--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel.features;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import intervalstore.nonc.IntervalStore;
+
+/**
+ * An adaption of FeatureStore that is efficient and lightweight, accelerating
+ * processing speed in JavaScript.
+ *
+ * It could be used in Java as well, with significant acceleration, but all this
+ * is so fast anyway that it probably will not be noticed in Java to speed it up
+ * by a factor of two or three. So for now, at least, this implementation is
+ * just in JavaScript. The flag for this is in SequenceFeatures.
+ *
+ * This implementation uses the IntervalStore developed by Bob Hanson, found at
+ * https://github.com/BobHanson/IntervalStoreJ, forked from the one developed by
+ * Mungo Carstairs at https://github.com/bartongroup/IntervalStoreJ.
+ *
+ * See the discussion folder at https://github.com/BobHanson/IntervalStoreJ for
+ * details.
+ *
+ * @author gmcarstairs
+ * @author Bob Hanson 2019.08.03-2019.08.16
+ *
+ */
+public class FeatureStoreJS extends FeatureStore
+{
+ private IntervalStore<SequenceFeature> featureStore;
+
+ public FeatureStoreJS()
+ {
+ // the only reference to features field in this class -- for the superclass
+
+ // linked-list no-NCList IntervalStore with presort
+
+ features = featureStore = new IntervalStore<>(true);
+ }
+
+ /**
+ * 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. This method allows duplicate features to be added, so test before
+ * calling to avoid this.
+ *
+ * @param feature
+ * @return true
+ */
+ @Override
+ protected synchronized boolean addContactFeature(SequenceFeature feature)
+ {
+ if (contactFeatureStarts == null)
+ {
+ contactFeatureStarts = new ArrayList<>();
+ contactFeatureEnds = new ArrayList<>();
+ }
+ contactFeatureStarts.add(
+ findFirstBegin(contactFeatureStarts, feature.begin), feature);
+ contactFeatureEnds.add(findFirstEnd(contactFeatureEnds, feature.end),
+ feature);
+ return true;
+ }
+
+
+ /**
+ * Add a feature to the IntervalStore, not allowing for duplicates.
+ *
+ *
+ * @return false if could not add it (late check for duplicate)
+ */
+ @Override
+ protected synchronized boolean addPositionalFeature(
+ SequenceFeature feature)
+ {
+ return featureStore.add(feature, false);
+ }
+
+ /**
+ * Initial check in FeatureStore.add(feature) that in other implementations
+ * does a containment check, but in this implementation just returns false to
+ * indicate that we should continue. This implementation will do this check as
+ * part of the add() method for greater efficiency (one binary search instead
+ * of two).
+ *
+ * @return false -- meaning "maybe not contained; continue adding"
+ */
+ @Override
+ protected boolean checkContainsPositionalFeatureForAdd(
+ SequenceFeature feature)
+ {
+ return false;
+ }
+
+ /**
+ * Check to see if a feature (or its equivalent based on
+ * IntervalI.equalsInterval) is already in this store. This method should be
+ * avoided except when necessary, as it involves a binary search with identity
+ * check.
+ *
+ * @return true if this feature or its equivalent (based on equalsInterval) is
+ * present already in the collection.
+ */
+ @Override
+ protected boolean containsFeature(SequenceFeature feature)
+ {
+ return featureStore.contains(feature);
+ }
+
+ @Override
+ protected boolean findAndRemoveNonContactFeature(SequenceFeature sf)
+ {
+ return featureStore.remove(sf);
+ }
+
+ /**
+ * Add contact features to the result list where either the second or the
+ * first contact position lies within the target range, inclusively.
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ @Override
+ protected void findContactFeatures(long from, long to,
+ List<SequenceFeature> result)
+ {
+ getContactStartOverlaps(from, to, result);
+ getContactEndOverlaps(from, to, result);
+ }
+
+ /**
+ * Locate the first feature start in a standard ArrayList that is at or after
+ * this position.
+ *
+ */
+
+ @Override
+ protected int findFirstBegin(List<SequenceFeature> list, long pos)
+ {
+ int matched = list.size();
+ int end = matched - 1;
+ int start = (end < 0 || list.get(end).begin < pos ? matched : 0);
+ while (start <= end)
+ {
+ int mid = (start + end) / 2;
+ if (list.get(mid).begin >= pos)
+ {
+ matched = mid;
+ end = mid - 1;
+ }
+ else
+ {
+ start = mid + 1;
+ }
+ }
+ return matched;
+ }
+
+ /**
+ * Locate the feature end in a standard ArrayList that is after or at this
+ * position.
+ *
+ */
+
+ @Override
+ protected int findFirstEnd(List<SequenceFeature> list, long pos)
+ {
+ int matched = list.size();
+ int end = matched - 1;
+ int start = 0;
+ while (start <= end)
+ {
+ int mid = (start + end) / 2;
+ if (list.get(mid).end >= pos)
+ {
+ matched = mid;
+ end = mid - 1;
+ }
+ else
+ {
+ start = mid + 1;
+ }
+ }
+ return matched;
+ }
+
+ /**
+ * Returns a (possibly empty) list of features whose extent overlaps the given
+ * range. The returned list is ordered as follows:
+ *
+ * (1) ContactFeature starts
+ *
+ * (2) ContactFeature ends (that are not also starts)
+ *
+ * (3) noncontact SequenceFeatures, in reverse start order
+ *
+ * (This last reverse order is for efficiency in processing only.)
+ *
+ *
+ *
+ * @param start
+ * start position of overlap range (inclusive)
+ * @param end
+ * end position of overlap range (inclusive)
+ *
+ * @param result
+ * optional result list; for highest efficiency, provide this
+ * parameter
+ * @return result same as result parameter, or a new ArrayList if that is null
+ */
+
+ @Override
+ public List<SequenceFeature> findOverlappingFeatures(long start, long end,
+ List<SequenceFeature> result)
+ {
+ if (result == null)
+ {
+ result = new ArrayList<>();
+ }
+ if (contactFeatureStarts != null)
+ {
+ if (start == end)
+ {
+ getContactPointStarts(contactFeatureStarts, start, result);
+ getContactPointEnds(contactFeatureEnds, end, result);
+ }
+ else
+ {
+ findContactFeatures(start, end, result);
+ }
+ }
+ if (featureStore.size() > 0)
+ {
+ featureStore.findOverlaps(start, end, result);
+ }
+ return result;
+ }
+
+ /**
+ * Adds to the result list any contact features having end (second contact
+ * point), but not start (first contact point), in the query from-to range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+
+ private void getContactEndOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ // find the first contact feature (if any)
+ // with end point not before the target range
+
+ for (int i = findFirstEnd(contactFeatureEnds,
+ from), n = contactFeatureEnds.size(); i < n; i++)
+ {
+ SequenceFeature sf = contactFeatureEnds.get(i);
+ if (sf.begin >= from && sf.begin <= to)
+ {
+ // this feature's first contact position lies in the search range
+ // so we don't include it in results a second time
+ continue;
+ }
+
+ if (sf.end > 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);
+ }
+ }
+
+ /**
+ * Binary search for contact start or end matching a specific position. This
+ * efficient search was designed specifically for rapid return for the
+ * OverviewPanel. It's implementation sped processing of that panel by 2300%.
+ *
+ * @param l
+ * @param pos
+ * @param result
+ * @param isStart
+ *
+ * @author Bob Hanson 2019.07.30
+ */
+ private void getContactPointStarts(List<SequenceFeature> l, long pos,
+ List<SequenceFeature> result)
+ {
+ int low = 0;
+ int high = l.size() - 1;
+ while (low <= high)
+ {
+ int mid = (low + high) >>> 1;
+ SequenceFeature f = l.get(mid);
+ switch (Long.signum(f.begin - pos))
+ {
+ case -1:
+ low = mid + 1;
+ continue;
+ case 1:
+ high = mid - 1;
+ continue;
+ case 0:
+ int m = mid;
+ result.add(f);
+ // could be "5" in 12345556788 ?
+ while (++mid <= high && (f = l.get(mid)) != null && f.begin == pos)
+ {
+ result.add(f);
+ }
+ while (--m >= low && (f = l.get(m)) != null && f.begin == pos)
+ {
+ result.add(f);
+ }
+ return;
+ }
+ }
+ }
+
+ private void getContactPointEnds(List<SequenceFeature> l, long pos,
+ List<SequenceFeature> result)
+ {
+ int low = 0;
+ int high = l.size() - 1;
+ while (low <= high)
+ {
+ int mid = (low + high) >>> 1;
+ SequenceFeature f = l.get(mid);
+ switch (Long.signum(f.end - pos))
+ {
+ case -1:
+ low = mid + 1;
+ continue;
+ case 1:
+ high = mid - 1;
+ continue;
+ case 0:
+ int m = mid;
+ if (f.begin != f.end)
+ {
+ result.add(f);
+ }
+ // could be "5" in 12345556788 ?
+ while (++mid <= high && (f = l.get(mid)) != null
+ && f.end == pos)
+ {
+ if (f.begin != f.end)
+ {
+ result.add(f);
+ }
+ }
+ while (--m >= low && (f = l.get(m)) != null
+ && f.end == pos)
+ {
+ if (f.begin != f.end)
+ {
+ result.add(f);
+ }
+ }
+ return;
+ }
+ }
+ }
+
+ /**
+ * Adds contact features whose start position lies in the from-to range to the
+ * result list
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+
+ private void getContactStartOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ for (int i = findFirstBegin(contactFeatureStarts,
+ from), n = contactFeatureStarts.size(); i < n; i++)
+ {
+ SequenceFeature sf = contactFeatureStarts.get(i);
+ if (sf.begin > to)
+ {
+ break;
+ }
+ result.add(sf);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff