import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
-public abstract class FeatureStore implements FeatureStoreI
-{
-
- /**
- * track last start for quick insertion of ordered features
- */
- protected int lastStart = -1, lastContactStart = -1;
-
- /**
- * Answers the 'length' of the feature, counting 0 for non-positional features
- * and 1 for contact features
- *
- * @param feature
- * @return
- */
- protected static int getFeatureLength(SequenceFeature feature)
- {
- if (feature.isNonPositional())
- {
- return 0;
- }
- if (feature.isContactFeature())
- {
- return 1;
- }
- return 1 + feature.getEnd() - feature.getBegin();
- }
-
- /**
- * Answers true if the list contains the feature, else false. This method is
- * optimised for the condition that the list is sorted on feature start
- * position ascending, and will give unreliable results if this does not hold.
- *
- * @param list
- * @param feature
- * @return
- */
- @Override
- public boolean listContains(List<SequenceFeature> list,
- SequenceFeature feature)
- {
- if (list == null || feature == null)
- {
- return false;
- }
-
- return (getEquivalentFeatureIndex(list, feature) >= 0);
- }
-
- /**
- * Binary search for the index (>= 0) of a feature in a list.
- *
- * @param list
- * @param feature
- * @return index if found; -1 if not
- */
- protected int getEquivalentFeatureIndex(List<SequenceFeature> list,
- SequenceFeature feature)
- {
-
- /*
- * locate the first entry in the list which does not precede the feature
- */
- int begin = feature.begin;
- int pos = findFirstBegin(list, begin);
- int len = list.size();
- while (pos < len)
- {
- SequenceFeature sf = list.get(pos);
- if (sf.begin > begin)
- {
- return -1; // no match found
- }
- if (sf.equals(feature))
- {
- return pos;
- }
- pos++;
- }
- return -1;
- }
-
- /**
- * A helper method to return the maximum of two floats, where a non-NaN value
- * is treated as 'greater than' a NaN value (unlike Math.max which does the
- * opposite)
- *
- * @param f1
- * @param f2
- */
- protected static float max(float f1, float f2)
- {
- if (Float.isNaN(f1))
- {
- return Float.isNaN(f2) ? f1 : f2;
- }
- else
- {
- return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
- }
- }
-
- /**
- * A helper method to return the minimum of two floats, where a non-NaN value
- * is treated as 'less than' a NaN value (unlike Math.min which does the
- * opposite)
- *
- * @param f1
- * @param f2
- */
- protected static float min(float f1, float f2)
- {
- if (Float.isNaN(f1))
- {
- return Float.isNaN(f2) ? f1 : f2;
- }
- else
- {
- return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
- }
- }
+import intervalstore.api.IntervalStoreI;
+import intervalstore.impl.BinarySearcher;
+import intervalstore.impl.IntervalStore;
+/**
+ * A data store for a set of sequence features that supports efficient lookup of
+ * features overlapping a given range. Intended for (but not limited to) storage
+ * of features for one sequence and feature type.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class FeatureStore
+{
/*
* Non-positional features have no (zero) start/end position.
* Kept as a separate list in case this criterion changes in future.
* IntervalStore holds remaining features and provides efficient
* query for features overlapping any given interval
*/
- Collection<SequenceFeature> features;
+ IntervalStoreI<SequenceFeature> features;
/*
* Feature groups represented in stored positional features
*/
public FeatureStore()
{
+ features = new IntervalStore<>();
positionalFeatureGroups = new HashSet<>();
nonPositionalFeatureGroups = new HashSet<>();
positionalMinScore = Float.NaN;
}
/**
- * Add a contact feature to the lists that hold them ordered by start (first
- * contact) and by end (second contact) position, ensuring the lists remain
- * ordered, and returns true. This method allows duplicate features to be
- * added, so test before calling to avoid this.
