X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStore.java;h=ccd8b66af9774e88b13d58b6720b3f6feb91484a;hb=8406f2ced29d2c04dbabaf1cde80b1a7fa8ce8ce;hp=951b7a5e0859b384e2b3dd9346123550506d58e5;hpb=5929abf0b458a833c936a2f34895e29600354a54;p=jalview.git

diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index 951b7a5..ccd8b66 100644
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -20,97 +20,114 @@
  */
 package jalview.datamodel.features;
 
-import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-/**
- * 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
 {
+
   /**
-   * a class providing criteria for performing a binary search of a list
+   * Answers the 'length' of the feature, counting 0 for non-positional features
+   * and 1 for contact features
+   * 
+   * @param feature
+   * @return
    */
-  abstract static class SearchCriterion
+  protected static int getFeatureLength(SequenceFeature feature)
   {
-    /**
-     * Answers true if the entry passes the search criterion test
-     * 
-     * @param entry
-     * @return
-     */
-    abstract boolean compare(SequenceFeature entry);
-
-    /**
-     * serves a search condition for finding the first feature whose start
-     * position follows a given target location
-     * 
-     * @param target
-     * @return
-     */
-    static SearchCriterion byStart(final long target)
+    if (feature.isNonPositional())
+    {
+      return 0;
+    }
+    if (feature.isContactFeature())
     {
-      return new SearchCriterion() {
+      return 1;
+    }
+    return 1 + feature.getEnd() - feature.getBegin();
+  }
 
-        @Override
-        boolean compare(SequenceFeature entry)
-        {
-          return entry.getBegin() >= target;
-        }
-      };
+  /**
+   * 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
+   */
+  @Override
+  public boolean listContains(List<SequenceFeature> features,
+          SequenceFeature feature)
+  {
+    if (features == null || feature == null)
+    {
+      return false;
     }
 
-    /**
-     * serves a search condition for finding the first feature whose end
-     * position is at or follows a given target location
-     * 
-     * @param target
-     * @return
+    /*
+     * locate the first entry in the list which does not precede the feature
      */
-    static SearchCriterion byEnd(final long target)
+    int pos = findFirstBegin(features, feature.begin);
+    int len = features.size();
+    while (pos < len)
     {
-      return new SearchCriterion()
+      SequenceFeature sf = features.get(pos);
+      if (sf.getBegin() > feature.getBegin())
       {
-
-        @Override
-        boolean compare(SequenceFeature entry)
-        {
-          return entry.getEnd() >= target;
-        }
-      };
+        return false; // no match found
+      }
+      if (sf.equals(feature))
+      {
+        return true;
+      }
+      pos++;
     }
+    return false;
+  }
 
-    /**
-     * serves a search condition for finding the first feature which follows the
-     * given range as determined by a supplied comparator
-     * 
-     * @param target
-     * @return
-     */
-    static SearchCriterion byFeature(final ContiguousI to,
-            final Comparator<ContiguousI> rc)
+  /**
+   * 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 new SearchCriterion()
-      {
+      return Float.isNaN(f2) ? f1 : f2;
+    }
+    else
+    {
+      return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
+    }
+  }
 
-        @Override
-        boolean compare(SequenceFeature entry)
-        {
-          return rc.compare(entry, to) >= 0;
-        }
-      };
+  /**
+   * 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);
     }
   }
 
@@ -121,14 +138,6 @@ public class FeatureStore
   List<SequenceFeature> nonPositionalFeatures;
 
   /*
-   * An ordered list of features, with the promise that no feature in the list 
-   * properly contains any other. This constraint allows bounded linear search
-   * of the list for features overlapping a region.
-   * Contact features are not included in this list.
-   */
-  List<SequenceFeature> nonNestedFeatures;
-
-  /*
    * contact features ordered by first contact position
    */
   List<SequenceFeature> contactFeatureStarts;
@@ -139,13 +148,10 @@ public class FeatureStore
   List<SequenceFeature> contactFeatureEnds;
 
   /*
-   * Nested Containment List is used to hold any features that are nested 
-   * within (properly contained by) any other feature. This is a recursive tree
-   * which supports depth-first scan for features overlapping a range.
-   * It is used here as a 'catch-all' fallback for features that cannot be put
-   * into a simple ordered list without invalidating the search methods.
+   * IntervalStore holds remaining features and provides efficient
+   * query for features overlapping any given interval
    */
-  NCList<SequenceFeature> nestedFeatures;
+  Collection<SequenceFeature> features;
 
