feature
*/
public void testContains()
{
FeatureStore fs = new FeatureStore();
- SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, "group1");
- SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, "group2");
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ "group1");
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ "group2");
SequenceFeature sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
"group1");
SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f,
/*
* add a nested feature
*/
- SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16,
- Float.NaN, "group1");
+ SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16, Float.NaN,
+ "group1");
fs.addFeature(sf7);
assertTrue(fs.contains(sf7));
assertTrue(fs.contains(new SequenceFeature(sf7)));
git://source.jalview.org / jalview.git / blobdiff