package jalview.datamodel.features;
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
* @author gmcarstairs
*
*/
-public class SequenceFeatures
+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>();
}
/**
- * 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
+ * {@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 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<SequenceFeature>();
+
+ for (String featureType : varargToTypes(type))
{
- return Collections.emptyList();
+ FeatureStore features = featureStore.get(featureType);
+ if (features != null)
+ {
+ result.addAll(features.findOverlappingFeatures(from, to));
+ }
}
- return features.findOverlappingFeatures(from, to);
+
+ return result;
}
/**
- * Answers a list of all features stored (including non-positional), in no
- * particular guaranteed order
- *
- * @return
+ * {@inheritDoc}
*/
- public List<SequenceFeature> getFeatures()
+ @Override
+ public List<SequenceFeature> getAllFeatures(String... type)
{
List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- for (FeatureStore featureSet : featureStore.values())
+
+ result.addAll(getPositionalFeatures(type));
+
+ result.addAll(getNonPositionalFeatures());
+
+ return result;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
+ {
+ if (ontologyTerm == null || ontologyTerm.length == 0)
{
- result.addAll(featureSet.getFeatures());
+ return new ArrayList<SequenceFeature>();
}
- return result;
+
+ Set<String> featureTypes = getFeatureTypes(ontologyTerm);
+ 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 (String featureType : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ FeatureStore featureSet = featureStore.get(featureType);
+ if (featureSet != null)
+ {
+ 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 (String featureType : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ FeatureStore featureSet = featureStore.get(featureType);
+ if (featureSet != null)
+ {
+ 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)
+
+ for (String featureType : varargToTypes(type))
{
- result.addAll(featureSet.getFeatures());
+ FeatureStore featureSet = featureStore.get(featureType);
+ if (featureSet != null)
+ {
+ result.addAll(featureSet.getPositionalFeatures());
+ }
}
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, replacing the value with the stored feature types if it is null
+ * or empty
*
+ * @param type
* @return
*/
- public List<SequenceFeature> getContactFeatures(String type)
+ protected Iterable<String> varargToTypes(String... type)
+ {
+ if (type == null || type.length == 0)
+ {
+ /*
+ * no vararg parameter supplied
+ */
+ return featureStore.keySet();
+ }
+
+ /*
+ * else make a copy of the list, and remove any null value just in case,
+ * as it would cause errors looking up the features Map
+ * sort in alphabetical order for consistent output behaviour
+ */
+ List<String> types = new ArrayList<String>(Arrays.asList(type));
+ types.remove(null);
+ Collections.sort(types);
+ return types;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<SequenceFeature> getContactFeatures(String... type)
{
List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- FeatureStore featureSet = featureStore.get(type);
- if (featureSet != null)
+
+ for (String featureType : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ FeatureStore featureSet = featureStore.get(featureType);
+ if (featureSet != null)
+ {
+ result.addAll(featureSet.getContactFeatures());
+ }
}
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)
+
+ for (String featureType : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ FeatureStore featureSet = featureStore.get(featureType);
+ if (featureSet != null)
+ {
+ 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())
}
return false;
}
-}
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Set<String> getFeatureGroups(boolean positionalFeatures,
+ String... type)
+ {
+ Set<String> groups = new HashSet<String>();
+
+ Iterable<String> types = varargToTypes(type);
+
+ for (String featureType : types)
+ {
+ FeatureStore featureSet = featureStore.get(featureType);
+ if (featureSet != null)
+ {
+ groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
+ }
+ }
+
+ return groups;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
+ String... groups)
+ {
+ Set<String> result = new HashSet<String>();
+
+ for (Entry<String, FeatureStore> 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<String>();
+ 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<SequenceFeature>();
+ Iterable<String> types = varargToTypes(type);
+
+ for (String featureType : types)
+ {
+ /*
+ * check whether the feature type is present, and also
+ * whether it has features for the specified group
+ */
+ FeatureStore features = featureStore.get(featureType);
+ if (features != null
+ && features.getFeatureGroups(positional).contains(group))
+ {
+ result.addAll(features.getFeaturesForGroup(positional, group));
+ }
+ }
+ return result;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean shiftFeatures(int shift)
+ {
+ boolean modified = false;
+ for (FeatureStore fs : featureStore.values())
+ {
+ modified |= fs.shiftFeatures(shift);
+ }
+ return modified;
+ }
+}
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