add .gitignore

.gitignore

@@ -0,0 +1,2 @@
+.coverage
+*.pyc

nilmdb/RedBlackTree.cc

@@ -1,605 +0,0 @@
-
-
-
-// The RedBlackEntry class is an Abstract Base Class.  This means that no
-// instance of the RedBlackEntry class can exist.  Only classes which
-// inherit from the RedBlackEntry class can exist.  Furthermore any class
-// which inherits from the RedBlackEntry class must define the member
-// function GetKey().  The Print() member function does not have to
-// be defined because a default definition exists.
-//
-// The GetKey() function should return an integer key for that entry.
-// The key for an entry should never change otherwise bad things might occur.
-
-class RedBlackEntry {
-public:
-  RedBlackEntry();
-  virtual ~RedBlackEntry();
-  virtual int GetKey() const = 0;
-  virtual void Print() const;
-};
-
-class RedBlackTreeNode {
-  friend class RedBlackTree;
-public:
-  void Print(RedBlackTreeNode*,
-	     RedBlackTreeNode*) const;
-  RedBlackTreeNode();
-  RedBlackTreeNode(RedBlackEntry *);
-  RedBlackEntry * GetEntry() const;
-  ~RedBlackTreeNode();
-protected:
-  RedBlackEntry * storedEntry;
-  int key;
-  int red; /* if red=0 then the node is black */
-  RedBlackTreeNode * left;
-  RedBlackTreeNode * right;
-  RedBlackTreeNode * parent;
-};
-
-
-
-class RedBlackTree {
-public:
-  RedBlackTree();
-  ~RedBlackTree();
-  void Print() const;
-  RedBlackEntry * DeleteNode(RedBlackTreeNode *);
-  RedBlackTreeNode * Insert(RedBlackEntry *);
-  RedBlackTreeNode * GetPredecessorOf(RedBlackTreeNode *) const;
-  RedBlackTreeNode * GetSuccessorOf(RedBlackTreeNode *) const;
-  RedBlackTreeNode * Search(int key);
-  TemplateStack<RedBlackTreeNode *> * Enumerate(int low, int high) ;
-  void CheckAssumptions() const;
-protected:
-  /*  A sentinel is used for root and for nil.  These sentinels are */
-  /*  created when RedBlackTreeCreate is caled.  root->left should always */
-  /*  point to the node which is the root of the tree.  nil points to a */
-  /*  node which should always be black but has aribtrary children and */
-  /*  parent and no key or info.  The point of using these sentinels is so */
-  /*  that the root and nil nodes do not require special cases in the code */
-  RedBlackTreeNode * root;
-  RedBlackTreeNode * nil;
-  void LeftRotate(RedBlackTreeNode *);
-  void RightRotate(RedBlackTreeNode *);
-  void TreeInsertHelp(RedBlackTreeNode *);
-  void TreePrintHelper(RedBlackTreeNode *) const;
-  void FixUpMaxHigh(RedBlackTreeNode *);
-  void DeleteFixUp(RedBlackTreeNode *);
-};
-
-const int MIN_INT=-MAX_INT;
-
-RedBlackTreeNode::RedBlackTreeNode(){
-};
-
-RedBlackTreeNode::RedBlackTreeNode(RedBlackEntry * newEntry)
-  : storedEntry (newEntry) , key(newEntry->GetKey()) {
-};
-
-RedBlackTreeNode::~RedBlackTreeNode(){
-};
-
-RedBlackEntry * RedBlackTreeNode::GetEntry() const {return storedEntry;}
-
-RedBlackEntry::RedBlackEntry(){
-};
-RedBlackEntry::~RedBlackEntry(){
-};
-void RedBlackEntry::Print() const {
-  cout << "No Print Method defined. Using Default: " << GetKey() << endl;
-}
-
-RedBlackTree::RedBlackTree()
-{
-  nil = new RedBlackTreeNode;
-  nil->left = nil->right = nil->parent = nil;
-  nil->red = 0;
-  nil->key = MIN_INT;
-  nil->storedEntry = NULL;
-
-  root = new RedBlackTreeNode;
-  root->parent = root->left = root->right = nil;
-  root->key = MAX_INT;
-  root->red=0;
-  root->storedEntry = NULL;
-}
-
-/***********************************************************************/
-/*  FUNCTION:  LeftRotate */
-/**/
-/*  INPUTS:  the node to rotate on */
-/**/
-/*  OUTPUT:  None */
-/**/
-/*  Modifies Input: this, x */
-/**/
-/*  EFFECTS:  Rotates as described in _Introduction_To_Algorithms by */
-/*            Cormen, Leiserson, Rivest (Chapter 14).  Basically this */
-/*            makes the parent of x be to the left of x, x the parent of */
-/*            its parent before the rotation and fixes other pointers */
-/*            accordingly.  */
-/***********************************************************************/
-
-void RedBlackTree::LeftRotate(RedBlackTreeNode* x) {
-  RedBlackTreeNode* y;
-
-  /*  I originally wrote this function to use the sentinel for */
-  /*  nil to avoid checking for nil.  However this introduces a */
-  /*  very subtle bug because sometimes this function modifies */
-  /*  the parent pointer of nil.  This can be a problem if a */
-  /*  function which calls LeftRotate also uses the nil sentinel */
-  /*  and expects the nil sentinel's parent pointer to be unchanged */
