package jalview.datamodel.features;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.HashMap;
+import java.util.Comparator;
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;
/**
* A class that stores sequence features in a way that supports efficient
*/
public class SequenceFeatures implements SequenceFeaturesI
{
+ /**
+ * a comparator for sorting features by start position ascending
+ */
+ private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
+ {
+ @Override
+ public int compare(ContiguousI o1, ContiguousI o2)
+ {
+ return Integer.compare(o1.getBegin(), o2.getBegin());
+ }
+ };
+
+ /**
+ * a comparator for sorting features by end position descending
+ */
+ private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
+ {
+ @Override
+ public int compare(ContiguousI o1, ContiguousI o2)
+ {
+ return Integer.compare(o2.getEnd(), o1.getEnd());
+ }
+ };
/*
* map from feature type to structured store of features for that type
*/
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<String, FeatureStore>();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#add(jalview.datamodel.SequenceFeature)
+ /**
+ * 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)
{
return featureStore.get(type).addFeature(sf);
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#findFeatures(int, int, java.lang.String)
+ /**
+ * {@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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getAllFeatures(java.lang.String)
+ /**
+ * {@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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureCount(boolean, java.lang.String)
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
+ {
+ if (ontologyTerm == null || ontologyTerm.length == 0)
+ {
+ return new ArrayList<>();
+ }
+
+ Set<String> featureTypes = getFeatureTypes(ontologyTerm);
+ return getAllFeatures(featureTypes.toArray(new String[featureTypes
+ .size()]));
+ }
+
+ /**
+ * {@inheritDoc}
*/
@Override
public int getFeatureCount(boolean positional, String... type)
{
int result = 0;
- for (FeatureStore fs : featureStore.values())
+
+ for (FeatureStore featureSet : varargToTypes(type))
{
- result += fs.size(positional);
+ 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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getPositionalFeatures(java.lang.String)
+ /**
+ * {@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 in key order
*
* @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<>();
+ List<String> args = Arrays.asList(type);
+ for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+ {
+ if (args.contains(featureType.getKey()))
+ {
+ types.add(featureType.getValue());
+ }
+ }
+ return types;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getContactFeatures(java.lang.String)
+ /**
+ * {@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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getNonPositionalFeatures(java.lang.String)
+ /**
+ * {@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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#delete(jalview.datamodel.SequenceFeature)
+ /**
+ * {@inheritDoc}
*/
@Override
public boolean delete(SequenceFeature sf)
return false;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#hasFeatures()
+ /**
+ * {@inheritDoc}
*/
@Override
public boolean hasFeatures()
return false;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureGroups(boolean, java.lang.String)
+ /**
+ * {@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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureTypesForGroups(boolean, java.lang.String)
+ /**
+ * {@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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureTypes()
+ /**
+ * {@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 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.
+ *
+ * @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 (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<SequenceFeature> features,
+ final boolean forwardStrand)
+ {
+ Collections.sort(features, forwardStrand ? FORWARD_STRAND
+ : REVERSE_STRAND);
+ }
+
+ /**
+ * {@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 Set<String> getFeatureTypes()
+ public void deleteAll()
{
- return Collections.unmodifiableSet(featureStore.keySet());
+ featureStore.clear();
}
}