package jalview.datamodel.features;
import jalview.datamodel.SequenceFeature;
-import jalview.util.Platform;
import java.util.ArrayList;
import java.util.Collection;
public class FeatureStore
{
+ public enum IntervalStoreType
+ {
+ /**
+ * original NCList-based IntervalStore
+ */
+ INTERVAL_STORE_NCLIST,
+
+ /**
+ * linked-list IntervalStore
+ */
+ INTERVAL_STORE_LINKED_LIST,
+
+ /**
+ * NCList as array buffer IntervalStore
+ */
+ INTERVAL_STORE_NCARRAY
+ }
+
/*
- * track last start for quick insertion of ordered features
+ * track largest start for quick insertion of ordered features
*/
- protected int lastStart = -1;
+ protected int maxStart = -1;
- protected int lastContactStart = -1;
+ protected int maxContactStart = -1;
/*
* Non-positional features have no (zero) start/end position.
float nonPositionalMaxScore;
- public final static int INTERVAL_STORE_DEFAULT = -1;
-
- /**
- * original NCList-based IntervalStore
- */
- public final static int INTERVAL_STORE_NCLIST_OBJECT = 0;
-
- /**
- * linked-list IntervalStore
- */
- public final static int INTERVAL_STORE_LINKED_LIST = 1;
-
- /**
- * NCList as array buffer IntervalStore
- */
- public final static int INTERVAL_STORE_NCARRAY = 3;
-
- static final int intervalStoreJavaOption = INTERVAL_STORE_NCLIST_OBJECT;
-
- private final static boolean useJSOption = false;
-
- private final static boolean isJSLinkedTest = true;
-
- static final int intervalStoreJSOption = (!useJSOption
- ? intervalStoreJavaOption
- : isJSLinkedTest
- ? INTERVAL_STORE_LINKED_LIST
- : INTERVAL_STORE_NCARRAY);
-
- // TODO: compare performance in real situations using
- // INTERVAL_STORE_LINKED_LIST;
-
/**
* Answers the 'length' of the feature, counting 0 for non-positional features
* and 1 for contact features
* @param feature
* @return
*/
- public boolean listContains(List<SequenceFeature> list,
+ public static boolean listContains(List<SequenceFeature> list,
SequenceFeature feature)
{
if (list == null || feature == null)
}
/**
- * standard constructor
+ * Constructor that defaults to using NCList IntervalStore
*/
public FeatureStore()
{
- this(INTERVAL_STORE_DEFAULT);
+ this(IntervalStoreType.INTERVAL_STORE_NCLIST);
}
/**
- * constructor for testing only
+ * Constructor that allows an alternative IntervalStore implementation to be
+ * chosen
*/
- public FeatureStore(int intervalStoreType)
+ public FeatureStore(IntervalStoreType intervalStoreType)
{
- features =
- // Platform.isJS()
- // ? new intervalstore.nonc.IntervalStore<>(true)
- // : new intervalstore.impl.IntervalStore<>();
- getIntervalStore(intervalStoreType);
+ features = getIntervalStore(intervalStoreType);
positionalFeatureGroups = new HashSet<>();
nonPositionalFeatureGroups = new HashSet<>();
positionalMinScore = Float.NaN;
nonPositionalMinScore = Float.NaN;
nonPositionalMaxScore = Float.NaN;
- // we only construct nonPositionalFeatures, contactFeatures if we need to
+ // only construct nonPositionalFeatures or contactFeatures if needed
}
- private IntervalStoreI<SequenceFeature> getIntervalStore(int type)
+ /**
+ * Returns a new instance of IntervalStoreI of implementation as selected by
+ * the type parameter
+ *
+ * @param type
+ * @return
+ */
+ private IntervalStoreI<SequenceFeature> getIntervalStore(
+ IntervalStoreType type)
{
- switch (type != INTERVAL_STORE_DEFAULT ? type : //
- Platform.isJS() //
- ? intervalStoreJSOption
- : intervalStoreJavaOption)
+ switch (type)
{
default:
- case INTERVAL_STORE_NCLIST_OBJECT:
+ case INTERVAL_STORE_NCLIST:
return new intervalstore.impl.IntervalStore<>();
case INTERVAL_STORE_NCARRAY:
- // TODO: Couldn't figure out how to get rid of this warning
- return new intervalstore.nonc.IntervalStoreImpl<>();
+ return new intervalstore.nonc.IntervalStore<>();
case INTERVAL_STORE_LINKED_LIST:
- return new intervalstore.nonc.IntervalStore0Impl<>();
+ return new intervalstore.nonc.IntervalStore0<>();
}
}
return false;
}
positionalFeatureGroups.add(feature.getFeatureGroup());
- if (feature.begin > lastContactStart)
+ if (feature.begin > maxContactStart)
{
- lastContactStart = feature.begin;
+ maxContactStart = feature.begin;
}
addContactFeature(feature);
}
return false;
}
positionalFeatureGroups.add(feature.getFeatureGroup());
- if (feature.begin > lastStart)
+ if (feature.begin > maxStart)
{
- lastStart = feature.begin;
+ maxStart = feature.begin;
}
}
return true;
}
+ /**
+ * A helper method that adds to the result list any features from the
+ * collection provided whose feature group matches the specified group
+ *
+ * @param group
+ * @param sfs
+ * @param result
+ */
private void addFeaturesForGroup(String group,
Collection<SequenceFeature> sfs, List<SequenceFeature> result)
{
}
return containsPositionalFeature(feature);
-
}
private boolean containsPositionalFeature(SequenceFeature feature)
{
- return features == null || feature.begin > lastStart ? false
+ return features == null || feature.begin > maxStart ? false
: features.contains(feature);
}
*/
private boolean containsContactFeature(SequenceFeature feature)
{
- return contactFeatureStarts != null && feature.begin <= lastContactStart
+ return contactFeatureStarts != null && feature.begin <= maxContactStart
&& listContains(contactFeatureStarts, feature);
}
return removed;
}
- public List<SequenceFeature> findOverlappingFeatures(long start, long end)
+ public List<SequenceFeature> findFeatures(long start, long end)
{
- return findOverlappingFeatures(start, end, null);
+ return findFeatures(start, end, null);
}
+ /**
+ * Returns a (possibly empty) list of features whose extent overlaps the given
+ * range. The returned list is not ordered. Contact features are included if
+ * either of the contact points lies within the range. If the {@code result}
+ * parameter is not null, new entries are added to this list and the (possibly
+ * extended) list returned.
+ *
+ * @param start
+ * start position of overlap range (inclusive)
+ * @param end
+ * end position of overlap range (inclusive)
+ * @param result
+ * @return
+ */
+ public List<SequenceFeature> findFeatures(long start, long end,
+ List<SequenceFeature> result)
+ {
+ if (result == null)
+ {
+ result = new ArrayList<>();
+ }
+
+ findContactFeatures(start, end, result);
+ features.findOverlaps(start, end, result);
+
+ return result;
+ }
+
+ /**
+ * Returns a (possibly empty) list of stored contact features
+ *
+ * @return
+ */
public List<SequenceFeature> getContactFeatures()
{
- return getContactFeatures(new ArrayList<>());
+ List<SequenceFeature> result = new ArrayList<>();
+ getContactFeatures(result);
+ return result;
}
/**
- * Answers a list of all contact features. If there are none, returns an
- * immutable empty list.
+ * Adds any stored contact features to the result list
*
* @return
*/
- public List<SequenceFeature> getContactFeatures(
- List<SequenceFeature> result)
+ public void getContactFeatures(List<SequenceFeature> result)
{
if (contactFeatureStarts != null)
{
result.addAll(contactFeatureStarts);
}
- return result;
}
/**
: nonPositionalFeatures.size();
}
- return (contactFeatureStarts == null ? 0 : contactFeatureStarts.size())
- + features.size();
+ int size = 0;
+
+ if (contactFeatureStarts != null)
+ {
+ // note a contact feature (start/end) counts as one
+ size += contactFeatureStarts.size();
+ }
+
+ if (features != null)
+ {
+ size += features.size();
+ }
+ return size;
}
/**
}
}
- public Collection<SequenceFeature> getFeatures()
- {
- return features;
- }
-
/**
* Answers a list of all either positional or non-positional features whose
* feature group matches the given group (which may be null)
return positional ? positionalMinScore : nonPositionalMinScore;
}
+ /**
+ * Answers a (possibly empty) list of all non-positional features
+ *
+ * @return
+ */
public List<SequenceFeature> getNonPositionalFeatures()
{
- return getNonPositionalFeatures(new ArrayList<>());
+ List<SequenceFeature> result = new ArrayList<>();
+ getNonPositionalFeatures(result);
+ return result;
}
/**
- * Answers a list of all non-positional features. If there are none, returns
- * an immutable empty list.
+ * Adds any stored non-positional features to the result list
*
* @return
*/
- public List<SequenceFeature> getNonPositionalFeatures(
- List<SequenceFeature> result)
+ public void getNonPositionalFeatures(List<SequenceFeature> result)
{
if (nonPositionalFeatures != null)
{
result.addAll(nonPositionalFeatures);
}
- return result;
}
+ /**
+ * Returns a (possibly empty) list of all positional features stored
+ *
+ * @return
+ */
public List<SequenceFeature> getPositionalFeatures()
{
- return getPositionalFeatures(new ArrayList<>());
+ List<SequenceFeature> result = new ArrayList<>();
+ getPositionalFeatures(result);
+
+ return result;
}
/**
- * Answers a list of all positional features stored, in no guaranteed order
- *
- * @return
+ * Adds all positional features stored to the result list, in no guaranteed
+ * order, and with no check for duplicates
*/
- public List<SequenceFeature> getPositionalFeatures(
- List<SequenceFeature> result)
+ public void getPositionalFeatures(List<SequenceFeature> result)
{
-
/*
* add any contact features - from the list by start position
*/
{
result.addAll(features);
}
-
- return result;
}
/**
&& !contactFeatureStarts.isEmpty())
|| (nonPositionalFeatures != null
&& !nonPositionalFeatures.isEmpty())
- || features.size() > 0;
+ || (features != null && features.size() > 0);
return !hasFeatures;
}
*/
if (nonPositionalFeatures != null)
{
- List<SequenceFeature> list = nonPositionalFeatures;
- for (int i = 0, n = list.size(); i < n; i++)
+ for (int i = 0, n = nonPositionalFeatures.size(); i < n; i++)
{
- SequenceFeature sf = list.get(i);
+ SequenceFeature sf = nonPositionalFeatures.get(i);
nonPositionalFeatureGroups.add(sf.getFeatureGroup());
float score = sf.getScore();
nonPositionalMinScore = min(nonPositionalMinScore, score);
}
}
- /*
- * scan positional features for groups, scores and extents
- */
-
rescanPositional(contactFeatureStarts);
rescanPositional(features);
}
+ /**
+ * Scans the given features and updates cached feature groups, minimum and
+ * maximum feature score, and total feature extent (length) for positional
+ * features
+ *
+ * @param sfs
+ */
private void rescanPositional(Collection<SequenceFeature> sfs)
{
if (sfs == null)
}
}
- /**
- * Returns a (possibly empty) list of features whose extent overlaps the given
- * range. The returned list is not ordered. Contact features are included if
- * either of the contact points lies within the range. If the {@code result}
- * parameter is not null, new entries are added to this list and the (possibly
- * extended) list returned.
- *
- * @param start
- * start position of overlap range (inclusive)
- * @param end
- * end position of overlap range (inclusive)
- * @param result
- * @return
- */
- public List<SequenceFeature> findOverlappingFeatures(long start, long end,
- List<SequenceFeature> result)
- {
- if (result == null)
- {
- result = new ArrayList<>();
- }
-
- findContactFeatures(start, end, result);
- features.findOverlaps(start, end, result);
-
- return result;
- }
-
}
git://source.jalview.org / jalview.git / blobdiff