- *
- * @param feature
- * @return
- */
- protected synchronized boolean addContactFeature(SequenceFeature feature)
- {
- if (contactFeatureStarts == null)
- {
- contactFeatureStarts = new ArrayList<>();
- contactFeatureEnds = new ArrayList<>();
- }
-
- /*
- * insert into list sorted by start (first contact position):
- * binary search the sorted list to find the insertion point
- */
- contactFeatureStarts.add(
- findFirstBegin(contactFeatureStarts, feature.begin), feature);
- /*
- * insert into list sorted by end (second contact position):
- * binary search the sorted list to find the insertion point
- */
- contactFeatureEnds.add(findFirstEnd(contactFeatureEnds, feature.end),
- feature);
-
- return true;
- }
-
- /**
* 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()
*
* @param feature
*/
-
- @Override
public boolean addFeature(SequenceFeature feature)
{
- // if (contains(feature))
- // {
- // return false;
- // }
-
- // /*
- // * keep a record of feature groups
- // */
- // if (!feature.isNonPositional())
- // {
- // positionalFeatureGroups.add(feature.getFeatureGroup());
- // }
+ if (contains(feature))
+ {
+ return false;
+ }
- if (feature.isContactFeature())
+ /*
+ * keep a record of feature groups
+ */
+ if (!feature.isNonPositional())
{
- if (containsContactFeature(feature))
- {
- return false;
- }
positionalFeatureGroups.add(feature.getFeatureGroup());
- if (feature.begin > lastContactStart)
- {
- lastContactStart = feature.begin;
- }
+ }
+
+ if (feature.isContactFeature())
+ {
addContactFeature(feature);
}
else if (feature.isNonPositional())
{
- if (containsNonPositional(feature))
- {
- return false;
- }
-
addNonPositionalFeature(feature);
}
else
{
- // allow for check with
- if (checkContainsPositionalFeatureForAdd(feature)
- || !addPositionalFeature(feature))
- {
- return false;
- }
- positionalFeatureGroups.add(feature.getFeatureGroup());
- // addPositionalFeature(feature);
- if (feature.begin > lastStart)
- {
- lastStart = feature.begin;
- }
+ addNestedFeature(feature);
}
/*
return true;
}
- private void addFeaturesForGroup(String group,
- Collection<SequenceFeature> sfs, List<SequenceFeature> result)
+ /**
+ * Answers true if this store contains the given feature (testing by
+ * SequenceFeature.equals), else false
+ *
+ * @param feature
+ * @return
+ */
+ public boolean contains(SequenceFeature feature)
{
- if (sfs == null)
+ if (feature.isNonPositional())
{
- return;
+ return nonPositionalFeatures == null ? false : nonPositionalFeatures
+ .contains(feature);
}
- for (SequenceFeature sf : sfs)
+
+ if (feature.isContactFeature())
{
- String featureGroup = sf.getFeatureGroup();
- if (group == null && featureGroup == null
- || group != null && group.equals(featureGroup))
- {
- result.add(sf);
- }
+ return contactFeatureStarts == null ? false : listContains(
+ contactFeatureStarts, feature);
}
+
+ return features == null ? false : features
+ .contains(feature);
}
/**
- * Adds one feature to the IntervalStore that can manage nested features
- * (creating the IntervalStore if necessary)
+ * Answers the 'length' of the feature, counting 0 for non-positional features
+ * and 1 for contact features
*
- * @return true if added -- allowing for late checking during addition
+ * @param feature
+ * @return
*/
- abstract protected boolean addPositionalFeature(SequenceFeature feature);
+ protected static int getFeatureLength(SequenceFeature feature)
+ {
+ if (feature.isNonPositional())
+ {
+ return 0;
+ }
+ if (feature.isContactFeature())
+ {
+ return 1;
+ }
+ return 1 + feature.getEnd() - feature.getBegin();
+ }
/**
* Adds the feature to the list of non-positional features (with lazy
}
/**
- * Answers true if this store contains the given feature (testing by
- * SequenceFeature.equals), else false
+ * Adds one feature to the IntervalStore that can manage nested features
+ * (creating the IntervalStore if necessary)
+ */
+ protected synchronized void addNestedFeature(SequenceFeature feature)
+ {
+ if (features == null)
+ {
+ features = new IntervalStore<>();
+ }
+ features.add(feature);
+ }
+
+ /**
+ * Add a contact feature to the lists that hold them ordered by start (first
+ * contact) and by end (second contact) position, ensuring the lists remain
+ * ordered, and returns true. This method allows duplicate features to be
+ * added, so test before calling to avoid this.