   /*
    * Feature groups represented in stored positional features 
@@ -178,254 +184,14 @@ public class FeatureStore
    */
   public FeatureStore()
   {
-    nonNestedFeatures = new ArrayList<SequenceFeature>();
-    positionalFeatureGroups = new HashSet<String>();
-    nonPositionalFeatureGroups = new HashSet<String>();
+    positionalFeatureGroups = new HashSet<>();
+    nonPositionalFeatureGroups = new HashSet<>();
     positionalMinScore = Float.NaN;
     positionalMaxScore = Float.NaN;
     nonPositionalMinScore = Float.NaN;
     nonPositionalMaxScore = Float.NaN;
 
-    // we only construct nonPositionalFeatures, contactFeatures
-    // or the NCList if we need to
-  }
-
-  /**
-   * 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 (contains(feature))
-    {
-      return false;
-    }
-
-    /*
-     * keep a record of feature groups
-     */
-    if (!feature.isNonPositional())
-    {
-      positionalFeatureGroups.add(feature.getFeatureGroup());
-    }
-
-    boolean added = false;
-
-    if (feature.isContactFeature())
-    {
-      added = addContactFeature(feature);
-    }
-    else if (feature.isNonPositional())
-    {
-      added = addNonPositionalFeature(feature);
-    }
-    else
-    {
-      added = addNonNestedFeature(feature);
-      if (!added)
-      {
-        /*
-         * detected a nested feature - put it in the NCList structure
-         */
-        added = addNestedFeature(feature);
-      }
-    }
-
-    if (added)
-    {
-      /*
-       * record the total extent of positional features, to make
-       * getTotalFeatureLength possible; we count the length of a 
-       * contact feature as 1
-       */
-      totalExtent += getFeatureLength(feature);
-
-      /*
-       * record the minimum and maximum score for positional
-       * and non-positional features
-       */
-      float score = feature.getScore();
-      if (!Float.isNaN(score))
-      {
-        if (feature.isNonPositional())
-        {
-          nonPositionalMinScore = min(nonPositionalMinScore, score);
-          nonPositionalMaxScore = max(nonPositionalMaxScore, score);
-        }
-        else
-        {
-          positionalMinScore = min(positionalMinScore, score);
-          positionalMaxScore = max(positionalMaxScore, score);
-        }
-      }
-    }
-
-    return added;
-  }
-
-  /**
-   * 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);
-    }
-
-    if (listContains(nonNestedFeatures, feature))
-    {
-      return true;
-    }
-
-    return nestedFeatures == null ? false : nestedFeatures
-            .contains(feature);
-  }
-
-  /**
-   * 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();
-  }
-
-  /**
-   * 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
-   * features. This method allows duplicate features, so test before calling to
-   * prevent this.
-   * 
-   * @param feature
-   */
-  protected boolean addNonPositionalFeature(SequenceFeature feature)
-  {
-    if (nonPositionalFeatures == null)
-    {
-      nonPositionalFeatures = new ArrayList<SequenceFeature>();
-    }
-
-    nonPositionalFeatures.add(feature);
-
-    nonPositionalFeatureGroups.add(feature.getFeatureGroup());
-
-    return true;
-  }
-
-  /**
-   * Adds one feature to the NCList that can manage nested features (creating
-   * the NCList if necessary), and returns true. If the feature is already
-   * stored in the NCList (by equality test), then it is not added, and this
-   * method returns false.
-   */
-  protected synchronized boolean addNestedFeature(SequenceFeature feature)
-  {
-    if (nestedFeatures == null)
-    {
-      nestedFeatures = new NCList<>(feature);
-      return true;
-    }
-    return nestedFeatures.add(feature, false);
-  }
-
-  /**
-   * Add a feature to the list of non-nested features, maintaining the ordering
-   * of the list. A check is made for whether the feature is nested in (properly
-   * contained by) an existing feature. If there is no nesting, the feature is
-   * added to the list and the method returns true. If nesting is found, the
-   * feature is not added and the method returns false.
-   * 
-   * @param feature
-   * @return
-   */
-  protected boolean addNonNestedFeature(SequenceFeature feature)
-  {
-    synchronized (nonNestedFeatures)
-    {
-      /*
-       * find the first stored feature which doesn't precede the new one
-       */
-      int insertPosition = binarySearch(nonNestedFeatures,
-              SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
-
-      /*
-       * fail if we detect feature enclosure - of the new feature by
-       * the one preceding it, or of the next feature by the new one
-       */
-      if (insertPosition > 0)
-      {
-        if (encloses(nonNestedFeatures.get(insertPosition - 1), feature))
-        {
-          return false;
-        }
-      }
-      if (insertPosition < nonNestedFeatures.size())
-      {
-        if (encloses(feature, nonNestedFeatures.get(insertPosition)))
-        {
-          return false;
-        }
-      }
-
-      /*
-       * checks passed - add the feature
-       */
-      nonNestedFeatures.add(insertPosition, feature);
-
-      return true;
-    }
-  }
-
-  /**
-   * Answers true if range1 properly encloses range2, else false
-   * 
-   * @param range1
-   * @param range2
-   * @return
-   */
-  protected boolean encloses(ContiguousI range1, ContiguousI range2)
-  {
-    int begin1 = range1.getBegin();
-    int begin2 = range2.getBegin();
-    int end1 = range1.getEnd();
-    int end2 = range2.getEnd();
-    if (begin1 == begin2 && end1 > end2)
-    {
-      return true;
-    }
-    if (begin1 < begin2 && end1 >= end2)
-    {
-      return true;
-    }
-    return false;
+    // we only construct nonPositionalFeatures, contactFeatures if we need to
   }
 
