JAL-2446 added contains, delete, checks for inclusion on add + tests

[jalview.git] / src / jalview / datamodel / features / NCList.java

diff --git a/src/jalview/datamodel/features/NCList.java b/src/jalview/datamodel/features/NCList.java
index 02f94b6..17e08eb 100644 (file)
--- a/src/jalview/datamodel/features/NCList.java
+++ b/src/jalview/datamodel/features/NCList.java
@@ -60,7 +60,7 @@ public class NCList<T extends ContiguousI>
      */
     Collections.sort(ranges, intervalSorter);
 
-    List<SubList> sublists = findSubranges(ranges);
+    List<SubList> sublists = buildSubranges(ranges);
 
     /*
      * convert each subrange to an NCNode consisting of a range and
@@ -95,7 +95,7 @@ public class NCList<T extends ContiguousI>
    * @param ranges
    * @return
    */
-  protected List<SubList> findSubranges(List<T> ranges)
+  protected List<SubList> buildSubranges(List<T> ranges)
   {
     List<SubList> sublists = new ArrayList<SubList>();
     
@@ -124,12 +124,31 @@ public class NCList<T extends ContiguousI>
   }
 
   /**
-   * Adds one entry to the stored set
+   * Adds one entry to the stored set (with duplicates allowed)
    * 
    * @param entry
    */
-  public synchronized void add(T 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 boolean add(T entry, boolean allowDuplicates)
+  {
+    if (!allowDuplicates && contains(entry))
+    {
+      return false;
+    }
+
     size++;
     long start = entry.getBegin();
     long end = entry.getEnd();
@@ -153,7 +172,7 @@ public class NCList<T extends ContiguousI>
        * all subranges precede this one - add it on the end
        */
       subranges.add(new NCNode<T>(entry));
-      return;
+      return true;
     }
 
     /*
@@ -175,7 +194,7 @@ public class NCList<T extends ContiguousI>
          * new entry lies between subranges j-1 j
          */
         subranges.add(j, new NCNode<T>(entry));
-        return;
+        return true;
       }
 
       if (subrange.getStart() <= start && subrange.getEnd() >= end)
@@ -184,7 +203,7 @@ public class NCList<T extends ContiguousI>
          * push new entry inside this subrange as it encloses it
          */
         subrange.add(entry);
-        return;
+        return true;
       }
       
       if (start <= subrange.getStart())
@@ -214,7 +233,7 @@ public class NCList<T extends ContiguousI>
              * entry encloses one or more preceding subranges
              */
             addEnclosingRange(entry, firstEnclosed, lastEnclosed);
-            return;
+            return true;
           }
           else
           {
@@ -223,7 +242,7 @@ public class NCList<T extends ContiguousI>
              * so just add it 
              */
             subranges.add(j, new NCNode<T>(entry));
-            return;
+            return true;
           }
         }
       }
@@ -245,9 +264,51 @@ public class NCList<T extends ContiguousI>
     {
       subranges.add(new NCNode<T>(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.getStart() > 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.
@@ -296,8 +357,7 @@ 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. 
@@ -494,4 +554,70 @@ public class NCList<T extends ContiguousI>
       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 
+         */
+        subranges.remove(i);
+        if (subRegions != null)
+        {
+          subranges.addAll(i, subRegions.subranges);
+        }
+        size--;
+        return true;
+      }
+      else
+      {
+        if (subRegions != null && subRegions.delete(entry))
+        {
+          size--;
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Answers true if this contains no ranges
+   * 
+   * @return
+   */
+  public boolean isEmpty()
+  {
+    return getSize() == 0;
+  }
+
+  /**
+   * Answer the list of subranges held in this NCList
+   * 
+   * @return
+   */
+  List<NCNode<T>> getSubregions()
+  {
+    return subranges;
+  }
 }