+/*
+ * 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 jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Platform;
import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
+import intervalstore.api.IntervalI;
/**
* A class that stores sequence features in a way that supports efficient
* @author gmcarstairs
*
*/
-public class SequenceFeatures
+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, FeatureStore> featureStore;
+ private Map<String, FeatureStoreI> featureStore;
+
+ /**
+ * original NCList-based IntervalStore
+ */
+ private final static int INTERVAL_STORE_NCLIST = 0;
+
+ /**
+ * linked-list deferred-sort IntervalStore - experimental only; unused
+ */
+ private final static int INTERVAL_STORE_LINKED_LIST_NO_PRESORT = 1;
+
+ /**
+ * linked-list IntervalStore option for JavaScript
+ */
+ 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
*/
public SequenceFeatures()
{
- featureStore = new HashMap<String, FeatureStore>();
+ /*
+ * use a TreeMap so that features are returned in alphabetical order of type
+ * ? wrap as a synchronized map for add and delete operations
+ */
+ // featureStore = Collections
+ // .synchronizedSortedMap(new TreeMap<String, FeatureStoreI>());
+ featureStore = new TreeMap<>();
}
/**
- * Adds one sequence feature to the store, and returns true, unless the
- * feature is already contained in the store, in which case this method
- * returns false. Containment is determined by SequenceFeature.equals()
- * comparison.
- *
- * @param sf
+ * Constructor given a list of features
*/
+ public SequenceFeatures(List<SequenceFeature> features)
+ {
+ this();
+ if (features != null)
+ {
+ for (SequenceFeature feature : features)
+ {
+ add(feature);
+ }
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
public boolean add(SequenceFeature sf)
{
String type = sf.getType();
+ if (type == null)
+ {
+ System.err.println("Feature type may not be null: " + sf.toString());
+ return false;
+ }
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();
+ }
+ }
+
/**
- * Returns a (possibly empty) list of features of the given type which overlap
- * the (inclusive) sequence position range
- *
- * @param type
- * @param from
- * @param to
- * @return
+ * {@inheritDoc}
*/
- public List<SequenceFeature> findFeatures(String type, int from,
- int to)
+ @Override
+ public List<SequenceFeature> findFeatures(int from, int to,
+ String... type)
{
- FeatureStore features = featureStore.get(type);
- if (features == null)
+ List<SequenceFeature> result = new ArrayList<>();
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- return Collections.emptyList();
+ // System.err.println("SF findFeature " + System.currentTimeMillis()
+ // + " " + from + " " + to + " "
+ // + featureSet.getPositionalFeatures().get(0).type);
+ //
+ result.addAll(featureSet.findOverlappingFeatures(from, to, null));
}
- return features.findOverlappingFeatures(from, to);
+ return result;
}
/**
- * Answers a list of all features stored (including non-positional), in no
- * particular guaranteed order
- *
- * @return
+ * {@inheritDoc}
+ */
+ @Override
+ public List<SequenceFeature> getAllFeatures(String... type)
+ {
+ List<SequenceFeature> result = new ArrayList<>();
+
+ result.addAll(getPositionalFeatures(type));
+
+ result.addAll(getNonPositionalFeatures());
+
+ return result;
+ }
+
+ /**
+ * {@inheritDoc}
*/
- public List<SequenceFeature> getFeatures()
+ @Override
+ public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- for (FeatureStore featureSet : featureStore.values())
+ if (ontologyTerm == null || ontologyTerm.length == 0)
{
- result.addAll(featureSet.getFeatures());
+ return new ArrayList<>();
}
- return result;
+
+ Set<String> featureTypes = getFeatureTypes(ontologyTerm);
+ if (featureTypes.isEmpty())
+ {
+ /*
+ * no features of the specified type or any sub-type
+ */
+ return new ArrayList<>();
+ }
+
+ return getAllFeatures(
+ featureTypes.toArray(new String[featureTypes.size()]));
}
/**
- * Answers a list of all non-positional features stored, in no particular
- * guaranteed order
- *
- * @return
+ * {@inheritDoc}
*/
- public List<SequenceFeature> getNonPositionalFeatures()
+ @Override
+ public int getFeatureCount(boolean positional, String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- for (FeatureStore featureSet : featureStore.values())
+ int result = 0;
+
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ result += featureSet.getFeatureCount(positional);
}
return result;
}
/**
- * Answers a list of all contact features stored, in no particular guaranteed
- * order
- *
- * @return
+ * {@inheritDoc}
*/
- public List<SequenceFeature> getContactFeatures()
+ @Override
+ public int getTotalFeatureLength(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- for (FeatureStore featureSet : featureStore.values())
+ int result = 0;
+
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ result += featureSet.getTotalFeatureLength();
}
return result;
}
/**
- * Answers a list of all features of the given type (including
- * non-positional), in no particular guaranteed order
- *
- * @return
+ * {@inheritDoc}
*/
- public List<SequenceFeature> getFeatures(String type)
+ @Override
+ public List<SequenceFeature> getPositionalFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- FeatureStore featureSet = featureStore.get(type);
- if (featureSet != null)
+ List<SequenceFeature> result = new ArrayList<>();
+
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getFeatures());
+ featureSet.getPositionalFeatures(result);
}
return result;
}
/**
- * Answers a list of all contact features of the given type, in no particular
- * guaranteed order
+ * A convenience method that converts a vararg for feature types to an
+ * Iterable over matched feature sets in key order
*