   /**
@@ -441,230 +207,105 @@ public class FeatureStore
   {
     if (contactFeatureStarts == null)
     {
-      contactFeatureStarts = new ArrayList<SequenceFeature>();
-    }
-    if (contactFeatureEnds == null)
-    {
-      contactFeatureEnds = new ArrayList<SequenceFeature>();
+      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
      */
-    int insertPosition = binarySearch(contactFeatureStarts,
-            SearchCriterion.byFeature(feature,
-                    RangeComparator.BY_START_POSITION));
-    contactFeatureStarts.add(insertPosition, feature);
-    // and resort to mak siccar...just in case insertion point not quite right
-    Collections.sort(contactFeatureStarts, RangeComparator.BY_START_POSITION);
-
-    insertPosition = binarySearch(contactFeatureStarts,
-            SearchCriterion.byFeature(feature,
-                    RangeComparator.BY_END_POSITION));
-    contactFeatureEnds.add(feature);
-    Collections.sort(contactFeatureEnds, RangeComparator.BY_END_POSITION);
+    contactFeatureEnds.add(findFirstEnd(contactFeatureEnds, feature.end),
+            feature);
 
     return true;
   }
 
   /**
-   * 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.
+   * 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 features
    * @param feature
-   * @return
    */
-  protected static boolean listContains(List<SequenceFeature> features,
-          SequenceFeature feature)
+
+  @Override
+  public boolean addFeature(SequenceFeature feature)
   {
-    if (features == null || feature == null)
+    if (contains(feature))
     {
       return false;
     }
 
     /*
-     * locate the first entry in the list which does not precede the feature
+     * keep a record of feature groups
      */
-    int pos = binarySearch(features,
-            SearchCriterion.byFeature(feature, RangeComparator.BY_START_POSITION));
-    int len = features.size();
-    while (pos < len)
+    if (!feature.isNonPositional())
     {
-      SequenceFeature sf = features.get(pos);
-      if (sf.getBegin() > feature.getBegin())
-      {
-        return false; // no match found
-      }
-      if (sf.equals(feature))
-      {
-        return true;
-      }
-      pos++;
+      positionalFeatureGroups.add(feature.getFeatureGroup());
     }
-    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<>();
-
-    findNonNestedFeatures(start, end, result);
-
-    findContactFeatures(start, end, result);
-
-    if (nestedFeatures != null)
+    if (feature.isContactFeature())
     {
-      result.addAll(nestedFeatures.findOverlaps(start, end));
+      addContactFeature(feature);
     }
-
-    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)
+    else if (feature.isNonPositional())
     {
-      findContactStartFeatures(from, to, result);
+      addNonPositionalFeature(feature);
     }
-    if (contactFeatureEnds != null)
+    else
     {
-      findContactEndFeatures(from, to, result);
+      addNestedFeature(feature);
     }
-  }
 
