*/
abstract boolean compare(SequenceFeature entry);
+ /**
+ * serves a search condition for finding the first feature whose start
+ * position follows a given target location
+ *
+ * @param target
+ * @return
+ */
static SearchCriterion byStart(final long target)
{
return new SearchCriterion() {
};
}
+ /**
+ * serves a search condition for finding the first feature whose end
+ * position follows a given target location
+ *
+ * @param target
+ * @return
+ */
static SearchCriterion byEnd(final long target)
{
return new SearchCriterion()
};
}
+ /**
+ * serves a search condition for finding the first feature which follows the
+ * given range as determined by a supplied comparator
+ *
+ * @param target
+ * @return
+ */
static SearchCriterion byFeature(final ContiguousI to,
final Comparator<ContiguousI> rc)
{
*/
public boolean addFeature(SequenceFeature feature)
{
+ if (contains(feature))
+ {
+ return false;
+ }
+
/*
* keep a record of feature groups
*/
}
else
{
- if (!contains(nonNestedFeatures, feature))
+ added = addNonNestedFeature(feature);
+ if (!added)
{
- added = addNonNestedFeature(feature);
- if (!added)
- {
- /*
- * detected a nested feature - put it in the NCList structure
- */
- added = addNestedFeature(feature);
- }
+ /*
+ * detected a nested feature - put it in the NCList structure
+ */
+ added = addNestedFeature(feature);
}
}
}
/**
+ * Answers true if this store contains the given feature (testing by
+ * SequenceFeature.equals), else false
+ *
+ * @param feature
+ * @return
+ */
+ public boolean contains(SequenceFeature feature)
+ {
+ if (feature.isNonPositional())
+ {
+ return nonPositionalFeatures == null ? false : nonPositionalFeatures
+ .contains(feature);
+ }
+
+ if (feature.isContactFeature())
+ {
+ return contactFeatureStarts == null ? false : listContains(
+ contactFeatureStarts, feature);
+ }
+
+ if (listContains(nonNestedFeatures, feature))
+ {
+ return true;
+ }
+
+ return nestedFeatures == null ? false : nestedFeatures
+ .contains(feature);
+ }
+
+ /**
* Answers the 'length' of the feature, counting 0 for non-positional features
* and 1 for contact features
*
/**
* Adds the feature to the list of non-positional features (with lazy
- * instantiation of the list if it is null), and returns true. If the
- * non-positional features already include the new feature (by equality test),
- * then it is not added, and this method returns false. The feature group is
- * added to the set of distinct feature groups for non-positional features.
+ * instantiation of the list if it is null), and returns true. The feature
+ * group is added to the set of distinct feature groups for non-positional
+ * features. This method allows duplicate features, so test before calling to
+ * prevent this.
*
* @param feature
*/
{
nonPositionalFeatures = new ArrayList<SequenceFeature>();
}
- if (nonPositionalFeatures.contains(feature))
- {
- return false;
- }
nonPositionalFeatures.add(feature);
/**
* Add a contact feature to the lists that hold them ordered by start (first
* contact) and by end (second contact) position, ensuring the lists remain
- * ordered, and returns true. If the contact feature lists already contain the
- * given feature (by test for equality), does not add it and returns false.
+ * ordered, and returns true. This method allows duplicate features to be
+ * added, so test before calling to avoid this.
*
* @param feature
* @return
contactFeatureEnds = new ArrayList<SequenceFeature>();
}
- if (contains(contactFeatureStarts, feature))
- {
- return false;
- }
-
/*
* binary search the sorted list to find the insertion point
*/
* @param feature
* @return
*/
- protected static boolean contains(List<SequenceFeature> features,
+ protected static boolean listContains(List<SequenceFeature> features,
SequenceFeature feature)
{
if (features == null || feature == null)
* Scans the list of non-nested features, starting from startIndex, to find
* those that overlap the from-to range, and adds them to the result list.
* Returns the index of the first feature whose start position is after the
- * target range (or the length of the whole list if none such feature exists).
+ * target range (or the length of the whole list if no such feature exists).