+ * @param type
* @return
*/
- public List<SequenceFeature> getContactFeatures(String type)
+ protected Iterable<FeatureStoreI> varargToTypes(String... type)
+ {
+ if (type == null || type.length == 0)
+ {
+ /*
+ * no vararg parameter supplied - return all
+ */
+ return featureStore.values();
+ }
+
+ List<FeatureStoreI> types = new ArrayList<>();
+ List<String> args = Arrays.asList(type);
+ for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
+ {
+ if (args.contains(featureType.getKey()))
+ {
+ types.add(featureType.getValue());
+ }
+ }
+ return types;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<SequenceFeature> getContactFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- FeatureStore featureSet = featureStore.get(type);
- if (featureSet != null)
+ List<SequenceFeature> result = new ArrayList<>();
+
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ featureSet.getContactFeatures(result);
}
return result;
}
/**
- * Answers a list of all non-positional features of the given type, in no
- * particular guaranteed order
- *
- * @return
+ * {@inheritDoc}
*/
- public List<SequenceFeature> getNonPositionalFeatures(String type)
+ @Override
+ public List<SequenceFeature> getNonPositionalFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- FeatureStore featureSet = featureStore.get(type);
- if (featureSet != null)
+ List<SequenceFeature> result = new ArrayList<>();
+
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ featureSet.getNonPositionalFeatures(result);
}
return result;
}
/**
- * Deletes the given feature from the store, returning true if it was found
- * (and deleted), else false. This method makes no assumption that the feature
- * is in the 'expected' place in the store, in case it has been modified since
- * it was added.
- *
- * @param sf
+ * {@inheritDoc}
*/
+ @Override
public boolean delete(SequenceFeature sf)
{
- for (FeatureStore featureSet : featureStore.values())
+ for (FeatureStoreI featureSet : featureStore.values())
{
if (featureSet.delete(sf))
{
}
return false;
}
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean hasFeatures()
+ {
+ for (FeatureStoreI featureSet : featureStore.values())
+ {
+ if (!featureSet.isEmpty())
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Set<String> getFeatureGroups(boolean positionalFeatures,
+ String... type)
+ {
+ Set<String> groups = new HashSet<>();
+
+ for (FeatureStoreI featureSet : varargToTypes(type))
+ {
+ groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
+ }
+
+ return groups;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
+ String... groups)
+ {
+ Set<String> result = new HashSet<>();
+
+ for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
+ {
+ Set<String> featureGroups = featureType.getValue()
+ .getFeatureGroups(positionalFeatures);
+ for (String group : groups)
+ {
+ if (featureGroups.contains(group))
+ {
+ /*
+ * yes this feature type includes one of the query groups
+ */
+ result.add(featureType.getKey());
+ break;
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Set<String> getFeatureTypes(String... soTerm)
+ {
+ Set<String> types = new HashSet<>();
+ for (Entry<String, FeatureStoreI> entry : featureStore.entrySet())
+ {
+ String type = entry.getKey();
+ if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
+ {
+ types.add(type);
+ }
+ }
+ return types;
+ }
+
+ /**
+ * 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
+ */
+ protected boolean isOntologyTerm(String type, String... soTerm)
+ {
+ if (soTerm == null || soTerm.length == 0)
+ {
+ return true;
+ }
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
+ for (String term : soTerm)
+ {
+ if (type.equals(term) || so.isA(type, term))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public float getMinimumScore(String type, boolean positional)
+ {
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMinimumScore(positional)
+ : Float.NaN;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public float getMaximumScore(String type, boolean positional)
+ {
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMaximumScore(positional)
+ : Float.NaN;
+ }
+
+ /**
+ * A convenience method to sort features by start position ascending (if on
+ * forward strand), or end position descending (if on reverse strand)
+ *
+ * @param features
+ * @param forwardStrand
+ */
+ public static void sortFeatures(List<? extends IntervalI> features,
+ final boolean forwardStrand)
+ {
+ IntervalI.sortIntervals(features, forwardStrand);
+ }
+
+ /**
+ * {@inheritDoc} This method is 'semi-optimised': it only inspects features
+ * for types that include the specified group, but has to inspect every
+ * feature of those types for matching feature group. This is efficient unless
+ * a sequence has features that share the same type but are in different
+ * groups - an unlikely case.
+ * <p>
+ * For example, if RESNUM feature is created with group = PDBID, then features
+ * would only be retrieved for those sequences associated with the target
+ * PDBID (group).
+ */
+ @Override
+ public List<SequenceFeature> getFeaturesForGroup(boolean positional,
+ String group, String... type)
+ {
+ List<SequenceFeature> result = new ArrayList<>();
+ for (FeatureStoreI featureSet : varargToTypes(type))
+ {
+ if (featureSet.getFeatureGroups(positional).contains(group))
+ {
+ result.addAll(featureSet.getFeaturesForGroup(positional, group));
+ }
+ }
+ return result;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean shiftFeatures(int fromPosition, int shiftBy)
+ {
+ boolean modified = false;
+ for (FeatureStoreI fs : featureStore.values())
+ {
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
+ }
+ return modified;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ 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);
+ }
+
}