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 intervalstore.api.IntervalStoreI;
import intervalstore.impl.BinarySearcher;
-import intervalstore.impl.IntervalStore;
+import intervalstore.impl.BinarySearcher.Compare;
-/**
- * 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 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 largest start for quick insertion of ordered features
+ */
+ protected int maxStart = -1;
+
+ protected int maxContactStart = -1;
+
/*
* Non-positional features have no (zero) start/end position.
* Kept as a separate list in case this criterion changes in future.
float nonPositionalMaxScore;
- private SequenceFeature[] temp = new SequenceFeature[3];
+ /**
+ * 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
+ */
+ public static boolean listContains(List<SequenceFeature> list,
+ SequenceFeature feature)
+ {
+ if (list == null || feature == null)
+ {
+ return false;
+ }
+
+ /*
+ * locate the first entry in the list which does not precede the feature
+ */
+ int begin = feature.begin;
+ int pos = BinarySearcher.findFirst(list, true, Compare.GE, begin);
+ int len = list.size();
+ while (pos < len)
+ {
+ SequenceFeature sf = list.get(pos);
+ if (sf.begin > begin)
+ {
+ return false; // no match found
+ }
+ if (sf.equals(feature))
+ {
+ return true;
+ }
+ pos++;
+ }
+ return false;
+ }
+
+ /**
+ * 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);
+ }
+ }
- private boolean isTainted;
+ /**
+ * 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);
+ }
+ }
/**
- * Constructor
+ * Constructor that defaults to using NCList IntervalStore
*/
public FeatureStore()
{
- features = new IntervalStore<>();
+ this(IntervalStoreType.INTERVAL_STORE_NCLIST);
+ }
+
+ /**
+ * Constructor that allows an alternative IntervalStore implementation to be
+ * chosen
+ */
+ public FeatureStore(IntervalStoreType 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
}
/**
- * 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()
- * comparison.
+ * 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)
+ {
+ default:
+ case INTERVAL_STORE_NCLIST:
+ return new intervalstore.impl.IntervalStore<>();
+ case INTERVAL_STORE_NCARRAY:
+ return new intervalstore.nonc.IntervalStore<>();
+ case INTERVAL_STORE_LINKED_LIST:
+ return new intervalstore.nonc.IntervalStore0<>();
+ }
+ }
+
+ /**
+ * 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
*/
- public boolean addFeature(SequenceFeature feature)
+ protected synchronized boolean addContactFeature(SequenceFeature feature)
{
- if (contains(feature))
+ if (contactFeatureStarts == null)
{
- return false;
+ contactFeatureStarts = new ArrayList<>();
+ contactFeatureEnds = new ArrayList<>();
}
/*
- * keep a record of feature groups
+ * insert into list sorted by start (first contact position):
+ * binary search the sorted list to find the insertion point
*/
- if (!feature.isNonPositional())
- {
- positionalFeatureGroups.add(feature.getFeatureGroup());
- }
+ int insertAt = BinarySearcher.findFirst(contactFeatureStarts, true,
+ Compare.GE, feature.begin);
+ contactFeatureStarts.add(insertAt, 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()
+ * comparison.