-  /*  after calling this function.  For example, when DeleteFixUP */
-  /*  calls LeftRotate it expects the parent pointer of nil to be */
-  /*  unchanged. */
-
-  y=x->right;
-  x->right=y->left;
-
-  if (y->left != nil) y->left->parent=x; /* used to use sentinel here */
-  /* and do an unconditional assignment instead of testing for nil */
-
-  y->parent=x->parent;
-
-  /* instead of checking if x->parent is the root as in the book, we */
-  /* count on the root sentinel to implicitly take care of this case */
-  if( x == x->parent->left) {
-    x->parent->left=y;
-  } else {
-    x->parent->right=y;
-  }
-  y->left=x;
-  x->parent=y;
-}
-
-/***********************************************************************/
-/*  FUNCTION:  RighttRotate */
-/**/
-/*  INPUTS:  node to rotate on */
-/**/
-/*  OUTPUT:  None */
-/**/
-/*  Modifies Input?: this, y */
-/**/
-/*  EFFECTS:  Rotates as described in _Introduction_To_Algorithms by */
-/*            Cormen, Leiserson, Rivest (Chapter 14).  Basically this */
-/*            makes the parent of x be to the left of x, x the parent of */
-/*            its parent before the rotation and fixes other pointers */
-/*            accordingly.  */
-/***********************************************************************/
-
-void RedBlackTree::RightRotate(RedBlackTreeNode* y) {
-  RedBlackTreeNode* x;
-
-  /*  I originally wrote this function to use the sentinel for */
-  /*  nil to avoid checking for nil.  However this introduces a */
-  /*  very subtle bug because sometimes this function modifies */
-  /*  the parent pointer of nil.  This can be a problem if a */
-  /*  function which calls LeftRotate also uses the nil sentinel */
-  /*  and expects the nil sentinel's parent pointer to be unchanged */
-  /*  after calling this function.  For example, when DeleteFixUP */
-  /*  calls LeftRotate it expects the parent pointer of nil to be */
-  /*  unchanged. */
-
-  x=y->left;
-  y->left=x->right;
-
-  if (nil != x->right)  x->right->parent=y; /*used to use sentinel here */
-  /* and do an unconditional assignment instead of testing for nil */
-
-  /* instead of checking if x->parent is the root as in the book, we */
-  /* count on the root sentinel to implicitly take care of this case */
-  x->parent=y->parent;
-  if( y == y->parent->left) {
-    y->parent->left=x;
-  } else {
-    y->parent->right=x;
-  }
-  x->right=y;
-  y->parent=x;
-}
-
-/***********************************************************************/
-/*  FUNCTION:  TreeInsertHelp  */
-/**/
-/*  INPUTS:  z is the node to insert */
-/**/
-/*  OUTPUT:  none */
-/**/
-/*  Modifies Input:  this, z */
-/**/
-/*  EFFECTS:  Inserts z into the tree as if it were a regular binary tree */
-/*            using the algorithm described in _Introduction_To_Algorithms_ */
-/*            by Cormen et al.  This funciton is only intended to be called */
-/*            by the Insert function and not by the user */
-/***********************************************************************/
-
-void RedBlackTree::TreeInsertHelp(RedBlackTreeNode* z) {
-  /*  This function should only be called by RedBlackTree::Insert */
-  RedBlackTreeNode* x;
-  RedBlackTreeNode* y;
-
-  z->left=z->right=nil;
-  y=root;
-  x=root->left;
-  while( x != nil) {
-    y=x;
-    if ( x->key > z->key) {
-      x=x->left;
-    } else { /* x->key <= z->key */
-      x=x->right;
-    }
-  }
-  z->parent=y;
-  if ( (y == root) ||
-       (y->key > z->key) ) {
-    y->left=z;
-  } else {
-    y->right=z;
-  }
-}
-
-/*  Before calling InsertNode  the node x should have its key set */
-
-/***********************************************************************/
-/*  FUNCTION:  InsertNode */
-/**/
-/*  INPUTS:  newEntry is the entry to insert*/
-/**/
-/*  OUTPUT:  This function returns a pointer to the newly inserted node */
-/*           which is guarunteed to be valid until this node is deleted. */
-/*           What this means is if another data structure stores this */
-/*           pointer then the tree does not need to be searched when this */
-/*           is to be deleted. */
-/**/
-/*  Modifies Input: tree */
-/**/
-/*  EFFECTS:  Creates a node node which contains the appropriate key and */
-/*            info pointers and inserts it into the tree. */
-/***********************************************************************/
-/* jim */
-RedBlackTreeNode * RedBlackTree::Insert(RedBlackEntry * newEntry)
-{
-  RedBlackTreeNode * y;
-  RedBlackTreeNode * x;
