X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FNCList.java;h=b8160d3c7077516d528477ed10a3ea53edc2470a;hb=c55e1fa5d2782cc46e515c11a91cf502f37386ab;hp=40b062a687c1bea85c1884c8d936b41f06dbaa6e;hpb=0ea61b395605ecf1854406f8e0c9a0be04404cb1;p=jalview.git

diff --git a/src/jalview/datamodel/features/NCList.java b/src/jalview/datamodel/features/NCList.java
index 40b062a..b8160d3 100644
--- a/src/jalview/datamodel/features/NCList.java
+++ b/src/jalview/datamodel/features/NCList.java
@@ -1,15 +1,20 @@
 package jalview.datamodel.features;
 
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.Range;
+
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.List;
 
 /**
  * An adapted implementation of NCList as described in the paper
  * 
  * <pre>
- * todo
+ * Nested Containment List (NCList): a new algorithm for accelerating
+ * interval query of genome alignment and interval databases
+ * - Alexander V. Alekseyenko, Christopher J. Lee
+ * https://doi.org/10.1093/bioinformatics/btl647
  * </pre>
  */
 public class NCList<T extends ContiguousI>
@@ -25,12 +30,6 @@ public class NCList<T extends ContiguousI>
    */
   private List<NCNode<T>> subranges;
 
-  /*
-   * a comparator to sort intervals by start position ascending, with
-   * longer (enclosing) intervals preceding those they enclose 
-   */
-  Comparator<ContiguousI> intervalSorter = new RangeComparator(true);
-
   /**
    * Constructor given a list of things that are each located on a contiguous
    * interval. Note that the constructor may reorder the list.
@@ -47,6 +46,9 @@ public class NCList<T extends ContiguousI>
   }
 
   /**
+   * Sort and group ranges into sublists where each sublist represents a region
+   * and its contained subregions
+   * 
    * @param ranges
    */
   protected void build(List<T> ranges)
@@ -55,18 +57,18 @@ public class NCList<T extends ContiguousI>
      * sort by start ascending so that contained intervals 
      * follow their containing interval
      */
-    Collections.sort(ranges, intervalSorter);
+    Collections.sort(ranges, RangeComparator.BY_START_POSITION);
 
-    List<SubList> sublists = findSubranges(ranges);
+    List<Range> sublists = buildSubranges(ranges);
 
     /*
      * convert each subrange to an NCNode consisting of a range and
      * (possibly) its contained NCList
      */
-    for (SubList sublist : sublists)
+    for (Range sublist : sublists)
     {
-      subranges.add(new NCNode<T>(ranges.subList(sublist.startIndex,
-              sublist.endIndex + 1)));
+      subranges.add(new NCNode<T>(ranges.subList(sublist.start,
+              sublist.end + 1)));
     }
 
     size = ranges.size();
@@ -75,9 +77,8 @@ public class NCList<T extends ContiguousI>
   public NCList(T entry)
   {
     this();
-    List<T> ranges = new ArrayList<T>();
-    ranges.add(entry);
-    build(ranges);
+    subranges.add(new NCNode<>(entry));
+    size = 1;
   }
 
   public NCList()
@@ -92,10 +93,15 @@ public class NCList<T extends ContiguousI>
    * @param ranges
    * @return
    */
-  protected List<SubList> findSubranges(List<T> ranges)
+  protected List<Range> buildSubranges(List<T> ranges)
   {
-    List<SubList> sublists = new ArrayList<SubList>();
+    List<Range> sublists = new ArrayList<>();
     
+    if (ranges.isEmpty())
+    {
+      return sublists;
+    }
+
     int listStartIndex = 0;
     long lastEndPos = Long.MAX_VALUE;
 
@@ -110,23 +116,42 @@ public class NCList<T extends ContiguousI>
          * this interval is not contained in the preceding one 
          * close off the last sublist
          */
-        sublists.add(new SubList(listStartIndex, i - 1));
+        sublists.add(new Range(listStartIndex, i - 1));
         listStartIndex = i;
       }
       lastEndPos = nextEnd;
     }
 
-    sublists.add(new SubList(listStartIndex, ranges.size() - 1));
+    sublists.add(new Range(listStartIndex, ranges.size() - 1));
     return sublists;
   }
 
   /**
-   * Adds one entry to the stored set
+   * Adds one entry to the stored set (with duplicates allowed)
+   * 
+   * @param entry
+   */
+  public void add(T entry)
+  {
+    add(entry, true);
+  }
+
+  /**
+   * Adds one entry to the stored set, and returns true, unless allowDuplicates
+   * is set to false and it is already contained (by object equality test), in
+   * which case it is not added and this method returns false.
    * 
    * @param entry
+   * @param allowDuplicates
+   * @return
    */
-  public synchronized void add(T entry)
+  public synchronized boolean add(T entry, boolean allowDuplicates)
   {
+    if (!allowDuplicates && contains(entry))
+    {
+      return false;
+    }
+
     size++;
     long start = entry.getBegin();
     long end = entry.getEnd();
@@ -149,8 +174,8 @@ public class NCList<T extends ContiguousI>
       /*
        * all subranges precede this one - add it on the end
        */
-      subranges.add(new NCNode<T>(entry));
-      return;
+      subranges.add(new NCNode<>(entry));
+      return true;
     }
 