-  /**
-   * 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 findContactEndFeatures(long from, long to,
-          List<SequenceFeature> result)
-  {
     /*
-     * find the first contact feature (if any) that does not lie 
-     * entirely before the target range
+     * record the total extent of positional features, to make
+     * getTotalFeatureLength possible; we count the length of a 
+     * contact feature as 1
      */
-    int startPosition = binarySearch(contactFeatureEnds,
-            SearchCriterion.byEnd(from));
-    for (; startPosition < contactFeatureEnds.size(); startPosition++)
-    {
-      SequenceFeature sf = contactFeatureEnds.get(startPosition);
-      if (!sf.isContactFeature())
-      {
-        System.err.println("Error! non-contact feature type "
-                + sf.getType() + " in contact features list");
-        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
-         */
-        continue;
-      }
-
-      int end = sf.getEnd();
-      if (end >= from && end <= to)
-      {
-        result.add(sf);
-      }
-      if (end > to)
-      {
-        break;
-      }
-    }
-  }
+    totalExtent += getFeatureLength(feature);
 
-  /**
-   * Adds non-nested features to the result list that lie within the target
-   * range. Non-positional features (start=end=0), contact features and nested
-   * features are excluded.
-   * 
-   * @param from
-   * @param to
-   * @param result
-   */
-  protected void findNonNestedFeatures(long from, long to,
-          List<SequenceFeature> result)
-  {
     /*
-     * find the first feature whose end position is
-     * after the target range start
+     * record the minimum and maximum score for positional
+     * and non-positional features
      */
-    int startIndex = binarySearch(nonNestedFeatures,
-            SearchCriterion.byEnd(from));
-
-    final int startIndex1 = startIndex;
-    int i = startIndex1;
-    while (i < nonNestedFeatures.size())
+    float score = feature.getScore();
+    if (!Float.isNaN(score))
     {
-      SequenceFeature sf = nonNestedFeatures.get(i);
-      if (sf.getBegin() > to)
+      if (feature.isNonPositional())
       {
-        break;
+        nonPositionalMinScore = min(nonPositionalMinScore, score);
+        nonPositionalMaxScore = max(nonPositionalMaxScore, score);
       }
-      if (sf.getBegin() <= to && sf.getEnd() >= from)
+      else
       {
-        result.add(sf);
+        positionalMinScore = min(positionalMinScore, score);
+        positionalMaxScore = max(positionalMaxScore, score);
       }
-      i++;
     }
+
+    return true;
   }
 
-  /**
-   * Adds contact features whose start position lies in the from-to range to the
-   * result list
-   * 
-   * @param from
-   * @param to
-   * @param result
-   */
-  protected void findContactStartFeatures(long from, long to,
-          List<SequenceFeature> result)
+  private void addFeaturesForGroup(String group,
+          Collection<SequenceFeature> sfs, List<SequenceFeature> result)
   {
-    int startPosition = binarySearch(contactFeatureStarts,
-            SearchCriterion.byStart(from));
-
-    for (; startPosition < contactFeatureStarts.size(); startPosition++)
+    if (sfs == null)
     {
-      SequenceFeature sf = contactFeatureStarts.get(startPosition);
-      if (!sf.isContactFeature())
-      {
-        System.err.println("Error! non-contact feature type "
-                + sf.getType() + " in contact features list");
-        continue;
-      }
-      int begin = sf.getBegin();
-      if (begin >= from && begin <= to)
+      return;
+    }
+    for (SequenceFeature sf : sfs)
+    {
+      String featureGroup = sf.getFeatureGroup();
+      if (group == null && featureGroup == null
+              || group != null && group.equals(featureGroup))
       {
         result.add(sf);
       }
@@ -672,67 +313,62 @@ public class FeatureStore
   }
 
   /**
-   * Answers a list of all positional features stored, in no guaranteed order
+   * Adds one feature to the IntervalStore that can manage nested features
+   * (creating the IntervalStore if necessary)
+   */
+  abstract protected void addNestedFeature(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
+   * features. This method allows duplicate features, so test before calling to
+   * prevent this.
    * 
-   * @return
+   * @param feature
    */
-  public List<SequenceFeature> getPositionalFeatures()
+  protected boolean addNonPositionalFeature(SequenceFeature feature)
   {
-    /*
-     * add non-nested features (may be all features for many cases)
-     */
-    List<SequenceFeature> result = new ArrayList<>();
-    result.addAll(nonNestedFeatures);
-
-    /*
-     * add any contact features - from the list by start position
-     */
-    if (contactFeatureStarts != null)
+    if (nonPositionalFeatures == null)
     {
-      result.addAll(contactFeatureStarts);
+      nonPositionalFeatures = new ArrayList<>();
     }
 