-  RedBlackTreeNode * newNode;
-
-  x = new RedBlackTreeNode(newEntry);
-  TreeInsertHelp(x);
-  newNode = x;
-  x->red=1;
-  while(x->parent->red) { /* use sentinel instead of checking for root */
-    if (x->parent == x->parent->parent->left) {
-      y=x->parent->parent->right;
-      if (y->red) {
-	x->parent->red=0;
-	y->red=0;
-	x->parent->parent->red=1;
-	x=x->parent->parent;
-      } else {
-	if (x == x->parent->right) {
-	  x=x->parent;
-	  LeftRotate(x);
-	}
-	x->parent->red=0;
-	x->parent->parent->red=1;
-	RightRotate(x->parent->parent);
-      }
-    } else { /* case for x->parent == x->parent->parent->right */
-             /* this part is just like the section above with */
-             /* left and right interchanged */
-      y=x->parent->parent->left;
-      if (y->red) {
-	x->parent->red=0;
-	y->red=0;
-	x->parent->parent->red=1;
-	x=x->parent->parent;
-      } else {
-	if (x == x->parent->left) {
-	  x=x->parent;
-	  RightRotate(x);
-	}
-	x->parent->red=0;
-	x->parent->parent->red=1;
-	LeftRotate(x->parent->parent);
-      }
-    }
-  }
-  root->left->red=0;
-  return(newNode);
-}
-
-/***********************************************************************/
-/*  FUNCTION:  GetSuccessorOf  */
-/**/
-/*    INPUTS:  x is the node we want the succesor of */
-/**/
-/*    OUTPUT:  This function returns the successor of x or NULL if no */
-/*             successor exists. */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    Note:  uses the algorithm in _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-RedBlackTreeNode * RedBlackTree::GetSuccessorOf(RedBlackTreeNode * x) const
-{
-  RedBlackTreeNode* y;
-
-  if (nil != (y = x->right)) { /* assignment to y is intentional */
-    while(y->left != nil) { /* returns the minium of the right subtree of x */
-      y=y->left;
-    }
-    return(y);
-  } else {
-    y=x->parent;
-    while(x == y->right) { /* sentinel used instead of checking for nil */
-      x=y;
-      y=y->parent;
-    }
-    if (y == root) return(nil);
-    return(y);
-  }
-}
-
-/***********************************************************************/
-/*  FUNCTION:  GetPredecessorOf  */
-/**/
-/*    INPUTS:  x is the node to get predecessor of */
-/**/
-/*    OUTPUT:  This function returns the predecessor of x or NULL if no */
-/*             predecessor exists. */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    Note:  uses the algorithm in _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-RedBlackTreeNode * RedBlackTree::GetPredecessorOf(RedBlackTreeNode * x) const {
-  RedBlackTreeNode* y;
-
-  if (nil != (y = x->left)) { /* assignment to y is intentional */
-    while(y->right != nil) { /* returns the maximum of the left subtree of x */
-      y=y->right;
-    }
-    return(y);
-  } else {
-    y=x->parent;
-    while(x == y->left) {
-      if (y == root) return(nil);
-      x=y;
-      y=y->parent;
-    }
-    return(y);
-  }
-}
-
-/***********************************************************************/
-/*  FUNCTION:  Print */
-/**/
-/*    INPUTS:  none */
-/**/
-/*    OUTPUT:  none  */
-/**/
-/*    EFFECTS:  This function recursively prints the nodes of the tree */
-/*              inorder. */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    Note:    This function should only be called from ITTreePrint */
-/***********************************************************************/
-
-void RedBlackTreeNode::Print(RedBlackTreeNode * nil,
-			     RedBlackTreeNode * root) const {
-  storedEntry->Print();
-  printf(", key=%i ",key);
-  printf("  l->key=");
-  if( left == nil) printf("NULL"); else printf("%i",left->key);
-  printf("  r->key=");
-  if( right == nil) printf("NULL"); else printf("%i",right->key);
-  printf("  p->key=");
-  if( parent == root) printf("NULL"); else printf("%i",parent->key);
-  printf("  red=%i\n",red);
-}
-
-void RedBlackTree::TreePrintHelper( RedBlackTreeNode* x) const {
-
-  if (x != nil) {
-    TreePrintHelper(x->left);
-    x->Print(nil,root);
-    TreePrintHelper(x->right);
-  }
-}
-
-/***********************************************************************/
-/*  FUNCTION:  Print */
-/**/
-/*    INPUTS:  none */
-/**/
-/*    OUTPUT:  none */
-/**/
-/*    EFFECT:  This function recursively prints the nodes of the tree */
-/*             inorder. */
-/**/
-/*    Modifies Input: none */
-/**/
-/***********************************************************************/
-
-void RedBlackTree::Print() const {
