*/
package jalview.datamodel.features;
-import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Platform;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
+import intervalstore.api.IntervalI;
+
/**
* A class that stores sequence features in a way that supports efficient
* querying by type and location (overlap). Intended for (but not limited to)
*/
public class SequenceFeatures implements SequenceFeaturesI
{
+
+ /*
+ * map from feature type to structured store of features for that type
+ * null types are permitted (but not a good idea!)
+ */
+ private Map<String, FeatureStoreI> featureStore;
+
/**
- * a comparator for sorting features by start position ascending
+ * original NCList-based IntervalStore
*/
- private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o1.getBegin(), o2.getBegin());
- }
- };
+ private final static int INTERVAL_STORE_NCLIST = 0;
/**
- * a comparator for sorting features by end position descending
+ * linked-list deferred-sort IntervalStore - experimental only; unused
*/
- private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o2.getEnd(), o1.getEnd());
- }
- };
+ private final static int INTERVAL_STORE_LINKED_LIST_NO_PRESORT = 1;
- /*
- * map from feature type to structured store of features for that type
- * null types are permitted (but not a good idea!)
+ /**
+ * linked-list IntervalStore option for JavaScript
*/
- private Map<String, FeatureStore> featureStore;
+ private final static int INTERVAL_STORE_LINKED_LIST = -1;
+
+ /**
+ * mode for Java or JavaScript; can be set differently for testing, but
+ * default is LINKED_LIST for JalviewJS and NCLIST for Java
+ */
+ private final int INTERVAL_STORE_MODE = (
+ // true || //
+ Platform.isJS() ? //
+ INTERVAL_STORE_LINKED_LIST //
+ : INTERVAL_STORE_NCLIST//
+ );
/**
* Constructor
* ? wrap as a synchronized map for add and delete operations
*/
// featureStore = Collections
- // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
- featureStore = new TreeMap<String, FeatureStore>();
+ // .synchronizedSortedMap(new TreeMap<String, FeatureStoreI>());
+ featureStore = new TreeMap<>();
}
/**
if (featureStore.get(type) == null)
{
- featureStore.put(type, new FeatureStore());
+ featureStore.put(type, newFeatureStore());
}
return featureStore.get(type).addFeature(sf);
}
+ private FeatureStoreI newFeatureStore()
+ {
+ switch (INTERVAL_STORE_MODE)
+ {
+ default:
+ case INTERVAL_STORE_NCLIST:
+ return new FeatureStoreImpl(true);
+ case INTERVAL_STORE_LINKED_LIST_NO_PRESORT:
+ return new FeatureStoreImpl(false);
+ case INTERVAL_STORE_LINKED_LIST:
+ return new FeatureStoreJS();
+ }
+ }
+
/**
* {@inheritDoc}
*/
String... type)
{
List<SequenceFeature> result = new ArrayList<>();
-
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.findOverlappingFeatures(from, to));
+ // System.err.println("SF findFeature " + System.currentTimeMillis()
+ // + " " + from + " " + to + " "
+ // + featureSet.getPositionalFeatures().get(0).type);
+ //
+ result.addAll(featureSet.findOverlappingFeatures(from, to, null));
}
-
return result;
}
return new ArrayList<>();
}
- return getAllFeatures(featureTypes.toArray(new String[featureTypes
- .size()]));
+ return getAllFeatures(
+ featureTypes.toArray(new String[featureTypes.size()]));
}
/**
{
int result = 0;
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
result += featureSet.getFeatureCount(positional);
}
{
int result = 0;
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
result += featureSet.getTotalFeatureLength();
}
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getPositionalFeatures());
+ featureSet.getPositionalFeatures(result);
}
return result;
}
* @param type
* @return
*/
- protected Iterable<FeatureStore> varargToTypes(String... type)
+ protected Iterable<FeatureStoreI> varargToTypes(String... type)
{
if (type == null || type.length == 0)
{
return featureStore.values();
}
- List<FeatureStore> types = new ArrayList<>();
+ List<FeatureStoreI> types = new ArrayList<>();
List<String> args = Arrays.asList(type);
- for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+ for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
{
if (args.contains(featureType.getKey()))
{
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ featureSet.getContactFeatures(result);
}
return result;
}
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ featureSet.getNonPositionalFeatures(result);
}
return result;
}
@Override
public boolean delete(SequenceFeature sf)
{
- for (FeatureStore featureSet : featureStore.values())
+ for (FeatureStoreI featureSet : featureStore.values())
{
if (featureSet.delete(sf))
{
@Override
public boolean hasFeatures()
{
- for (FeatureStore featureSet : featureStore.values())
+ for (FeatureStoreI featureSet : featureStore.values())
{
if (!featureSet.isEmpty())
{
{
Set<String> groups = new HashSet<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
}
{
Set<String> result = new HashSet<>();
- for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+ for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
{
- Set<String> featureGroups = featureType.getValue().getFeatureGroups(
- positionalFeatures);
+ Set<String> featureGroups = featureType.getValue()
+ .getFeatureGroups(positionalFeatures);
for (String group : groups)
{
if (featureGroups.contains(group))
public Set<String> getFeatureTypes(String... soTerm)
{
Set<String> types = new HashSet<>();
- for (Entry<String, FeatureStore> entry : featureStore.entrySet())
+ for (Entry<String, FeatureStoreI> entry : featureStore.entrySet())
{
String type = entry.getKey();
if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
}
/**
- * Answers true if the given type is one of the specified sequence ontology
- * terms (or a sub-type of one), or if no terms are supplied. Answers false if
- * filter terms are specified and the given term does not match any of them.