+ *
+ * @param feature
+ */
+ public boolean addFeature(SequenceFeature feature)
+ {
if (feature.isContactFeature())
{
+ if (containsContactFeature(feature))
+ {
+ return false;
+ }
+ positionalFeatureGroups.add(feature.getFeatureGroup());
+ if (feature.begin > maxContactStart)
+ {
+ maxContactStart = feature.begin;
+ }
addContactFeature(feature);
}
else if (feature.isNonPositional())
{
+ if (containsNonPositionalFeature(feature))
+ {
+ return false;
+ }
+
addNonPositionalFeature(feature);
}
else
{
- addNestedFeature(feature);
+ if (!features.add(feature, false))
+ {
+ return false;
+ }
+ positionalFeatureGroups.add(feature.getFeatureGroup());
+ if (feature.begin > maxStart)
+ {
+ maxStart = feature.begin;
+ }
}
/*
}
/**
- * Answers true if this store contains the given feature (testing by
- * SequenceFeature.equals), else false
- *
- * @param feature
- * @return
- */
- public boolean contains(SequenceFeature feature)
- {
- if (feature.isNonPositional())
- {
- return nonPositionalFeatures == null ? false : nonPositionalFeatures
- .contains(feature);
- }
-
- if (feature.isContactFeature())
- {
- return contactFeatureStarts == null ? false : listContains(
- contactFeatureStarts, feature);
- }
-
- return features == null ? false : features
- .contains(feature);
- }
-
- /**
- * Answers the 'length' of the feature, counting 0 for non-positional features
- * and 1 for contact features
+ * A helper method that adds to the result list any features from the
+ * collection provided whose feature group matches the specified group
*
- * @param feature
- * @return
+ * @param group
+ * @param sfs
+ * @param result
*/
- protected static int getFeatureLength(SequenceFeature feature)
+ private void addFeaturesForGroup(String group,
+ Collection<SequenceFeature> sfs, List<SequenceFeature> result)
{
- if (feature.isNonPositional())
+ if (sfs == null)
{
- return 0;
+ return;
}
- if (feature.isContactFeature())
+ for (SequenceFeature sf : sfs)
{
- return 1;
+ String featureGroup = sf.getFeatureGroup();
+ if (group == null && featureGroup == null
+ || group != null && group.equals(featureGroup))
+ {
+ result.add(sf);
+ }
}
- return 1 + feature.getEnd() - feature.getBegin();
}
/**
}
/**
- * 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);
- isTainted = 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, and returns true. This method allows duplicate features to be
- * added, so test before calling to avoid this.
+ * Answers true if this store contains the given feature (testing by
+ * SequenceFeature.equals), else false
*
* @param feature
* @return
*/
- protected synchronized boolean addContactFeature(SequenceFeature feature)
+ public boolean contains(SequenceFeature feature)
{
- if (contactFeatureStarts == null)
+ if (feature.isNonPositional())
{
- contactFeatureStarts = new ArrayList<>();
+ return containsNonPositionalFeature(feature);
}
- if (contactFeatureEnds == null)
+
+ if (feature.isContactFeature())
{
- contactFeatureEnds = new ArrayList<>();
+ return containsContactFeature(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);
-
+ return containsPositionalFeature(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);
+ private boolean containsPositionalFeature(SequenceFeature feature)
+ {
+ return features == null || feature.begin > maxStart ? false
+ : features.contains(feature);
+ }
- return true;
+ /**
+ * Answers true if this store already contains a contact feature equal to the
+ * given feature (by {@code SequenceFeature.equals()} test), else false
+ *
+ * @param feature
+ * @return
+ */
+ private boolean containsContactFeature(SequenceFeature feature)
+ {
+ return contactFeatureStarts != null && feature.begin <= maxContactStart
+ && listContains(contactFeatureStarts, feature);
}
/**
- * 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.
+ * Answers true if this store already contains a non-positional feature equal
+ * to the given feature (by {@code SequenceFeature.equals()} test), else false
*
- * @param features
* @param feature
* @return
*/
- protected static boolean listContains(List<SequenceFeature> features,
- SequenceFeature feature)
+ private boolean containsNonPositionalFeature(SequenceFeature 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++;
- }
- }
-
- /**
- * Answers a list of all positional features stored, in no guaranteed order
- *
- * @return
- */
- public List<SequenceFeature> getPositionalFeatures()
- {
- 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;
- }
-
- /**
- * Answers a list of all contact features. If there are none, returns an
- * immutable empty list.
- *
- * @return
- */
- public List<SequenceFeature> getContactFeatures()
- {
- if (contactFeatureStarts == null)
- {
- return Collections.emptyList();
- }
- return new ArrayList<>(contactFeatureStarts);
- }
-
- /**
- * Answers a list of all non-positional features. If there are none, returns
- * an immutable empty list.