-  TreePrintHelper(root->left);
-}
-
-/***********************************************************************/
-/*  FUNCTION:  DeleteFixUp */
-/**/
-/*    INPUTS:  x is the child of the spliced */
-/*             out node in DeleteNode. */
-/**/
-/*    OUTPUT:  none */
-/**/
-/*    EFFECT:  Performs rotations and changes colors to restore red-black */
-/*             properties after a node is deleted */
-/**/
-/*    Modifies Input: this, x */
-/**/
-/*    The algorithm from this function is from _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-void RedBlackTree::DeleteFixUp(RedBlackTreeNode* x) {
-  RedBlackTreeNode * w;
-  RedBlackTreeNode * rootLeft = root->left;
-
-  while( (!x->red) && (rootLeft != x)) {
-    if (x == x->parent->left) {
-
-//
-      w=x->parent->right;
-      if (w->red) {
-	w->red=0;
-	x->parent->red=1;
-	LeftRotate(x->parent);
-	w=x->parent->right;
-      }
-      if ( (!w->right->red) && (!w->left->red) ) {
-	w->red=1;
-	x=x->parent;
-      } else {
-	if (!w->right->red) {
-	  w->left->red=0;
-	  w->red=1;
-	  RightRotate(w);
-	  w=x->parent->right;
-	}
-	w->red=x->parent->red;
-	x->parent->red=0;
-	w->right->red=0;
-	LeftRotate(x->parent);
-	x=rootLeft; /* this is to exit while loop */
-      }
-//
-
-    } else { /* the code below is has left and right switched from above */
-      w=x->parent->left;
-      if (w->red) {
-	w->red=0;
-	x->parent->red=1;
-	RightRotate(x->parent);
-	w=x->parent->left;
-      }
-      if ( (!w->right->red) && (!w->left->red) ) {
-	w->red=1;
-	x=x->parent;
-      } else {
-	if (!w->left->red) {
-	  w->right->red=0;
-	  w->red=1;
-	  LeftRotate(w);
-	  w=x->parent->left;
-	}
-	w->red=x->parent->red;
-	x->parent->red=0;
-	w->left->red=0;
-	RightRotate(x->parent);
-	x=rootLeft; /* this is to exit while loop */
-      }
-    }
-  }
-  x->red=0;
-
-}
-
-
-/***********************************************************************/
-/*  FUNCTION:  DeleteNode */
-/**/
-/*    INPUTS:  tree is the tree to delete node z from */
-/**/
-/*    OUTPUT:  returns the RedBlackEntry stored at deleted node */
-/**/
-/*    EFFECT:  Deletes z from tree and but don't call destructor */
-/**/
-/*    Modifies Input:  z */
-/**/
-/*    The algorithm from this function is from _Introduction_To_Algorithms_ */
-/***********************************************************************/
-
-RedBlackEntry * RedBlackTree::DeleteNode(RedBlackTreeNode * z){
-  RedBlackTreeNode* y;
-  RedBlackTreeNode* x;
-  RedBlackEntry * returnValue = z->storedEntry;
-
-  y= ((z->left == nil) || (z->right == nil)) ? z : GetSuccessorOf(z);
-  x= (y->left == nil) ? y->right : y->left;
-  if (root == (x->parent = y->parent)) { /* assignment of y->p to x->p is intentional */
-    root->left=x;
-  } else {
-    if (y == y->parent->left) {
-      y->parent->left=x;
-    } else {
-      y->parent->right=x;
-    }
-  }
-  if (y != z) { /* y should not be nil in this case */
-
-    /* y is the node to splice out and x is its child */
-
-    y->left=z->left;
-    y->right=z->right;
-    y->parent=z->parent;
-    z->left->parent=z->right->parent=y;
-    if (z == z->parent->left) {
-      z->parent->left=y;
-    } else {
-      z->parent->right=y;
-    }
-    if (!(y->red)) {
-      y->red = z->red;
-      DeleteFixUp(x);
-    } else
-      y->red = z->red;
-    delete z;
-  } else {
-    if (!(y->red)) DeleteFixUp(x);
-    delete y;
-  }
-  return returnValue;
-}
-
-
-/***********************************************************************/
-/*  FUNCTION:  Enumerate */
-/**/
-/*    INPUTS:  tree is the tree to look for keys between [low,high] */
-/**/
-/*    OUTPUT:  stack containing pointers to the nodes between [low,high] */
-/**/
-/*    Modifies Input: none */
-/**/
-/*    EFFECT:  Returns a stack containing pointers to nodes containing */
-/*             keys which in [low,high]/ */
-/**/
-/***********************************************************************/
-
-TemplateStack<RedBlackTreeNode *> * RedBlackTree::Enumerate(int low,
-							    int high)  {
-  TemplateStack<RedBlackTreeNode *> * enumResultStack =
-    new TemplateStack<RedBlackTreeNode *>(4);
-
-  RedBlackTreeNode* x=root->left;
-  RedBlackTreeNode* lastBest=NULL;
-
-  while(nil != x) {
-    if ( x->key > high ) {
-      x=x->left;
-    } else {
-      lastBest=x;
-      x=x->right;
-    }
-  }
-  while ( (lastBest) && (low <= lastBest->key) ) {
-    enumResultStack->Push(lastBest);
-    lastBest=GetPredecessorOf(lastBest);
-  }
-  return(enumResultStack);
-}