     /*
@@ -166,25 +191,25 @@ public class NCList<T extends ContiguousI>
     {
       NCNode<T> subrange = subranges.get(j);
 
-      if (end < subrange.getStart() && !overlapping && !enclosing)
+      if (end < subrange.getBegin() && !overlapping && !enclosing)
       {
         /*
          * new entry lies between subranges j-1 j
          */
-        subranges.add(j, new NCNode<T>(entry));
-        return;
+        subranges.add(j, new NCNode<>(entry));
+        return true;
       }
 
-      if (subrange.getStart() <= start && subrange.getEnd() >= end)
+      if (subrange.getBegin() <= start && subrange.getEnd() >= end)
       {
         /*
          * push new entry inside this subrange as it encloses it
          */
         subrange.add(entry);
-        return;
+        return true;
       }
       
-      if (start <= subrange.getStart())
+      if (start <= subrange.getBegin())
       {
         if (end >= subrange.getEnd())
         {
@@ -211,7 +236,7 @@ public class NCList<T extends ContiguousI>
              * entry encloses one or more preceding subranges
              */
             addEnclosingRange(entry, firstEnclosed, lastEnclosed);
-            return;
+            return true;
           }
           else
           {
@@ -219,8 +244,8 @@ public class NCList<T extends ContiguousI>
              * entry spans two subranges but doesn't enclose any
              * so just add it 
              */
-            subranges.add(j, new NCNode<T>(entry));
-            return;
+            subranges.add(j, new NCNode<>(entry));
+            return true;
           }
         }
       }
@@ -232,14 +257,61 @@ public class NCList<T extends ContiguousI>
 
     /*
      * drops through to here if new range encloses all others
+     * or overlaps the last one
      */
     if (enclosing)
     {
       addEnclosingRange(entry, firstEnclosed, lastEnclosed);
     }
+    else
+    {
+      subranges.add(new NCNode<>(entry));
+    }
+
+    return true;
   }
   
   /**
+   * Answers true if this NCList contains the given entry (by object equality
+   * test), else false
+   * 
+   * @param entry
+   * @return
+   */
+  public boolean contains(T entry)
+  {
+    /*
+     * find the first sublist that might overlap, i.e. 
+     * the first whose end position is >= from
+     */
+    int candidateIndex = findFirstOverlap(entry.getBegin());
+
+    if (candidateIndex == -1)
+    {
+      return false;
+    }
+
+    int to = entry.getEnd();
+
+    for (int i = candidateIndex; i < subranges.size(); i++)
+    {
+      NCNode<T> candidate = subranges.get(i);
+      if (candidate.getBegin() > to)
+      {
+        /*
+         * we are past the end of our target range
+         */
+        break;
+      }
+      if (candidate.contains(entry))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
    * Update the tree so that the range of the new entry encloses subranges i to
    * j (inclusive). That is, replace subranges i-j (inclusive) with a new
    * subrange that contains them.
@@ -251,9 +323,9 @@ public class NCList<T extends ContiguousI>
   protected synchronized void addEnclosingRange(T entry, final int i,
           final int j)
   {
-    NCList<T> newNCList = new NCList<T>();
-    newNCList.subranges.addAll(subranges.subList(i, j + 1));
-    NCNode<T> newNode = new NCNode<T>(entry, newNCList);
+    NCList<T> newNCList = new NCList<>();
+    newNCList.addNodes(subranges.subList(i, j + 1));
+    NCNode<T> newNode = new NCNode<>(entry, newNCList);
     for (int k = j; k >= i; k--)
     {
       subranges.remove(k);
@@ -261,6 +333,15 @@ public class NCList<T extends ContiguousI>
     subranges.add(i, newNode);
   }
 
+  protected void addNodes(List<NCNode<T>> nodes)
+  {
+    for (NCNode<T> node : nodes)
+    {
+      subranges.add(node);
+      size += node.size();
+    }
+  }
+
   /**
    * Returns a (possibly empty) list of items whose extent overlaps the given
    * range
@@ -273,7 +354,7 @@ public class NCList<T extends ContiguousI>
    */
   public List<T> findOverlaps(long from, long to)
   {
-    List<T> result = new ArrayList<T>();
+    List<T> result = new ArrayList<>();
 
     findOverlaps(from, to, result);
     