- *
- * @return
- */
- public List<SequenceFeature> getNonPositionalFeatures()
- {
- if (nonPositionalFeatures == null)
- {
- return Collections.emptyList();
- }
- return new ArrayList<>(nonPositionalFeatures);
- }
+ return nonPositionalFeatures == null ? false
+ : nonPositionalFeatures.contains(feature);
+ }
/**
* Deletes the given feature from the store, returning true if it was found
}
}
- boolean removedNonPositional = false;
-
/*
* if not found, try non-positional features
*/
if (!removed && nonPositionalFeatures != null)
{
- removedNonPositional = nonPositionalFeatures.remove(sf);
- removed = removedNonPositional;
+ removed = nonPositionalFeatures.remove(sf);
}
/*
return removed;
}
+ public List<SequenceFeature> findFeatures(long start, long end)
+ {
+ return findFeatures(start, end, null);
+ }
+
/**
- * 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.
+ * 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
*/
- protected synchronized void rescanAfterDelete()
+ public List<SequenceFeature> findFeatures(long start, long end,
+ List<SequenceFeature> result)
{
- positionalFeatureGroups.clear();
- nonPositionalFeatureGroups.clear();
- totalExtent = 0;
- positionalMinScore = Float.NaN;
- positionalMaxScore = Float.NaN;
- nonPositionalMinScore = Float.NaN;
- nonPositionalMaxScore = Float.NaN;
- isTainted = true;
- /*
- * scan non-positional features for groups and scores
- */
- for (SequenceFeature sf : getNonPositionalFeatures())
+ if (result == null)
{
- nonPositionalFeatureGroups.add(sf.getFeatureGroup());
- float score = sf.getScore();
- nonPositionalMinScore = min(nonPositionalMinScore, score);
- nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ result = new ArrayList<>();
}
- /*
- * 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);
- }
+ findContactFeatures(start, end, result);
+ features.findOverlaps(start, end, result);
+
+ return result;
}
/**
- * 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)
+ * Returns a (possibly empty) list of stored contact features
*
- * @param f1
- * @param f2
+ * @return
*/
- protected static float min(float f1, float f2)
+ public List<SequenceFeature> getContactFeatures()
{
- if (Float.isNaN(f1))
- {
- return Float.isNaN(f2) ? f1 : f2;
- }
- else
- {
- return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
- }
+ List<SequenceFeature> result = new ArrayList<>();
+ getContactFeatures(result);
+ return result;
}
/**
- * 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)
+ * Adds any stored contact features to the result list
*
- * @param f1
- * @param f2
+ * @return
*/
- protected static float max(float f1, float f2)
+ public void getContactFeatures(List<SequenceFeature> result)
{
- if (Float.isNaN(f1))
- {
- return Float.isNaN(f2) ? f1 : f2;
- }
- else
+ if (contactFeatureStarts != null)
{
- return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
+ result.addAll(contactFeatureStarts);
}
}
/**
- * Answers true if this store has no features, else false
+ * Answers the number of positional (or non-positional) features stored.
+ * Contact features count as 1.
*
+ * @param positional
* @return
*/
- public boolean isEmpty()
+ public int getFeatureCount(boolean positional)
{
- boolean hasFeatures = (contactFeatureStarts != null
- && !contactFeatureStarts
- .isEmpty())
- || (nonPositionalFeatures != null && !nonPositionalFeatures
- .isEmpty())
- || (features != null && features.size() > 0);
+ if (!positional)
+ {
+ return nonPositionalFeatures == null ? 0
+ : nonPositionalFeatures.size();
+ }
+
+ int size = 0;
+
+ if (contactFeatureStarts != null)
+ {
+ // note a contact feature (start/end) counts as one
+ size += contactFeatureStarts.size();
+ }
- return !hasFeatures;
+ if (features != null)
+ {
+ size += features.size();
+ }
+ return size;
}
/**
}
else
{
- return nonPositionalFeatureGroups == null ? Collections
- .<String> emptySet() : Collections
- .unmodifiableSet(nonPositionalFeatureGroups);
+ return nonPositionalFeatureGroups == null
+ ? Collections.<String> emptySet()
+ : Collections.unmodifiableSet(nonPositionalFeatureGroups);
}
}
/**
- * 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)
+ 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 (contactFeatureStarts != null)
+ if (positional)
{
- // note a contact feature (start/end) counts as one
- size += contactFeatureStarts.size();
+ addFeaturesForGroup(group, contactFeatureStarts, result);
+ addFeaturesForGroup(group, features, result);
}
-
- if (features != null)
+ else
{
- size += features.size();
+ addFeaturesForGroup(group, nonPositionalFeatures, result);
}
-
- return size;
+ 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.
+ * 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
*/
- public int getTotalFeatureLength()
+ public float getMaximumScore(boolean positional)
{
- return totalExtent;
+ return positional ? positionalMaxScore : nonPositionalMaxScore;
}
/**
}
/**
- * 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 a (possibly empty) list of all non-positional features
*
- * @param positional
* @return
*/
- public float getMaximumScore(boolean positional)
+ public List<SequenceFeature> getNonPositionalFeatures()
{
- return positional ? positionalMaxScore : nonPositionalMaxScore;
+ List<SequenceFeature> result = new ArrayList<>();
+ getNonPositionalFeatures(result);
+ return result;
}
/**
- * Answers a list of all either positional or non-positional features whose
- * feature group matches the given group (which may be null)
+ * Adds any stored non-positional features to the result list
*
- * @param positional
- * @param group
* @return
*/
- public List<SequenceFeature> getFeaturesForGroup(boolean positional,
- String group)
+ public void getNonPositionalFeatures(List<SequenceFeature> result)
+ {
+ if (nonPositionalFeatures != null)
+ {
+ result.addAll(nonPositionalFeatures);
+ }
+ }
+
+ /**
+ * Returns a (possibly empty) list of all positional features stored
+ *
+ * @return
+ */
+ public List<SequenceFeature> getPositionalFeatures()
{
List<SequenceFeature> result = new ArrayList<>();
+ getPositionalFeatures(result);
+
+ return result;
+ }
+ /**
+ * Adds all positional features stored to the result list, in no guaranteed
+ * order, and with no check for duplicates
+ */
+ public void getPositionalFeatures(List<SequenceFeature> result)
+ {
/*
- * if we know features don't include the target group, no need
- * to inspect them for matches
+ * add any contact features - from the list by start position
*/
- if (positional && !positionalFeatureGroups.contains(group)
- || !positional && !nonPositionalFeatureGroups.contains(group))
+ if (contactFeatureStarts != null)
{
- return result;
+ result.addAll(contactFeatureStarts);
}
- List<SequenceFeature> sfs = positional ? getPositionalFeatures()
- : getNonPositionalFeatures();
- for (SequenceFeature sf : sfs)
+ /*
+ * add any nested features
+ */
+ if (features != null)
{
- String featureGroup = sf.getFeatureGroup();
- if (group == null && featureGroup == null || group != null
- && group.equals(featureGroup))
+ result.addAll(features);
+ }
+ }
+
+ /**
+ * Answers the total length of positional features (or zero if there are
+ * none). Contact features contribute a value of 1 to the total.
+ *
+ * @return
+ */
+ public int getTotalFeatureLength()
+ {
+ return totalExtent;
+ }
+
+ /**
+ * Answers true if this store has no features, else false
+ *
+ * @return
+ */
+ public boolean isEmpty()
+ {
+ boolean hasFeatures = (contactFeatureStarts != null
+ && !contactFeatureStarts.isEmpty())
+ || (nonPositionalFeatures != null
+ && !nonPositionalFeatures.isEmpty())
+ || (features != null && 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)
+ {
+ for (int i = 0, n = nonPositionalFeatures.size(); i < n; i++)
{
- result.add(sf);
+ SequenceFeature sf = nonPositionalFeatures.get(i);
+ nonPositionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
}
}
- return result;
+
+ 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)
+ {
+ return;
+ }
+ for (SequenceFeature sf : sfs)
+ {
+ positionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ positionalMinScore = min(positionalMinScore, score);
+ positionalMaxScore = max(positionalMaxScore, score);
+ totalExtent += getFeatureLength(sf);
+ }
}
/**
* (Although a simple shift of all values would preserve data integrity!)
