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JAL-3383 removed FeatureStore.getFeatures() as 'breaks encapsulation'
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 3 Oct 2019 11:41:09 +0000
(12:41 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 3 Oct 2019 11:41:09 +0000
(12:41 +0100)
src/jalview/datamodel/features/FeatureStore.java
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test/jalview/datamodel/features/FeatureStoreLinkedTest.java
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test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
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test/jalview/datamodel/features/FeatureStoreTest.java
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diff --git
a/src/jalview/datamodel/features/FeatureStore.java
b/src/jalview/datamodel/features/FeatureStore.java
index
fff7127
..
c582e56
100644
(file)
--- a/
src/jalview/datamodel/features/FeatureStore.java
+++ b/
src/jalview/datamodel/features/FeatureStore.java
@@
-566,11
+566,6
@@
public class FeatureStore
}
}
}
}
- public Collection<SequenceFeature> getFeatures()
- {
- return features;
- }
-
/**
* Answers a list of all either positional or non-positional features whose
* feature group matches the given group (which may be null)
/**
* Answers a list of all either positional or non-positional features whose
* feature group matches the given group (which may be null)
@@
-732,10
+727,9
@@
public class FeatureStore
*/
if (nonPositionalFeatures != null)
{
*/
if (nonPositionalFeatures != null)
{
- List<SequenceFeature> list = nonPositionalFeatures;
- for (int i = 0, n = list.size(); i < n; i++)
+ for (int i = 0, n = nonPositionalFeatures.size(); i < n; i++)
{
{
- SequenceFeature sf = list.get(i);
+ SequenceFeature sf = nonPositionalFeatures.get(i);
nonPositionalFeatureGroups.add(sf.getFeatureGroup());
float score = sf.getScore();
nonPositionalMinScore = min(nonPositionalMinScore, score);
nonPositionalFeatureGroups.add(sf.getFeatureGroup());
float score = sf.getScore();
nonPositionalMinScore = min(nonPositionalMinScore, score);
@@
-743,14
+737,17
@@
public class FeatureStore
}
}
}
}
- /*
- * scan positional features for groups, scores and extents
- */
-
rescanPositional(contactFeatureStarts);
rescanPositional(features);
}
rescanPositional(contactFeatureStarts);
rescanPositional(features);
}
+ /**
+ * Scans the given features and updates cached feature groups, minimum and
+ * maximum feature score, and total feature extent (length) for positional
+ * features
+ *
+ * @param sfs
+ */
private void rescanPositional(Collection<SequenceFeature> sfs)
{
if (sfs == null)
private void rescanPositional(Collection<SequenceFeature> sfs)
{
if (sfs == null)
diff --git
a/test/jalview/datamodel/features/FeatureStoreLinkedTest.java
b/test/jalview/datamodel/features/FeatureStoreLinkedTest.java
index
e53ae3c
..
df4e983
100644
(file)
--- a/
test/jalview/datamodel/features/FeatureStoreLinkedTest.java
+++ b/
test/jalview/datamodel/features/FeatureStoreLinkedTest.java
@@
-9,11
+9,14
@@
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.features.FeatureStore.IntervalStoreType;
import java.util.ArrayList;
import jalview.datamodel.features.FeatureStore.IntervalStoreType;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Set;
import org.testng.annotations.Test;
import java.util.List;
import java.util.Set;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
/**
* Tests that exercise the 'linked list' version of IntervalStore
*/
/**
* Tests that exercise the 'linked list' version of IntervalStore
*/
@@
-431,7
+434,9
@@
public class FeatureStoreLinkedTest
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
- assertEquals(fs.getFeatures().size(), 2);
+ Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+ .getValue(fs, "features");
+ assertEquals(intervalStore.size(), 2);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
@@
-836,8
+841,10
@@
public class FeatureStoreLinkedTest
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
- assertTrue(store.getFeatures().contains(sf1));
- assertTrue(store.getFeatures().contains(sf2));
+ Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+ .getValue(store, "features");
+ assertTrue(intervalStore.contains(sf1));
+ assertTrue(intervalStore.contains(sf2));
/*
* delete the first feature
/*
* delete the first feature
diff --git
a/test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
b/test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
index
527beb8
..
5cf74bc
100644
(file)
--- a/
test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
+++ b/
test/jalview/datamodel/features/FeatureStoreNCListBufferTest.java
@@
-9,11
+9,14
@@
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.features.FeatureStore.IntervalStoreType;
import java.util.ArrayList;
import jalview.datamodel.features.FeatureStore.IntervalStoreType;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Set;
import org.testng.annotations.Test;
import java.util.List;
import java.util.Set;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
/**
* Tests that exercise the 'NC array' implementation of IntervalStore
*/
/**
* Tests that exercise the 'NC array' implementation of IntervalStore
*/
@@
-427,7
+430,9
@@
public class FeatureStoreNCListBufferTest
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
- assertEquals(fs.getFeatures().size(), 2);
+ Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+ .getValue(fs, "features");
+ assertEquals(intervalStore.size(), 2);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
@@
-832,8
+837,10
@@
public class FeatureStoreNCListBufferTest
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
- assertTrue(store.getFeatures().contains(sf1));
- assertTrue(store.getFeatures().contains(sf2));
+ Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+ .getValue(store, "features");
+ assertTrue(intervalStore.contains(sf1));
+ assertTrue(intervalStore.contains(sf2));
/*
* delete the first feature
/*
* delete the first feature
diff --git
a/test/jalview/datamodel/features/FeatureStoreTest.java
b/test/jalview/datamodel/features/FeatureStoreTest.java
index
8342018
..
bc179f6
100644
(file)
--- a/
test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/
test/jalview/datamodel/features/FeatureStoreTest.java
@@
-8,11
+8,14
@@
import static org.testng.Assert.assertTrue;
import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Set;
import org.testng.annotations.Test;
import java.util.List;
import java.util.Set;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class FeatureStoreTest
{
private FeatureStore newFeatureStore()
public class FeatureStoreTest
{
private FeatureStore newFeatureStore()
@@
-415,7
+418,9
@@
public class FeatureStoreTest
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
- assertEquals(fs.getFeatures().size(), 2);
+ Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+ .getValue(fs, "features");
+ assertEquals(intervalStore.size(), 2);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
@@
-820,8
+825,10
@@
public class FeatureStoreTest
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
- assertTrue(store.getFeatures().contains(sf1));
- assertTrue(store.getFeatures().contains(sf2));
+ Collection<SequenceFeature> intervalStore = (Collection<SequenceFeature>) PA
+ .getValue(store, "features");
+ assertTrue(intervalStore.contains(sf1));
+ assertTrue(intervalStore.contains(sf2));
/*
* delete the first feature
/*
* delete the first feature