@@ -288,8 +369,7 @@ public class NCList<T extends ContiguousI>
    * @param to
    * @param result
    */
-  protected void findOverlaps(long from, long to,
- List<T> result)
+  protected void findOverlaps(long from, long to, List<T> result)
   {
     /*
      * find the first sublist that might overlap, i.e. 
@@ -305,14 +385,14 @@ public class NCList<T extends ContiguousI>
     for (int i = candidateIndex; i < subranges.size(); i++)
     {
       NCNode<T> candidate = subranges.get(i);
-      if (candidate.getStart() > to)
+      if (candidate.getBegin() > to)
       {
         /*
          * we are past the end of our target range
          */
         break;
       }
-      candidate.addOverlaps(from, to, result);
+      candidate.findOverlaps(from, to, result);
     }
 
   }
@@ -328,8 +408,12 @@ public class NCList<T extends ContiguousI>
    */
   protected int findFirstOverlap(long from)
   {
-    // TODO binary search
-    // for now quick cheat linear search
+    /*
+     * The NCList paper describes binary search for this step,
+     * but this not implemented here as (a) I haven't understood it yet
+     * and (b) it seems to imply complications for adding to an NCList
+     */
+
     int i = 0;
     if (subranges != null)
     {
@@ -359,7 +443,7 @@ public class NCList<T extends ContiguousI>
   }
 
   /**
-   * Returns a string representation of the data where containment is shown bgy
+   * Returns a string representation of the data where containment is shown by
    * indentation on new lines
    * 
    * @return
@@ -370,6 +454,7 @@ public class NCList<T extends ContiguousI>
     int offset = 0;
     int indent = 2;
     prettyPrint(sb, offset, indent);
+    sb.append(System.lineSeparator());
     return sb.toString();
   }
 
@@ -420,7 +505,7 @@ public class NCList<T extends ContiguousI>
     int lastStart = start;
     for (NCNode<T> subrange : subranges)
     {
-      if (subrange.getStart() < lastStart)
+      if (subrange.getBegin() < lastStart)
       {
         System.err.println("error in NCList: range " + subrange.toString()
                 + " starts before " + lastStart);
@@ -432,7 +517,7 @@ public class NCList<T extends ContiguousI>
                 + " ends after " + end);
         return false;
       }
-      lastStart = subrange.getStart();
+      lastStart = subrange.getBegin();
 
       if (!subrange.isValid())
       {
@@ -449,7 +534,7 @@ public class NCList<T extends ContiguousI>
    */
   public int getStart()
   {
-    return subranges.isEmpty() ? 0 : subranges.get(0).getStart();
+    return subranges.isEmpty() ? 0 : subranges.get(0).getBegin();
   }
 
   /**
@@ -457,8 +542,85 @@ public class NCList<T extends ContiguousI>
    * 
    * @return
    */
-  public int getSize()
+  public int size()
   {
     return size;
   }
+
+  /**
+   * Returns a list of all entries stored
+   * 
+   * @return
+   */
+  public List<T> getEntries()
+  {
+    List<T> result = new ArrayList<>();
+    getEntries(result);
+    return result;
+  }
+
+  /**
+   * Adds all contained entries to the given list
+   * 
+   * @param result
+   */
+  void getEntries(List<T> result)
+  {
+    for (NCNode<T> subrange : subranges)
+    {
+      subrange.getEntries(result);
+    }
+  }
+
+  /**
+   * Deletes the given entry from the store, returning true if it was found (and
+   * deleted), else false. This method makes no assumption that the entry is in
+   * the 'expected' place in the store, in case it has been modified since it
+   * was added. Only the first 'same object' match is deleted, not 'equal' or
+   * multiple objects.
+   * 
+   * @param entry
+   */
+  public synchronized boolean delete(T entry)
+  {
+    if (entry == null)
+    {
+      return false;
+    }
+    for (int i = 0; i < subranges.size(); i++)
+    {
+      NCNode<T> subrange = subranges.get(i);
+      NCList<T> subRegions = subrange.getSubRegions();
+
+      if (subrange.getRegion() == entry)
+      {
+        /*
+         * if the subrange is rooted on this entry, promote its
+         * subregions (if any) to replace the subrange here;
+         * NB have to resort subranges after doing this since e.g.
+         * [10-30 [12-20 [16-18], 13-19]]
+         * after deleting 12-20, 16-18 is promoted to sibling of 13-19
+         * but should follow it in the list of subranges of 10-30 
+         */
+        subranges.remove(i);
+        if (subRegions != null)
+        {
+          subranges.addAll(subRegions.subranges);
+          Collections.sort(subranges, RangeComparator.BY_START_POSITION);
+        }
+        size--;
+        return true;
+      }
+      else
+      {
+        if (subRegions != null && subRegions.delete(entry))
+        {
+          size--;
+          subrange.deleteSubRegionsIfEmpty();
+          return true;
+        }
+      }
+    }
+    return false;
+  }
 }