*
* @param startIndex
* @param from
{
break;
}
- int start = sf.getBegin();
- int end = sf.getEnd();
- if (start <= to && end >= from)
+ if (sf.getBegin() <= to && sf.getEnd() >= from)
{
result.add(sf);
}
/*
* add contact
*/
- SequenceFeature sf5 = new SequenceFeature("Disulfide bond", "", 0, 0,
+ SequenceFeature sf5 = new SequenceFeature("Disulfide bond", "", 10, 20,
Float.NaN, null);
assertTrue(fs.addFeature(sf5));
assertEquals(fs.getFeatureCount(true), 2); // positional - add 1 for contact
assertEquals(fs.getFeatureCount(false), 1); // non-positional
- SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "", 0, 0,
+ SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "", 10, 20,
Float.NaN, null);
assertFalse(fs.addFeature(sf6)); // already stored
assertEquals(fs.getFeatureCount(true), 2); // no change
}
@Test(groups = "Functional")
- public void testContains()
+ public void testListContains()
{
- assertFalse(FeatureStore.contains(null, null));
+ assertFalse(FeatureStore.listContains(null, null));
List<SequenceFeature> features = new ArrayList<SequenceFeature>();
- assertFalse(FeatureStore.contains(features, null));
+ assertFalse(FeatureStore.listContains(features, null));
SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
"group1");
- assertFalse(FeatureStore.contains(null, sf1));
- assertFalse(FeatureStore.contains(features, sf1));
+ assertFalse(FeatureStore.listContains(null, sf1));
+ assertFalse(FeatureStore.listContains(features, sf1));
features.add(sf1);
SequenceFeature sf2 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
"group1");
// sf2.equals(sf1) so contains should return true
- assertTrue(FeatureStore.contains(features, sf2));
- assertFalse(FeatureStore.contains(features, sf3));
+ assertTrue(FeatureStore.listContains(features, sf2));
+ assertFalse(FeatureStore.listContains(features, sf3));
}
@Test(groups = "Functional")
assertEquals(pos.get(1).getBegin(), 13);
assertEquals(pos.get(1).getEnd(), 22);
}
+
+ @Test(groups = "Functional")
+ public void testDelete_readd()
+ {
+ /*
+ * add a feature and a nested feature
+ */
+ FeatureStore store = new FeatureStore();
+ SequenceFeature sf1 = addFeature(store, 10, 20);
+ // sf2 is nested in sf1 so will be stored in nestedFeatures
+ SequenceFeature sf2 = addFeature(store, 12, 14);
+ List<SequenceFeature> features = store.getPositionalFeatures();
+ assertEquals(features.size(), 2);
+ assertTrue(features.contains(sf1));
+ assertTrue(features.contains(sf2));
+ assertTrue(store.nonNestedFeatures.contains(sf1));
+ assertTrue(store.nestedFeatures.contains(sf2));
+
+ /*
+ * delete the first feature
+ */
+ assertTrue(store.delete(sf1));
+ features = store.getPositionalFeatures();
+ assertFalse(features.contains(sf1));
+ assertTrue(features.contains(sf2));
+
+ /*
+ * re-add the 'nested' feature; is it now duplicated?
+ */
+ store.addFeature(sf2);
+ features = store.getPositionalFeatures();
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf2));
+ }
+
+ @Test(groups = "Functional")
+ 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 sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
+ "group1");
+ SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f,
+ "group1");
+ SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "", 5, 15,
+ Float.NaN, "group1");
+ SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "", 5, 15,
+ Float.NaN, "group2");
+
+ fs.addFeature(sf1);
+ fs.addFeature(sf3);
+ fs.addFeature(sf5);
+ assertTrue(fs.contains(sf1)); // positional feature
+ assertTrue(fs.contains(new SequenceFeature(sf1))); // identical feature
+ assertFalse(fs.contains(sf2)); // different group
+ assertTrue(fs.contains(sf3)); // non-positional
+ assertTrue(fs.contains(new SequenceFeature(sf3)));
+ assertFalse(fs.contains(sf4)); // different score
+ assertTrue(fs.contains(sf5)); // contact feature
+ assertTrue(fs.contains(new SequenceFeature(sf5)));
+ assertFalse(fs.contains(sf6)); // different group
+
+ /*
+ * add a nested feature
+ */
+ SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16,
+ Float.NaN, "group1");
+ fs.addFeature(sf7);
+ assertTrue(fs.contains(sf7));
+ assertTrue(fs.contains(new SequenceFeature(sf7)));
+
+ /*
+ * delete the outer (enclosing, non-nested) feature
+ */
+ fs.delete(sf1);
+ assertFalse(fs.contains(sf1));
+ assertTrue(fs.contains(sf7));
+ }
}
git://source.jalview.org / jalview.git / commitdiff