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;
@Override
public List<SequenceFeature> getAllFeatures(String... type)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
result.addAll(getPositionalFeatures(type));
{
if (ontologyTerm == null || ontologyTerm.length == 0)
{
- return new ArrayList<SequenceFeature>();
+ return new ArrayList<>();
}
Set<String> featureTypes = getFeatureTypes(ontologyTerm);
{
int result = 0;
- for (String featureType : varargToTypes(type))
+ for (FeatureStore featureSet : varargToTypes(type))
{
- FeatureStore featureSet = featureStore.get(featureType);
- if (featureSet != null)
- {
- result += featureSet.getFeatureCount(positional);
- }
+ result += featureSet.getFeatureCount(positional);
}
return result;
}
{
int result = 0;
- for (String featureType : varargToTypes(type))
+ for (FeatureStore featureSet : varargToTypes(type))
{
- FeatureStore featureSet = featureStore.get(featureType);
- if (featureSet != null)
- {
- result += featureSet.getTotalFeatureLength();
- }
+ result += featureSet.getTotalFeatureLength();
}
return result;
-
}
/**
@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)
{
if (type == null || type.length == 0)
{
/*
- * no vararg parameter supplied
+ * no vararg parameter supplied - return all
*/
- return featureStore.keySet();
+ return featureStore.values();
}
- /*
- * 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);
+ 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;
}
@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;
}
@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;
}
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;
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())
{
@Override
public Set<String> getFeatureTypes(String... soTerm)
{
- Set<String> types = new HashSet<String>();
+ Set<String> types = new HashSet<>();
for (Entry<String, FeatureStore> entry : featureStore.entrySet())
{
String type = entry.getKey();
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)
+ List<SequenceFeature> result = new ArrayList<>();
+ for (FeatureStore featureSet : varargToTypes(type))
{
- /*
- * 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))
+ if (featureSet.getFeatureGroups(positional).contains(group))
{
- result.addAll(features.getFeaturesForGroup(positional, group));
+ result.addAll(featureSet.getFeaturesForGroup(positional, group));
}
}
return result;