import java.util.Set;
import intervalstore.api.IntervalStoreI;
+import intervalstore.impl.BinarySearcher;
+import intervalstore.impl.BinarySearcher.Compare;
-public abstract class FeatureStore implements FeatureStoreI
+public class FeatureStore
{
-
- /**
+ /*
* track last start for quick insertion of ordered features
*/
protected int lastStart = -1;
* @param feature
* @return
*/
- @Override
public boolean listContains(List<SequenceFeature> list,
SequenceFeature feature)
{
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 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 -1; // no match found
+ return false; // no match found
}
if (sf.equals(feature))
{
- return pos;
+ return true;
}
pos++;
}
- return -1;
+ return false;
}
/**
*/
public FeatureStore(int intervalStoreType)
{
- features = getIntervalStore(intervalStoreType);
+ features =
+ // Platform.isJS()
+ // ? new intervalstore.nonc.IntervalStore<>(true)
+ // : new intervalstore.impl.IntervalStore<>();
+ getIntervalStore(intervalStoreType);
positionalFeatureGroups = new HashSet<>();
nonPositionalFeatureGroups = new HashSet<>();
positionalMinScore = Float.NaN;
private IntervalStoreI<SequenceFeature> getIntervalStore(int type)
{
switch (type != INTERVAL_STORE_DEFAULT ? type : //
- Platform.isJS() //
- ? intervalStoreJSOption
- : intervalStoreJavaOption)
+ Platform.isJS() //
+ ? intervalStoreJSOption
+ : intervalStoreJavaOption)
{
default:
case INTERVAL_STORE_NCLIST_OBJECT:
* 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);
+ 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
*
* @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 (feature.isContactFeature())
{
if (containsContactFeature(feature))
}
else if (feature.isNonPositional())
{
- if (containsNonPositional(feature))
+ if (containsNonPositionalFeature(feature))
{
return false;
}
}
else
{
- // allow for check with
- if (checkContainsPositionalFeatureForAdd(feature)
- || !addPositionalFeature(feature))
+ if (!features.add(feature, false))
{
return false;
}
}
/**
- * Adds one feature to the IntervalStore that can manage nested features
- * (creating the IntervalStore if necessary)
- *
- * @return true if added -- allowing for late checking during addition
- */
- abstract protected boolean addPositionalFeature(SequenceFeature feature);
-
- /**
* Adds the feature to the list of non-positional features (with lazy
* instantiation of the list if it is null), and returns true. The feature
* group is added to the set of distinct feature groups for non-positional
* @param feature
* @return
*/
- @Override
public boolean contains(SequenceFeature feature)
{
if (feature.isNonPositional())
{
- return containsNonPositional(feature);
-
+ return containsNonPositionalFeature(feature);
}
if (feature.isContactFeature())
{
return containsContactFeature(feature);
-
}
return containsPositionalFeature(feature);
}
- /**
- * A check that can be overridden if the check is being done during the add
- * operation itself.
- *
- * @param feature
- * @return
- */
- protected boolean checkContainsPositionalFeatureForAdd(
- SequenceFeature feature)
- {
- return containsPositionalFeature(feature);
- }
-
private boolean containsPositionalFeature(SequenceFeature feature)
{
return features == null || feature.begin > lastStart ? false
- : containsFeature(feature);
+ : features.contains(feature);
}
+ /**
+ * 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 <= lastContactStart
&& listContains(contactFeatureStarts, feature);
}
- private boolean containsNonPositional(SequenceFeature feature)
+ /**
+ * Answers true if this store already contains a non-positional feature equal
+ * to the given feature (by {@code SequenceFeature.equals()} test), else false
+ *
+ * @param feature
+ * @return
+ */
+ private boolean containsNonPositionalFeature(SequenceFeature feature)
{
return nonPositionalFeatures == null ? false
: nonPositionalFeatures.contains(feature);
}
- 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;
*/
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);
-
- abstract protected int findFirstEnd(List<SequenceFeature> list, long pos);
-
- @Override
public List<SequenceFeature> findOverlappingFeatures(long start, long end)
{
return findOverlappingFeatures(start, end, null);
}
- @Override
public List<SequenceFeature> getContactFeatures()
{
return getContactFeatures(new ArrayList<>());
*
* @return
*/
-
- @Override
public List<SequenceFeature> getContactFeatures(
List<SequenceFeature> result)
{
* @param positional
* @return
*/
-
- @Override
public int getFeatureCount(boolean positional)
{
if (!positional)
return (contactFeatureStarts == null ? 0 : contactFeatureStarts.size())
+ features.size();
-
}
/**
* @param positionalFeatures
* @return
*/
-
- @Override
public Set<String> getFeatureGroups(boolean positionalFeatures)
{
if (positionalFeatures)
}
}
- @Override
public Collection<SequenceFeature> getFeatures()
{
return features;
* @param group
* @return
*/
-
- @Override
public List<SequenceFeature> getFeaturesForGroup(boolean positional,
String group)
{
* @param positional
* @return
*/
-
- @Override
public float getMaximumScore(boolean positional)
{
return positional ? positionalMaxScore : nonPositionalMaxScore;
* @param positional
* @return
*/
-
- @Override
public float getMinimumScore(boolean positional)
{
return positional ? positionalMinScore : nonPositionalMinScore;
}
- @Override
public List<SequenceFeature> getNonPositionalFeatures()
{
return getNonPositionalFeatures(new ArrayList<>());
*
* @return
*/
-
- @Override
public List<SequenceFeature> getNonPositionalFeatures(
List<SequenceFeature> result)
{
return result;
}
- @Override
public List<SequenceFeature> getPositionalFeatures()
{
return getPositionalFeatures(new ArrayList<>());
*
* @return
*/
-
- @Override
public List<SequenceFeature> getPositionalFeatures(
List<SequenceFeature> result)
{
*
* @return
*/
-
- @Override
public int getTotalFeatureLength()
{
return totalExtent;
*
* @return
*/
-
- @Override
public boolean isEmpty()
{
boolean hasFeatures = (contactFeatureStarts != null
* @param shiftBy
* @return
*/
-
- @Override
public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
{
/*
return modified;
}
+ /**
+ * 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
+ */
+ 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)
+ {
+ findContactStartOverlaps(from, to, result);
+ 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
+ */
+ private 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 = findFirstEnd(contactFeatureEnds, from);
+
+ int n = contactFeatureEnds.size();
+ while (index < n)
+ {
+ 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
+ */
+ private void findContactStartOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ int index = BinarySearcher.findFirst(contactFeatureStarts, true,
+ Compare.GE, (int) 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++;
+ }
+ }
+
+ /**
+ * 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;
+ }
+
}
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