nilmdb/bxintersect.pyx

@@ -1,26 +1,7 @@
 # cython: profile=False
-# This is from bx-python 554:07aca5a9f6fc (BSD licensed), modified to
+# This is based on bxintersect in bx-python 554:07aca5a9f6fc (BSD licensed);
-# store interval ranges as doubles rather than 32-bit integers.
+# modified to store interval ranges as doubles rather than 32-bit integers,
-
+# use fully closed intervals, support deletion, etc.
-"""
-Data structure for performing intersect queries on a set of intervals which
-preserves all information about the intervals (unlike bitset projection methods).
-
-:Authors: James Taylor (james@jamestaylor.org),
-          Ian Schenk (ian.schenck@gmail.com),
-          Brent Pedersen (bpederse@gmail.com)
-"""
-
-# Historical note:
-#    This module original contained an implementation based on sorted endpoints
-#    and a binary search, using an idea from Scott Schwartz and Piotr Berman.
-#    Later an interval tree implementation was implemented by Ian for Galaxy's
-#    join tool (see `bx.intervals.operations.quicksect.py`). This was then
-#    converted to Cython by Brent, who also added support for
-#    upstream/downstream/neighbor queries. This was modified by James to
-#    handle half-open intervals strictly, to maintain sort order, and to
-#    implement the same interface as the original Intersecter.
-
 #cython: cdivision=True
 
 import operator
@@ -194,76 +175,6 @@ cdef class IntervalNode:
             self.cright._intersect( start, end, results )
 