*
* @param feature
* @return
*/
- @Override
- public boolean contains(SequenceFeature feature)
+ protected synchronized boolean addContactFeature(SequenceFeature feature)
{
- if (feature.isNonPositional())
+ if (contactFeatureStarts == null)
{
- return containsNonPositional(feature);
-
+ contactFeatureStarts = new ArrayList<>();
}
-
- if (feature.isContactFeature())
+ if (contactFeatureEnds == null)
{
- return containsContactFeature(feature);
-
+ contactFeatureEnds = new ArrayList<>();
}
- return containsPositionalFeature(feature);
+ /*
+ * insert into list sorted by start (first contact position):
+ * binary search the sorted list to find the insertion point
+ */
+ int insertPosition = BinarySearcher.findFirst(contactFeatureStarts,
+ f -> f.getBegin() >= feature.getBegin());
+ contactFeatureStarts.add(insertPosition, feature);
+
+ /*
+ * insert into list sorted by end (second contact position):
+ * binary search the sorted list to find the insertion point
+ */
+ insertPosition = BinarySearcher.findFirst(contactFeatureEnds,
+ f -> f.getEnd() >= feature.getEnd());
+ contactFeatureEnds.add(insertPosition, feature);
+
+ return true;
}
/**
- * A check that can be overridden if the check is being done during the add
- * operation itself.
+ * Answers true if the list contains the feature, else false. This method is
+ * optimised for the condition that the list is sorted on feature start
+ * position ascending, and will give unreliable results if this does not hold.
*
+ * @param features
* @param feature
* @return
*/
- protected boolean checkContainsPositionalFeatureForAdd(
+ protected static boolean listContains(List<SequenceFeature> features,
SequenceFeature feature)
{
- return containsPositionalFeature(feature);
+ if (features == null || feature == null)
+ {
+ return false;
+ }
+
+ /*
+ * locate the first entry in the list which does not precede the feature
+ */
+ // int pos = binarySearch(features,
+ // SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
+ int pos = BinarySearcher.findFirst(features,
+ val -> val.getBegin() >= feature.getBegin());
+ int len = features.size();
+ while (pos < len)
+ {
+ SequenceFeature sf = features.get(pos);
+ if (sf.getBegin() > feature.getBegin())
+ {
+ return false; // no match found
+ }
+ if (sf.equals(feature))
+ {
+ return true;
+ }
+ pos++;
+ }
+ return false;
+ }
+
+ /**
+ * 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.
+ *
+ * @param start
+ * start position of overlap range (inclusive)
+ * @param end
+ * end position of overlap range (inclusive)
+ * @return
+ */
+ public List<SequenceFeature> findOverlappingFeatures(long start, long end)
+ {
+ List<SequenceFeature> result = new ArrayList<>();
+
+ findContactFeatures(start, end, result);
+
+ if (features != null)
+ {
+ result.addAll(features.findOverlaps(start, end));
+ }
+
+ return result;
+ }
+
+ /**
+ * Adds contact features to the result list where either the second or the
+ * first contact position lies within the target range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ protected void findContactFeatures(long from, long to,
+ List<SequenceFeature> result)
+ {
+ if (contactFeatureStarts != null)
+ {
+ findContactStartOverlaps(from, to, result);
+ }
+ if (contactFeatureEnds != null)
+ {
+ findContactEndOverlaps(from, to, result);
+ }
+ }
+
+ /**
+ * Adds to the result list any contact features whose end (second contact
+ * point), but not start (first contact point), lies in the query from-to
+ * range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ protected void findContactEndOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ /*
+ * find the first contact feature (if any)
+ * whose end point is not before the target range
+ */
+ int index = BinarySearcher.findFirst(contactFeatureEnds,
+ f -> f.getEnd() >= from);
+
+ while (index < contactFeatureEnds.size())
+ {
+ SequenceFeature sf = contactFeatureEnds.get(index);
+ if (!sf.isContactFeature())
+ {
+ System.err.println("Error! non-contact feature type "
+ + sf.getType() + " in contact features list");
+ index++;
+ continue;
+ }
+
+ int begin = sf.getBegin();
+ if (begin >= from && begin <= to)
+ {
+ /*
+ * this feature's first contact position lies in the search range
+ * so we don't include it in results a second time
+ */
+ index++;
+ continue;
+ }
+
+ if (sf.getEnd() > to)
+ {
+ /*
+ * this feature (and all following) has end point after the target range
+ */
+ break;
+ }
+
+ /*
+ * feature has end >= from and end <= to
+ * i.e. contact end point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
+ }
+ }
+
+ /**
+ * Adds contact features whose start position lies in the from-to range to the
+ * result list
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ protected void findContactStartOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ int index = BinarySearcher.findFirst(contactFeatureStarts,
+ f -> f.getBegin() >= from);
+
+ while (index < contactFeatureStarts.size())
+ {
+ SequenceFeature sf = contactFeatureStarts.get(index);
+ if (!sf.isContactFeature())
+ {
+ System.err.println("Error! non-contact feature " + sf.toString()
+ + " in contact features list");
+ index++;
+ continue;
+ }
+ if (sf.getBegin() > to)
+ {
+ /*
+ * this feature's start (and all following) follows the target range
+ */
+ break;
+ }
+
+ /*
+ * feature has begin >= from and begin <= to
+ * i.e. contact start point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
+ }
}
- private boolean containsPositionalFeature(SequenceFeature feature)
+ /**
+ * Answers a list of all positional features stored, in no guaranteed order
+ *
+ * @return
+ */
+ public List<SequenceFeature> getPositionalFeatures()
{
- return features == null || feature.begin > lastStart ? false
- : containsFeature(feature);
+ List<SequenceFeature> result = new ArrayList<>();
+
+ /*
+ * add any contact features - from the list by start position
+ */
+ if (contactFeatureStarts != null)
+ {
+ result.addAll(contactFeatureStarts);
+ }
+
+ /*
+ * add any nested features
+ */
+ if (features != null)
+ {
+ result.addAll(features);
+ }
+
+ return result;
}
- private boolean containsContactFeature(SequenceFeature feature)
+ /**
+ * Answers a list of all contact features. If there are none, returns an
+ * immutable empty list.
+ *
+ * @return
+ */
+ public List<SequenceFeature> getContactFeatures()
{
- return contactFeatureStarts != null && feature.begin <= lastContactStart
- && listContains(contactFeatureStarts, feature);
+ if (contactFeatureStarts == null)
+ {
+ return Collections.emptyList();
+ }
+ return new ArrayList<>(contactFeatureStarts);
}
- private boolean containsNonPositional(SequenceFeature feature)
+ /**
+ * Answers a list of all non-positional features. If there are none, returns
+ * an immutable empty list.
+ *
+ * @return
+ */
+ public List<SequenceFeature> getNonPositionalFeatures()
{
- return nonPositionalFeatures == null ? false
- : nonPositionalFeatures.contains(feature);
+ if (nonPositionalFeatures == null)
+ {
+ return Collections.emptyList();
+ }
+ return new ArrayList<>(nonPositionalFeatures);
}
- abstract protected boolean containsFeature(SequenceFeature feature);
-
/**
* 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
*
* @param sf
*/
-
- @Override
public synchronized boolean delete(SequenceFeature sf)
{
boolean removed = false;
}
}
+ boolean removedNonPositional = false;
+
/*
* if not found, try non-positional features
*/
if (!removed && nonPositionalFeatures != null)
{
- removed = nonPositionalFeatures.remove(sf);
+ removedNonPositional = nonPositionalFeatures.remove(sf);
+ removed = removedNonPositional;
}
/*
*/
if (!removed && features != null)
{
- removed = findAndRemoveNonContactFeature(sf);
+ removed = features.remove(sf);
}
if (removed)
return removed;
}
- abstract protected boolean findAndRemoveNonContactFeature(SequenceFeature sf);
-
- abstract protected void findContactFeatures(long from, long to,
- List<SequenceFeature> result);
-
- abstract protected int findFirstBegin(List<SequenceFeature> list,
- long pos);
+ /**
+ * Rescan all features to recompute any cached values after an entry has been
+ * deleted. This is expected to be an infrequent event, so performance here is
+ * not critical.
+ */
+ protected synchronized void rescanAfterDelete()
+ {
+ positionalFeatureGroups.clear();
+ nonPositionalFeatureGroups.clear();
+ totalExtent = 0;
+ positionalMinScore = Float.NaN;
+ positionalMaxScore = Float.NaN;
+ nonPositionalMinScore = Float.NaN;
+ nonPositionalMaxScore = Float.NaN;
- abstract protected int findFirstEnd(List<SequenceFeature> list, long pos);
+ /*
+ * scan non-positional features for groups and scores
+ */
+ for (SequenceFeature sf : getNonPositionalFeatures())
+ {
+ nonPositionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ }
- @Override
- public List<SequenceFeature> findOverlappingFeatures(long start, long end)
- {
- return findOverlappingFeatures(start, end, null);
+ /*
+ * scan positional features for groups, scores and extents
+ */
+ for (SequenceFeature sf : getPositionalFeatures())
+ {
+ positionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ positionalMinScore = min(positionalMinScore, score);
+ positionalMaxScore = max(positionalMaxScore, score);
+ totalExtent += getFeatureLength(sf);
+ }
}
- @Override
- public List<SequenceFeature> getContactFeatures()
+ /**
+ * A helper method to return the minimum of two floats, where a non-NaN value
+ * is treated as 'less than' a NaN value (unlike Math.min which does the
+ * opposite)
+ *
+ * @param f1
+ * @param f2
+ */
+ protected static float min(float f1, float f2)
{
- return getContactFeatures(new ArrayList<>());
+ if (Float.isNaN(f1))
+ {
+ return Float.isNaN(f2) ? f1 : f2;
+ }
+ else
+ {
+ return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
+ }
}
/**
- * Answers a list of all contact features. If there are none, returns an
- * immutable empty list.
+ * A helper method to return the maximum of two floats, where a non-NaN value
+ * is treated as 'greater than' a NaN value (unlike Math.max which does the
+ * opposite)
*
- * @return
+ * @param f1
+ * @param f2
*/
-
- @Override
- public List<SequenceFeature> getContactFeatures(
- List<SequenceFeature> result)
+ protected static float max(float f1, float f2)
{
- if (contactFeatureStarts != null)
+ if (Float.isNaN(f1))
{
- result.addAll(contactFeatureStarts);
+ return Float.isNaN(f2) ? f1 : f2;
+ }
+ else
+ {
+ return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
}
- return result;
}
/**
- * Answers the number of positional (or non-positional) features stored.
- * Contact features count as 1.