+ * Answers true if the given type matches one of the specified terms (or is a
+ * sub-type of one in the Sequence Ontology), or if no terms are supplied.
+ * Answers false if filter terms are specified and the given term does not
+ * match any of them.
*
* @param type
* @param soTerm
{
return true;
}
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
for (String term : soTerm)
{
- if (so.isA(type, term))
+ if (type.equals(term) || so.isA(type, term))
{
return true;
}
@Override
public float getMinimumScore(String type, boolean positional)
{
- return featureStore.containsKey(type) ? featureStore.get(type)
- .getMinimumScore(positional) : Float.NaN;
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMinimumScore(positional)
+ : Float.NaN;
}
/**
@Override
public float getMaximumScore(String type, boolean positional)
{
- return featureStore.containsKey(type) ? featureStore.get(type)
- .getMaximumScore(positional) : Float.NaN;
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMaximumScore(positional)
+ : Float.NaN;
}
/**
* @param features
* @param forwardStrand
*/
- public static void sortFeatures(List<SequenceFeature> features,
+ public static void sortFeatures(List<? extends IntervalI> features,
final boolean forwardStrand)
{
- Collections.sort(features, forwardStrand ? FORWARD_STRAND
- : REVERSE_STRAND);
+ IntervalI.sortIntervals(features, forwardStrand);
}
/**
String group, String... type)
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
if (featureSet.getFeatureGroups(positional).contains(group))
{
public boolean shiftFeatures(int fromPosition, int shiftBy)
{
boolean modified = false;
- for (FeatureStore fs : featureStore.values())
+ for (FeatureStoreI fs : featureStore.values())
{
modified |= fs.shiftFeatures(fromPosition, shiftBy);
}
{
featureStore.clear();
}
+
+ /**
+ * Simplified find for features associated with a given position.
+ *
+ * JavaScript set to not use IntervalI, but easily testable by setting false
+ * to true in javadoc
+ *
+ * FeatureRenderer has checked already that featureStore does contain type.
+ *
+ * @author Bob Hanson 2019.07.30
+ */
+ @Override
+ public List<SequenceFeature> findFeatures(int pos, String type,
+ List<SequenceFeature> list)
+ {
+ FeatureStoreI fs = featureStore.get(type);
+ return fs.findOverlappingFeatures(pos, pos, list);
+ }
+
+ // Chrome; developer console closed
+
+ // BH 2019.08.01 useIntervalStore true, redraw false:
+ // Platform: timer mark 13.848 0.367 overviewrender 16000 pixels row:14
+ // Platform: timer mark 15.391 0.39 overviewrender 16000 pixels row:14
+ // Platform: timer mark 16.498 0.39 overviewrender 16000 pixels row:14
+ // Platform: timer mark 17.596 0.401 overviewrender 16000 pixels row:14
+ // Platform: timer mark 18.738 0.363 overviewrender 16000 pixels row:14
+ // Platform: timer mark 19.659 0.358 overviewrender 16000 pixels row:14
+ // Platform: timer mark 20.737 0.359 overviewrender 16000 pixels row:14
+ // Platform: timer mark 21.797 0.391 overviewrender 16000 pixels row:14
+ // Platform: timer mark 22.851 0.361 overviewrender 16000 pixels row:14
+ // Platform: timer mark 24.019 0.395 overviewrender 16000 pixels row:14
+
+ // BH 2019.08.01 useIntervalStore false, redraw false:
+ // Platform: timer mark 19.011 0.181 overviewrender 16000 pixels row:14
+ // Platform: timer mark 20.311 0.183 overviewrender 16000 pixels row:14
+ // Platform: timer mark 21.368 0.175 overviewrender 16000 pixels row:14
+ // Platform: timer mark 22.347 0.178 overviewrender 16000 pixels row:14
+ // Platform: timer mark 23.605 0.216 overviewrender 16000 pixels row:14
+ // Platform: timer mark 24.836 0.191 overviewrender 16000 pixels row:14
+ // Platform: timer mark 26.016 0.181 overviewrender 16000 pixels row:14
+ // Platform: timer mark 27.278 0.178 overviewrender 16000 pixels row:14
+ // Platform: timer mark 28.158 0.181 overviewrender 16000 pixels row:14
+ // Platform: timer mark 29.227 0.196 overviewrender 16000 pixels row:14
+ // Platform: timer mark 30.1 0.171 overviewrender 16000 pixels row:14
+ // Platform: timer mark 31.684 0.196 overviewrender 16000 pixels row:14
+ // Platform: timer mark 32.779 0.18 overviewrender 16000 pixels row:14
+ // Platform: timer mark 52.355 0.185 overviewrender 16000 pixels row:14
+ // Platform: timer mark 53.829 0.186 overviewrender 16000 pixels row:14
+
+ /**
+ * @author Bob Hanson 2019.08.01
+ */
+ @Override
+ public boolean hasFeatures(String type)
+ {
+ return featureStore.containsKey(type);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff