import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
-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
+public abstract class FeatureStore implements FeatureStoreI
{
+
/*
* 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
*/
- IntervalStoreI<SequenceFeature> features;
+ Collection<SequenceFeature> features;
+
+ @Override
+ public Collection<SequenceFeature> getFeatures()
+ {
+ return features;
+ }
/*
* Feature groups represented in stored positional features
float nonPositionalMaxScore;
- private ArrayList<SequenceFeature> featuresList;
-
/**
* Constructor
*/
public FeatureStore()
{
- features = new IntervalStore<>();
- featuresList = new ArrayList<>();
positionalFeatureGroups = new HashSet<>();
nonPositionalFeatureGroups = new HashSet<>();
positionalMinScore = Float.NaN;
* @param feature
*/
+ @Override
public boolean addFeature(SequenceFeature feature)
{
if (contains(feature))
* @param feature
* @return
*/
+ @Override
public boolean contains(SequenceFeature feature)
{
if (feature.isNonPositional())
if (feature.isContactFeature())
{
- return contactFeatureStarts == null ? false
- : listContains(contactFeatureStarts, feature);
+ return contactFeatureStarts != null
+ && listContains(contactFeatureStarts, feature);
}
return features == null ? false : features.contains(feature);
*/
protected synchronized void addNestedFeature(SequenceFeature feature)
{
- if (features == null)
- {
- features = new IntervalStore<>();
- }
features.add(feature);
- featuresList.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
if (contactFeatureStarts == null)
{
contactFeatureStarts = new ArrayList<>();
- }
- if (contactFeatureEnds == null)
- {
contactFeatureEnds = new ArrayList<>();
}
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++;
- }
- }
+ abstract protected void findContactFeatures(long from, long to,
+ List<SequenceFeature> result);
/**
* Answers a list of all positional features stored, in no guaranteed order
* @return
*/
- public List<SequenceFeature> getPositionalFeatures()
+ @Override
+ public List<SequenceFeature> getPositionalFeatures(
+ List<SequenceFeature> result)
{
- List<SequenceFeature> result = new ArrayList<>();
/*
* add any contact features - from the list by start position
* @return
*/
- public List<SequenceFeature> getContactFeatures()
+ @Override
+ public List<SequenceFeature> getContactFeatures(
+ List<SequenceFeature> result)
{
- if (contactFeatureStarts == null)
+ if (contactFeatureStarts != null)
{
- return Collections.emptyList();
+ result.addAll(contactFeatureStarts);
}
- return new ArrayList<>(contactFeatureStarts);
+ return result;
}
/**
* @return
*/
- public List<SequenceFeature> getNonPositionalFeatures()
+ @Override
+ public List<SequenceFeature> getNonPositionalFeatures(
+ List<SequenceFeature> result)
{
- if (nonPositionalFeatures == null)
+ if (nonPositionalFeatures != null)
{
- return Collections.emptyList();
+ result.addAll(nonPositionalFeatures);
}
- return new ArrayList<>(nonPositionalFeatures);
+ return result;
}
/**
* @param sf
*/
+ @Override
public synchronized boolean delete(SequenceFeature sf)
{
boolean removed = false;
if (!removed && features != null)
{
removed = features.remove(sf);
- featuresList.remove(sf);
}
if (removed)
/*
* scan non-positional features for groups and scores
*/
- for (SequenceFeature sf : getNonPositionalFeatures())
+ if (nonPositionalFeatures != null)
{
- nonPositionalFeatureGroups.add(sf.getFeatureGroup());
- float score = sf.getScore();
- nonPositionalMinScore = min(nonPositionalMinScore, score);
- nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ for (SequenceFeature sf : nonPositionalFeatures)
+ {
+ nonPositionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ }
}
/*
* scan positional features for groups, scores and extents
*/
- for (SequenceFeature sf : getPositionalFeatures())
+
+ 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();
}
}
+
/**
* 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 != null && features.size() > 0);
+ || features.size() > 0;
return !hasFeatures;
}
* @return
*/
+ @Override
public Set<String> getFeatureGroups(boolean positionalFeatures)
{
if (positionalFeatures)
}
/**
- * Answers the number of positional (or non-positional) features stored.
- * Contact features count as 1.
+ * 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
*/
- public int getFeatureCount(boolean positional)
+ @Override
+ public List<SequenceFeature> getFeaturesForGroup(boolean positional,
+ String group)
{
- if (!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))
{
- return nonPositionalFeatures == null ? 0
- : nonPositionalFeatures.size();
+ return result;
}
- int size = 0;
+ if (positional)
+ {
+ addFeaturesForGroup(group, contactFeatureStarts, result);
+ addFeaturesForGroup(group, features, result);
+ }
+ else
+ {
+ addFeaturesForGroup(group, nonPositionalFeatures, result);
+ }
+ return result;
+ }
- if (contactFeatureStarts != null)
+ private void addFeaturesForGroup(String group,
+ Collection<SequenceFeature> sfs, List<SequenceFeature> result)
+ {
+ if (sfs == null)
+ {
+ return;
+ }
+ for (SequenceFeature sf : sfs)
{
- // note a contact feature (start/end) counts as one
- size += contactFeatureStarts.size();
+ String featureGroup = sf.getFeatureGroup();
+ if (group == null && featureGroup == null
+ || group != null && group.equals(featureGroup))
+ {
+ result.add(sf);
+ }
}
+ }
- if (features != null)
+ /**
+ * Answers the number of positional (or non-positional) features stored.
+ * Contact features count as 1.
+ *
+ * @param positional
+ * @return
+ */
+
+ @Override
+ public int getFeatureCount(boolean positional)
+ {
+ if (!positional)
{
- size += features.size();
+ return nonPositionalFeatures == null ? 0
+ : nonPositionalFeatures.size();
}
- return size;
+ return (contactFeatureStarts == null ? 0 : contactFeatureStarts.size())
+ + features.size();
+
}
+
/**
* 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;
* @return
*/
+ @Override
public float getMinimumScore(boolean positional)
{
return positional ? positionalMinScore : nonPositionalMinScore;
* @return
*/
+ @Override
public float getMaximumScore(boolean positional)
{
return positional ? positionalMaxScore : nonPositionalMaxScore;
}
- /**
- * 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
- */
-
- public List<SequenceFeature> getFeaturesForGroup(boolean positional,
- String group)
- {
- 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))
- {
- return result;
- }
-
- List<SequenceFeature> sfs = positional ? getPositionalFeatures()
- : getNonPositionalFeatures();
- for (SequenceFeature sf : sfs)
- {
- String featureGroup = sf.getFeatureGroup();
- if (group == null && featureGroup == null
- || group != null && group.equals(featureGroup))
- {
- result.add(sf);
- }
- }
- return result;
- }
/**
* Adds the shift amount to the start and end of all positional features whose
* @return
*/
+ @Override
public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
{
/*
return modified;
}
- /////////////////////// added by Bob Hanson ///////////////////////
-
- // The following methods use a linked list of containment in features
- // rather than IntervalStore. Implemented only for OverviewPanel, because
- // only that makes calls for start == end in feature overlap requests.
- //
- //
- // There are two parts --- initialization, and overlap searching.
- //
- // Initialization involves two steps:
- //
- // (1) sorting of features by start position using a standard Array.sort with
- // Comparator.
- // (2) linking of features, effectively nesting them.
- //
- // Searching also involves two steps:
- //
- // (1) binary search for a position within the sorted features array.
- // (2) traversing the linked lists with an end check to read out the
- // overlapped features at this position.
- //
- // All of this is done with very simple standard methods.
-
- // single public method:
-
- /**
- * Find all features containing this position.
- *
- * @param pos
- * @return list of SequenceFeatures
- * @author Bob Hanson 2019.07.30
- */
-
- public List<SequenceFeature> findOverlappingFeatures(int pos,
- List<SequenceFeature> result)
- {
- if (result == null)
- {
- result = new ArrayList<>();
- }
-
- if (contactFeatureStarts != null)
- {
- findContacts(contactFeatureStarts, pos, result, true);
- findContacts(contactFeatureEnds, pos, result, false);
- }
- if (featuresList != null)
- {
- findOverlaps(featuresList, pos, result);
- }
- return result;
- }
-
- // Initialization
-
- /*
- * contact features ordered by first contact position
- */
- private SequenceFeature[] orderedFeatureStarts;
-
- private void rebuildArrays(int n)
- {
- if (startComp == null)
- {
- startComp = new StartComparator();
- }
- orderedFeatureStarts = new SequenceFeature[n];
- for (int i = n; --i >= 0;)
- {
- SequenceFeature sf = featuresList.get(i);
- sf.index = i; // for debugging only
- orderedFeatureStarts[i] = sf;
- }
- Arrays.sort(orderedFeatureStarts, startComp);
- linkFeatures(orderedFeatureStarts);
- }
-
- /**
- * just a standard Comparator
- */
- private static StartComparator startComp;
-
- class StartComparator implements Comparator<SequenceFeature>
- {
-
- @Override
- public int compare(SequenceFeature o1, SequenceFeature o2)
- {
- int p1 = o1.begin;
- int p2 = o2.begin;
- return (p1 < p2 ? -1 : p1 > p2 ? 1 : 0);
- }
-
- }
-
- /**
- * Run through the sorted sequence array once, building the containedBy linked
- * list references. Does a check first to make sure there is actually
- * something out there that is overlapping. A null for sf.containedBy means
- * there are no overlaps for this feature.
- *
- * @param intervals
- */
- private void linkFeatures(SequenceFeature[] intervals)
- {
- if (intervals.length < 2)
- {
- return;
- }
- int maxEnd = intervals[0].end;
- for (int i = 1, n = intervals.length; i < n; i++)
- {
- SequenceFeature sf = intervals[i];
- if (sf.begin <= maxEnd)
- {
- sf.containedBy = getContainedBy(intervals[i - 1], sf);
- }
- if (sf.end > maxEnd)
- {
- maxEnd = sf.end;
- }
- }
- }
-
- /**
- * Since we are traversing the sorted feature array in a forward direction,
- * all elements prior to the one we are working on have been fully linked. All
- * we are doing is following those links until we find the first array feature
- * with a containedBy element that has an end >= our begin point. It is
- * generally a very short list -- maybe one or two depths. But it might be
- * more than that.
- *
- * @param sf
- * @param sf0
- * @return
- */
- private SequenceFeature getContainedBy(SequenceFeature sf,
- SequenceFeature sf0)
- {
- int begin = sf0.begin;
- while (sf != null)
- {
- if (begin <= sf.end)
- {
- System.out.println("\nFS found " + sf0.index + ":" + sf0
- + "\nFS in " + sf.index + ":" + sf);
- return sf;
- }
- sf = sf.containedBy;
- }
- return null;
- }
-
- // search-stage methods
- /**
- * Binary search for contact start or end at a given (Overview) position.
- *
- * @param l
- * @param pos
- * @param result
- * @param isStart
- *
- * @author Bob Hanson 2019.07.30
- */
- private static void findContacts(List<SequenceFeature> l, int pos,
- List<SequenceFeature> result, boolean isStart)
+ @Override
+ public List<SequenceFeature> findOverlappingFeatures(long start, long end)
{
- int low = 0;
- int high = l.size() - 1;
- while (low <= high)
- {
- int mid = (low + high) >>> 1;
- SequenceFeature f = l.get(mid);
- switch (Long.signum((isStart ? f.begin : f.end) - 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
- && (isStart ? f.begin : f.end) == pos)
- {
- result.add(f);
- }
- while (--m >= low && (f = l.get(m)) != null
- && (isStart ? f.begin : f.end) == pos)
- {
- result.add(f);
- }
- return;
- }
- }
+ return findOverlappingFeatures(start, end, null);
}
- /**
- * Find all overlaps; special case when there is only one feature. The
- * required array of start-sorted SequenceFeature is created lazily.
- *
- * @param features
- * @param pos
- * @param result
- */
- private void findOverlaps(List<SequenceFeature> features, int pos,
- List<SequenceFeature> result)
+ @Override
+ public List<SequenceFeature> getPositionalFeatures()
{
- int n = featuresList.size();
- if (n == 1)
- {
- checkOne(featuresList.get(0), pos, result);
- return;
- }
- if (orderedFeatureStarts == null)
- {
- rebuildArrays(n);
- }
-
- // (1) Find the closest feature to this position.
-
- SequenceFeature sf = findClosestFeature(orderedFeatureStarts, pos);
-
- // (2) Traverse the containedBy field, checking for overlap.
-
- while (sf != null)
- {
- if (sf.end >= pos)
- {
- result.add(sf);
- }
- sf = sf.containedBy;
- }
+ return getPositionalFeatures(new ArrayList<>());
}
- /**
- * Quick check when we only have one feature.
- *
- * @param sf
- * @param pos
- * @param result
- */
- private void checkOne(SequenceFeature sf, int pos,
- List<SequenceFeature> result)
+ @Override
+ public List<SequenceFeature> getContactFeatures()
{
- if (sf.begin <= pos && sf.end >= pos)
- {
- result.add(sf);
- }
- return;
+ return getContactFeatures(new ArrayList<>());
}
- /**
- * A binary search identical to the one used for contact start/end, but here
- * we return the feature itself. Unlike Collection.BinarySearch, all we have
- * to be is close, not exact, and we make sure if there is a string of
- * identical starts, then we slide to the end so that we can check all of
- * them.
- *
- * @param l
- * @param pos
- * @return
- */
- private SequenceFeature findClosestFeature(SequenceFeature[] l, int pos)
+ @Override
+ public List<SequenceFeature> getNonPositionalFeatures()
{
- int low = 0;
- int high = l.length - 1;
- while (low <= high)
- {
- int mid = (low + high) >>> 1;
- SequenceFeature f = l[mid];
- switch (Long.signum(f.begin - pos))
- {
- case -1:
- low = mid + 1;
- continue;
- case 1:
- high = mid - 1;
- continue;
- case 0:
-
- while (++mid <= high && l[mid].begin == pos)
- {
- ;
- }
- return l[--mid];
- }
- }
- // -1 here?
- return (high < 0 || low >= l.length ? null : l[high]);
+ return getNonPositionalFeatures(new ArrayList<>());
}
-
}
git://source.jalview.org / jalview.git / blobdiff