+ * Answers true if this store has no features, else false
*
- * @param positional
* @return
*/
-
- @Override
- public int getFeatureCount(boolean positional)
+ public boolean isEmpty()
{
- if (!positional)
- {
- return nonPositionalFeatures == null ? 0
- : nonPositionalFeatures.size();
- }
-
- return (contactFeatureStarts == null ? 0 : contactFeatureStarts.size())
- + features.size();
+ boolean hasFeatures = (contactFeatureStarts != null
+ && !contactFeatureStarts
+ .isEmpty())
+ || (nonPositionalFeatures != null && !nonPositionalFeatures
+ .isEmpty())
+ || (features != null && features.size() > 0);
+ return !hasFeatures;
}
/**
* @param positionalFeatures
* @return
*/
-
- @Override
public Set<String> getFeatureGroups(boolean positionalFeatures)
{
if (positionalFeatures)
}
else
{
- return nonPositionalFeatureGroups == null
- ? Collections.<String> emptySet()
- : Collections.unmodifiableSet(nonPositionalFeatureGroups);
+ return nonPositionalFeatureGroups == null ? Collections
+ .<String> emptySet() : Collections
+ .unmodifiableSet(nonPositionalFeatureGroups);
}
}
- @Override
- 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)
+ * Answers the number of positional (or non-positional) features stored.
+ * Contact features count as 1.
*
* @param positional
- * @param group
* @return
*/
-
- @Override
- public List<SequenceFeature> getFeaturesForGroup(boolean positional,
- String group)
+ public int getFeatureCount(boolean positional)
{
- List<SequenceFeature> result = new ArrayList<>();
-
- /*
- * if we know features don't include the target group, no need
- * to inspect them for matches
- */
- if (positional && !positionalFeatureGroups.contains(group)
- || !positional && !nonPositionalFeatureGroups.contains(group))
+ if (!positional)
{
- return result;
+ return nonPositionalFeatures == null ? 0 : nonPositionalFeatures
+ .size();
}
- if (positional)
+ int size = 0;
+
+ if (contactFeatureStarts != null)
{
- addFeaturesForGroup(group, contactFeatureStarts, result);
- addFeaturesForGroup(group, features, result);
+ // note a contact feature (start/end) counts as one
+ size += contactFeatureStarts.size();
}
- else
+
+ if (features != null)
{
- addFeaturesForGroup(group, nonPositionalFeatures, result);
+ size += features.size();
}
- return result;
+
+ return size;
}
/**
- * Answers the maximum score held for positional or non-positional features.
- * This may be Float.NaN if there are no features, are none has a non-NaN
- * score.
+ * Answers the total length of positional features (or zero if there are
+ * none). Contact features contribute a value of 1 to the total.
*
- * @param positional
* @return
*/
-
- @Override
- public float getMaximumScore(boolean positional)
+ public int getTotalFeatureLength()
{
- return positional ? positionalMaxScore : nonPositionalMaxScore;
+ return totalExtent;
}
/**
* @param positional
* @return
*/
-
- @Override
public float getMinimumScore(boolean positional)
{
return positional ? positionalMinScore : nonPositionalMinScore;
}
- @Override
- public List<SequenceFeature> getNonPositionalFeatures()
- {
- return getNonPositionalFeatures(new ArrayList<>());
- }
-
/**
- * Answers a list of all non-positional features. If there are none, returns
- * an immutable empty list.
+ * Answers the maximum score held for positional or non-positional features.
+ * This may be Float.NaN if there are no features, are none has a non-NaN
+ * score.