*/
boolean modified = false;
- for (SequenceFeature sf : getPositionalFeatures())
+ List<SequenceFeature> list = getPositionalFeatures();
+ for (int i = 0, n = list.size(); i < n; i++)
{
+ SequenceFeature sf = list.get(i);
if (sf.getBegin() >= fromPosition)
{
modified = true;
}
/**
- * Find all features containing this position.
- * Uses isTainted field to know when to reconstruct its temporary array.
+ * Answers the position (0, 1...) in the list of the first entry whose end
+ * position is not less than {@ pos}. If no such entry is found, answers the
+ * length of the list.
*
+ * @param list
* @param pos
- * @return list of SequenceFeatures
- * @author Bob Hanson 2019.07.30
+ * @return
*/
- public void findOverlappingFeatures(int pos, List<SequenceFeature> result)
+ protected int findFirstEnd(List<SequenceFeature> list, long pos)
{
+ return BinarySearcher.findFirst(list, false, Compare.GE, (int) pos);
+ }
+ /**
+ * 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)
{
- findContacts(contactFeatureStarts, pos, result, true);
- findContacts(contactFeatureEnds, pos, result, false);
- }
- if (features != null)
- {
- int n = features.size();
- if (isTainted)
- {
- isTainted = false;
- if (temp.length < n)
- {
- temp = new SequenceFeature[n << 1];
- }
- features.toArray(temp);
- }
- findOverlaps(temp, n, pos, result);
+ findContactStartOverlaps(from, to, result);
+ findContactEndOverlaps(from, to, result);
}
}
/**
- * Binary search for contact start or end at a given (Overview) position.
+ * 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 l
- * @param pos
+ * @param from
+ * @param to
* @param result
- * @param isStart
- *
- * @author Bob Hanson 2019.07.30
*/
- private static void findContacts(List<SequenceFeature> l, int pos,
- List<SequenceFeature> result, boolean isStart)
+ private void findContactEndOverlaps(long from, long to,
+ List<SequenceFeature> result)
{
- int low = 0;
- int high = l.size() - 1;
- while (low <= high)
+ /*
+ * find the first contact feature (if any)
+ * whose end point is not before the target range
+ */
+ int index = findFirstEnd(contactFeatureEnds, from);
+
+ int n = contactFeatureEnds.size();
+ while (index < n)
{
- int mid = (low + high) >>> 1;
- SequenceFeature f = l.get(mid);
- switch (Long.signum((isStart ? f.begin : f.end) - pos))
+ SequenceFeature sf = contactFeatureEnds.get(index);
+ if (!sf.isContactFeature())
{
- case -1:
- low = mid + 1;
+ System.err.println("Error! non-contact feature type " + sf.getType()
+ + " in contact features list");
+ index++;
continue;
- case 1:
- high = mid - 1;
+ }
+
+ 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;
- 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;
}
+
+ 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++;
}
}
/**
- * Brute force point-interval overlap test
+ * Adds contact features whose start position lies in the from-to range to the
+ * result list
*
- * @param features
- * @param n
- * @param pos
+ * @param from
+ * @param to
* @param result
*/
- private static void findOverlaps(SequenceFeature[] features, int n,
- int pos,
+ private void findContactStartOverlaps(long from, long to,
List<SequenceFeature> result)
{
- // BH I know, brute force. We need a single-position overlap
- // method for IntervalStore, I think.
- for (int i = n; --i >= 0;)
+ int index = BinarySearcher.findFirst(contactFeatureStarts, true,
+ Compare.GE, (int) from);
+
+ while (index < contactFeatureStarts.size())
{
- SequenceFeature f = features[i];
- if (f.begin <= pos && f.end >= pos)
+ 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)
{
- result.add(f);
+ /*
+ * 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++;
}
}
git://source.jalview.org / jalview.git / blobdiff