-    /*
-     * add any nested features
-     */
-    if (nestedFeatures != null)
-    {
-      result.addAll(nestedFeatures.getEntries());
-    }
+    nonPositionalFeatures.add(feature);
 
-    return result;
+    nonPositionalFeatureGroups.add(feature.getFeatureGroup());
+
+    return true;
   }
 
   /**
-   * Answers a list of all contact features. If there are none, returns an
-   * immutable empty list.
+   * Answers true if this store contains the given feature (testing by
+   * SequenceFeature.equals), else false
    * 
+   * @param feature
    * @return
    */
-  public List<SequenceFeature> getContactFeatures()
+  @Override
+  public boolean contains(SequenceFeature feature)
   {
-    if (contactFeatureStarts == null)
+    if (feature.isNonPositional())
     {
-      return Collections.emptyList();
+      return nonPositionalFeatures == null ? false
+              : nonPositionalFeatures.contains(feature);
     }
-    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)
+    if (feature.isContactFeature())
     {
-      return Collections.emptyList();
+      return contactFeatureStarts != null
+              && listContains(contactFeatureStarts, feature);
     }
-    return new ArrayList<>(nonPositionalFeatures);
+
+    return features == null ? false : containsFeature(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
@@ -741,15 +377,14 @@ public class FeatureStore
    * 
    * @param sf
    */
+
+  @Override
   public synchronized boolean delete(SequenceFeature sf)
   {
-    /*
-     * try the non-nested positional features first
-     */
-    boolean removed = nonNestedFeatures.remove(sf);
+    boolean removed = false;
 
     /*
-     * if not found, try contact positions (and if found, delete
+     * try contact positions (and if found, delete
      * from both lists of contact positions)
      */
     if (!removed && contactFeatureStarts != null)
@@ -775,9 +410,9 @@ public class FeatureStore
     /*
      * if not found, try nested features
      */
-    if (!removed && nestedFeatures != null)
+    if (!removed && features != null)
     {
-      removed = nestedFeatures.delete(sf);
+      removed = features.remove(sf);
     }
 
     if (removed)
@@ -788,100 +423,64 @@ public class FeatureStore
     return removed;
   }
 
-  /**
-   * 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 void findContactFeatures(long from, long to,
+          List<SequenceFeature> result);
 
-    /*
-     * 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);
-    }
+  abstract protected int findFirstBegin(List<SequenceFeature> list,
+          long pos);
 
-    /*
-     * 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);
-    }
+  abstract protected int findFirstEnd(List<SequenceFeature> list, long pos);
+
+  @Override
+  public List<SequenceFeature> findOverlappingFeatures(long start, long end)
+  {
+    return findOverlappingFeatures(start, end, null);
   }
 
-  /**
-   * 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)
+  @Override
+  public List<SequenceFeature> getContactFeatures()
   {
-    if (Float.isNaN(f1))
-    {
-      return Float.isNaN(f2) ? f1 : f2;
-    }
-    else
-    {
-      return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
-    }
+    return getContactFeatures(new ArrayList<>());
   }
 
   /**
-   * 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)
+   * Answers a list of all contact features. If there are none, returns an
+   * immutable empty list.
    * 
-   * @param f1
-   * @param f2
+   * @return
    */
-  protected static float max(float f1, float f2)
+
+  @Override
+  public List<SequenceFeature> 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);
     }
+    return result;
   }
 
   /**
-   * 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()
+
+  @Override
+  public int getFeatureCount(boolean positional)
   {
-    boolean hasFeatures = !nonNestedFeatures.isEmpty()
-            || (contactFeatureStarts != null && !contactFeatureStarts
-                    .isEmpty())
-            || (nonPositionalFeatures != null && !nonPositionalFeatures
-                    .isEmpty())
-            || (nestedFeatures != null && nestedFeatures.size() > 0);
+    if (!positional)
+    {
+      return nonPositionalFeatures == null ? 0
+              : nonPositionalFeatures.size();
+    }
+
+    return (contactFeatureStarts == null ? 0 : contactFeatureStarts.size())
+            + features.size();
 