*
+ * @param positional
* @return
*/
-
- @Override
- public List<SequenceFeature> getNonPositionalFeatures(
- List<SequenceFeature> result)
- {
- if (nonPositionalFeatures != null)
- {
- result.addAll(nonPositionalFeatures);
- }
- return result;
- }
-
- @Override
- public List<SequenceFeature> getPositionalFeatures()
+ public float getMaximumScore(boolean positional)
{
- return getPositionalFeatures(new ArrayList<>());
+ return positional ? positionalMaxScore : nonPositionalMaxScore;
}
/**
- * Answers a list of all positional features stored, in no guaranteed order
+ * Answers a list of all either positional or non-positional features whose
+ * feature group matches the given group (which may be null)
*
+ * @param positional
+ * @param group
* @return
*/
-
- @Override
- public List<SequenceFeature> getPositionalFeatures(
- List<SequenceFeature> result)
+ public List<SequenceFeature> getFeaturesForGroup(boolean positional,
+ String group)
{
+ List<SequenceFeature> result = new ArrayList<>();
/*
- * add any contact features - from the list by start position
- */
- if (contactFeatureStarts != null)
- {
- result.addAll(contactFeatureStarts);
- }
-
- /*
- * add any nested features
+ * if we know features don't include the target group, no need
+ * to inspect them for matches
*/
- if (features != null)
+ if (positional && !positionalFeatureGroups.contains(group)
+ || !positional && !nonPositionalFeatureGroups.contains(group))
{
- result.addAll(features);
+ return result;
}
- return result;
- }
-
- /**
- * Answers the total length of positional features (or zero if there are
- * none). Contact features contribute a value of 1 to the total.
- *
- * @return
- */
-
- @Override
- public int getTotalFeatureLength()
- {
- return totalExtent;
- }
-
- /**
- * Answers true if this store has no features, else false
- *
- * @return
- */
-
- @Override
- public boolean isEmpty()
- {
- boolean hasFeatures = (contactFeatureStarts != null
- && !contactFeatureStarts.isEmpty())
- || (nonPositionalFeatures != null
- && !nonPositionalFeatures.isEmpty())
- || features.size() > 0;
-
- return !hasFeatures;
- }
-
- /**
- * Rescan all features to recompute any cached values after an entry has been
- * deleted. This is expected to be an infrequent event, so performance here is
- * not critical.
- */
- protected synchronized void rescanAfterDelete()
- {
- positionalFeatureGroups.clear();
- nonPositionalFeatureGroups.clear();
- totalExtent = 0;
- positionalMinScore = Float.NaN;
- positionalMaxScore = Float.NaN;
- nonPositionalMinScore = Float.NaN;
- nonPositionalMaxScore = Float.NaN;
- /*
- * scan non-positional features for groups and scores
- */
- if (nonPositionalFeatures != null)
+ List<SequenceFeature> sfs = positional ? getPositionalFeatures()
+ : getNonPositionalFeatures();
+ for (SequenceFeature sf : sfs)
{
- List<SequenceFeature> list = nonPositionalFeatures;
- for (int i = 0, n = list.size(); i < n; i++)
+ String featureGroup = sf.getFeatureGroup();
+ if (group == null && featureGroup == null || group != null
+ && group.equals(featureGroup))
{
- SequenceFeature sf = list.get(i);
- nonPositionalFeatureGroups.add(sf.getFeatureGroup());
- float score = sf.getScore();
- nonPositionalMinScore = min(nonPositionalMinScore, score);
- nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ result.add(sf);
}
}
-
- /*
- * scan positional features for groups, scores and extents
- */
-
- rescanPositional(contactFeatureStarts);
- rescanPositional(features);
- }
-
- private void rescanPositional(Collection<SequenceFeature> sfs)
- {
- if (sfs == null)
- {
- return;
- }
- for (SequenceFeature sf : sfs)
- {
- positionalFeatureGroups.add(sf.getFeatureGroup());
- float score = sf.getScore();
- positionalMinScore = min(positionalMinScore, score);
- positionalMaxScore = max(positionalMaxScore, score);
- totalExtent += getFeatureLength(sf);
- }
+ return result;
}
/**
* @param shiftBy
* @return
*/
-
- @Override
public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
{
/*
* (Although a simple shift of all values would preserve data integrity!)
*/
boolean modified = false;
- List<SequenceFeature> list = getPositionalFeatures();
- for (int i = 0, n = list.size(); i < n; i++)
+ for (SequenceFeature sf : getPositionalFeatures())
{
- SequenceFeature sf = list.get(i);
if (sf.getBegin() >= fromPosition)
{
modified = true;
}
return modified;
}
-
}
git://source.jalview.org / jalview.git / blobdiff