+/*
+ * 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 java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
+import java.util.Collections;
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;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
/**
* 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!)
*/
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, FeatureStore>());
+ 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)
{
}
/**
- * Returns a (possibly empty) list of features, optionally restricted to
- * specified types, which overlap the given (inclusive) sequence position
- * range
- *
- * @param from
- * @param to
- * @param type
- * @return
+ * {@inheritDoc}
*/
+ @Override
public List<SequenceFeature> findFeatures(int from, int to,
String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
- for (String featureType : varargToTypes(type))
+ for (FeatureStore featureSet : varargToTypes(type))
{
- FeatureStore features = featureStore.get(featureType);
- if (features != null)
- {
- result.addAll(features.findOverlappingFeatures(from, to));
- }
+ result.addAll(featureSet.findOverlappingFeatures(from, to));
}
return result;
}
/**
- * Answers a list of all features stored, optionally restricted to specified
- * types, in no particular guaranteed order
- *
- * @param type
- * @return
+ * {@inheritDoc}
*/
+ @Override
public List<SequenceFeature> getAllFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
result.addAll(getPositionalFeatures(type));
- result.addAll(getNonPositionalFeatures(type));
+ result.addAll(getNonPositionalFeatures());
return result;
}
/**
- * Answers a list of all positional features, optionally restricted to
- * specified types, in no particular guaranteed order
- *
- * @param type
- * @return
+ * {@inheritDoc}
*/
+ @Override
+ public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
+ {
+ if (ontologyTerm == null || ontologyTerm.length == 0)
+ {
+ return new ArrayList<>();
+ }
+
+ 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()]));
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public int getFeatureCount(boolean positional, String... type)
+ {
+ int result = 0;
+
+ for (FeatureStore featureSet : varargToTypes(type))
+ {
+ result += featureSet.getFeatureCount(positional);
+ }
+ return result;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public int getTotalFeatureLength(String... type)
+ {
+ int result = 0;
+
+ for (FeatureStore featureSet : varargToTypes(type))
+ {
+ result += featureSet.getTotalFeatureLength();
+ }
+ return result;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
public List<SequenceFeature> getPositionalFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
- for (String featureType : varargToTypes(type))
+ for (FeatureStore featureSet : varargToTypes(type))
{
- FeatureStore featureSet = featureStore.get(featureType);
- if (featureSet != null)
- {
- result.addAll(featureSet.getPositionalFeatures());
- }
+ result.addAll(featureSet.getPositionalFeatures());
}
return result;
}
/**
* A convenience method that converts a vararg for feature types to an
- * Iterable, replacing the value with the stored feature types if it is null
- * or empty
+ * Iterable over matched feature sets. If no types are specified, all feature
+ * sets are returned. If one or more types are specified, feature sets for
+ * those types are returned, preserving the order of the types.
*
* @param type
* @return
*/
- protected Iterable<String> varargToTypes(String... type)
+ protected Iterable<FeatureStore> varargToTypes(String... type)
{
- return type == null || type.length == 0 ? featureStore
- .keySet() : Arrays.asList(type);
+ if (type == null || type.length == 0)
+ {
+ /*
+ * no vararg parameter supplied - return all
+ */
+ return featureStore.values();
+ }
+
+ List<FeatureStore> types = new ArrayList<>();
+ for (String theType : type)
+ {
+ if (theType != null && featureStore.containsKey(theType))
+ {
+ types.add(featureStore.get(theType));
+ }
+ }
+ return types;
}
/**
- * Answers a list of all contact features, optionally restricted to specified
- * types, in no particular guaranteed order
- *
- * @return
+ * {@inheritDoc}
*/
+ @Override
public List<SequenceFeature> getContactFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
- for (String featureType : varargToTypes(type))
+ for (FeatureStore featureSet : varargToTypes(type))
{
- FeatureStore featureSet = featureStore.get(featureType);
- if (featureSet != null)
- {
- result.addAll(featureSet.getContactFeatures());
- }
+ result.addAll(featureSet.getContactFeatures());
}
return result;
}
/**
- * Answers a list of all non-positional features, optionally restricted to
- * specified types, in no particular guaranteed order
- *
- * @param type
- * if no type is specified, all are returned
- * @return
+ * {@inheritDoc}
*/
+ @Override
public List<SequenceFeature> getNonPositionalFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
- for (String featureType : varargToTypes(type))
+ for (FeatureStore featureSet : varargToTypes(type))
{
- FeatureStore featureSet = featureStore.get(featureType);
- if (featureSet != null)
- {
- result.addAll(featureSet.getNonPositionalFeatures());
- }
+ result.addAll(featureSet.getNonPositionalFeatures());
}
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())
}
/**
- * Answers true if this store contains at least one feature, else false
- *
- * @return
+ * {@inheritDoc}
*/
+ @Override
public boolean hasFeatures()
{
for (FeatureStore featureSet : featureStore.values())
}
/**
- * Returns a set of the distinct feature groups present in the collection. The
- * set may include null. The boolean parameter determines whether the groups
- * for positional or for non-positional features are returned. The optional
- * type parameter may be used to restrict to groups for specified feature
- * types.
- *
- * @param positionalFeatures
- * @param type
- * @return
+ * {@inheritDoc}
*/
+ @Override
public Set<String> getFeatureGroups(boolean positionalFeatures,
String... type)
{
- Set<String> groups = new HashSet<String>();
+ Set<String> groups = new HashSet<>();
- Iterable<String> types = varargToTypes(type);
-
- for (String featureType : types)
+ for (FeatureStore featureSet : varargToTypes(type))
{
- FeatureStore featureSet = featureStore.get(featureType);
- if (featureSet != null)
- {
- groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
- }
+ groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
}
return groups;
}
/**
- * Answers the set of distinct feature types for which there is at least one
- * feature with one of the given feature group(s). The parameter determines
- * whether the groups for positional or for non-positional features are
- * returned.
- *
- * @param positionalFeatures
- * @param groups
- * @return
+ * {@inheritDoc}
*/
+ @Override
public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
String... groups)
{
- Set<String> result = new HashSet<String>();
+ Set<String> result = new HashSet<>();
for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
{
return result;
}
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Set<String> getFeatureTypes(String... soTerm)
+ {
+ Set<String> types = new HashSet<>();
+ for (Entry<String, FeatureStore> 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.getInstance();
+ 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)
+ {
+ Collections.sort(features,
+ forwardStrand
+ ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+ : IntervalI.COMPARE_END_DESC);
+ }
+
+ /**
+ * {@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 (FeatureStore 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 (FeatureStore fs : featureStore.values())
+ {
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
+ }
+ return modified;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
+ }
}
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