-    return !hasFeatures;
   }
 
   /**
@@ -892,6 +491,8 @@ public class FeatureStore
    * @param positionalFeatures
    * @return
    */
+
+  @Override
   public Set<String> getFeatureGroups(boolean positionalFeatures)
   {
     if (positionalFeatures)
@@ -900,87 +501,68 @@ public class FeatureStore
     }
     else
     {
-      return nonPositionalFeatureGroups == null ? Collections
-              .<String> emptySet() : Collections
-              .unmodifiableSet(nonPositionalFeatureGroups);
+      return nonPositionalFeatureGroups == null
+              ? Collections.<String> emptySet()
+              : Collections.unmodifiableSet(nonPositionalFeatureGroups);
     }
   }
 
-  /**
-   * Performs a binary search of the (sorted) list to find the index of the
-   * first entry which returns true for the given comparator function. Returns
-   * the length of the list if there is no such entry.
-   * 
-   * @param features
-   * @param sc
-   * @return
-   */
-  protected static int binarySearch(List<SequenceFeature> features,
-          SearchCriterion sc)
+  @Override
+  public Collection<SequenceFeature> getFeatures()
   {
-    int start = 0;
-    int end = features.size() - 1;
-    int matched = features.size();
-
-    while (start <= end)
-    {
-      int mid = (start + end) / 2;
-      SequenceFeature entry = features.get(mid);
-      boolean compare = sc.compare(entry);
-      if (compare)
-      {
-        matched = mid;
-        end = mid - 1;
-      }
-      else
-      {
-        start = mid + 1;
-      }
-    }
-
-    return matched;
+    return features;
   }
 
   /**
-   * 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 = nonNestedFeatures.size();
-
-    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 (nestedFeatures != null)
+    else
     {
-      size += nestedFeatures.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()
+
+  @Override
+  public float getMaximumScore(boolean positional)
   {
-    return totalExtent;
+    return positional ? positionalMaxScore : nonPositionalMaxScore;
   }
 
   /**
@@ -991,59 +573,154 @@ public class FeatureStore
    * @param positional
    * @return
    */
+
+  @Override
   public float getMinimumScore(boolean positional)
   {
     return positional ? positionalMinScore : nonPositionalMinScore;
   }
 
+  @Override
+  public List<SequenceFeature> getNonPositionalFeatures()
+  {
+    return getNonPositionalFeatures(new ArrayList<>());
+  }
+
   /**
-   * 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 list of all non-positional features. If there are none, returns
+   * an immutable empty list.
    * 
-   * @param positional
    * @return
    */
-  public float getMaximumScore(boolean positional)
+
+  @Override
+  public List<SequenceFeature> getNonPositionalFeatures(
+          List<SequenceFeature> result)
   {
-    return positional ? positionalMaxScore : nonPositionalMaxScore;
+    if (nonPositionalFeatures != null)
+    {
+      result.addAll(nonPositionalFeatures);
+    }
+    return result;
+  }
+
+  @Override
+  public List<SequenceFeature> getPositionalFeatures()
+  {
+    return getPositionalFeatures(new ArrayList<>());
   }
 
   /**
-   * Answers a list of all either positional or non-positional features whose
-   * feature group matches the given group (which may be null)
+   * Answers a list of all positional features stored, in no guaranteed order
    * 
-   * @param positional
-   * @param group
    * @return
    */
-  public List<SequenceFeature> getFeaturesForGroup(boolean positional,
-          String group)
+
+  @Override
+  public List<SequenceFeature> getPositionalFeatures(
+          List<SequenceFeature> result)
   {
-    List<SequenceFeature> result = new ArrayList<>();
 
     /*
-     * 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);
+    }
+
+    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)
+    {
+      for (SequenceFeature sf : nonPositionalFeatures)
       {
-        result.add(sf);
+        nonPositionalFeatureGroups.add(sf.getFeatureGroup());
+        float score = sf.getScore();
+        nonPositionalMinScore = min(nonPositionalMinScore, score);
+        nonPositionalMaxScore = max(nonPositionalMaxScore, score);
       }
     }
-    return result;
+
+    /*
+     * 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);
+    }
   }
 
   /**
@@ -1055,6 +732,8 @@ public class FeatureStore
    * @param shiftBy
    * @return
    */
+
+  @Override
   public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
   {
     /*
@@ -1086,4 +765,5 @@ public class FeatureStore
     }
     return modified;
   }
+
 }