 
-    cdef void _seek_left(IntervalNode self, double position, list results, int n, double max_dist):
-        # we know we can bail in these 2 cases.
-        if self.maxend + max_dist < position:
-            return
-        if self.minstart > position:
-            return
-
-        # the ordering of these 3 blocks makes it so the results are
-        # ordered nearest to farest from the query position
-        if self.cright is not EmptyNode:
-            self.cright._seek_left(position, results, n, max_dist)
-
-        if -1 < position - self.end < max_dist:
-            results.append(self.interval)
-
-        # TODO: can these conditionals be more stringent?
-        if self.cleft is not EmptyNode:
-                self.cleft._seek_left(position, results, n, max_dist)
-
-
-
-    cdef void _seek_right(IntervalNode self, double position, list results, int n, double max_dist):
-        # we know we can bail in these 2 cases.
-        if self.maxend < position: return
-        if self.minstart - max_dist > position: return
-
-        #print "SEEK_RIGHT:",self, self.cleft, self.maxend, self.minstart, position
-
-        # the ordering of these 3 blocks makes it so the results are
-        # ordered nearest to farest from the query position
-        if self.cleft is not EmptyNode:
-                self.cleft._seek_right(position, results, n, max_dist)
-
-        if -1 < self.start - position < max_dist:
-            results.append(self.interval)
-
-        if self.cright is not EmptyNode:
-                self.cright._seek_right(position, results, n, max_dist)
-
-
-    cpdef left(self, position, int n=1, double max_dist=2500):
-        """
-        find n features with a start > than `position`
-        f: a Interval object (or anything with an `end` attribute)
-        n: the number of features to return
-        max_dist: the maximum distance to look before giving up.
-        """
-        cdef list results = []
-        # use start - 1 becuase .left() assumes strictly left-of
-        self._seek_left( position - 1, results, n, max_dist )
-        if len(results) == n: return results
-        r = results
-        r.sort(key=operator.attrgetter('end'), reverse=True)
-        return r[:n]
-
-    cpdef right(self, position, int n=1, double max_dist=2500):
-        """
-        find n features with a end < than position
-        f: a Interval object (or anything with a `start` attribute)
-        n: the number of features to return
-        max_dist: the maximum distance to look before giving up.
-        """
-        cdef list results = []
-        # use end + 1 becuase .right() assumes strictly right-of
-        self._seek_right(position + 1, results, n, max_dist)
-        if len(results) == n: return results
-        r = results
-        r.sort(key=operator.attrgetter('start'))
-        return r[:n]
-
     def traverse(self):
         if self.cleft is not EmptyNode:
             for node in self.cleft.traverse():
@@ -392,6 +303,7 @@ cdef class IntervalTree:
 
     # ---- Position based interfaces -----------------------------------------
 
+    ## KEEP
     def insert( self, double start, double end, object value=None ):
         """
         Insert the interval [start,end) associated with value `value`.
@@ -401,8 +313,14 @@ cdef class IntervalTree:
         else:
             self.root = self.root.insert( start, end, value )
 
-    add = insert
+    def delete( self, double start, double end, object value=None ):
-
+        """
+        Delete the interval [start,end) associated with value `value`.
+        """
+        if self.root is None:
+            self.root = IntervalNode( start, end, value )
+        else:
+            self.root = self.root.insert( start, end, value )
 
     def find( self, start, end ):
         """
@@ -412,26 +330,9 @@ cdef class IntervalTree:
             return []
         return self.root.find( start, end )
 
-    def before( self, position, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie before `position` and are no
-        further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.left( position, num_intervals, max_dist )
-
-    def after( self, position, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie after `position` and are no
-        further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.right( position, num_intervals, max_dist )
-
     # ---- Interval-like object based interfaces -----------------------------
 
+    ## KEEP
     def insert_interval( self, interval ):
         """
         Insert an "interval" like object (one with at least start and end
@@ -439,50 +340,6 @@ cdef class IntervalTree:
         """
         self.insert( interval.start, interval.end, interval )
 
-    add_interval = insert_interval
-
-    def before_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely before `interval`
-        and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.left( interval.start, num_intervals, max_dist )
-
-    def after_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely after `interval` and
-        are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        return self.root.right( interval.end, num_intervals, max_dist )
-
-    def upstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely upstream of
-        `interval` and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        if interval.strand == -1 or interval.strand == "-":
-            return self.root.right( interval.end, num_intervals, max_dist )
-        else:
-            return self.root.left( interval.start, num_intervals, max_dist )
-
-    def downstream_of_interval( self, interval, num_intervals=1, max_dist=2500 ):
-        """
-        Find `num_intervals` intervals that lie completely downstream of
-        `interval` and are no further than `max_dist` positions away
-        """
-        if self.root is None:
-            return []
-        if interval.strand == -1 or interval.strand == "-":
-            return self.root.left( interval.start, num_intervals, max_dist )
-        else:
-            return self.root.right( interval.end, num_intervals, max_dist )
-
     def traverse(self):
         """
         iterator that traverses the tree

nilmdb/interval.py

@@ -18,7 +18,9 @@ Intervals are closed, ie. they include timestamps [start, end]
 # Fourth version is an optimized rb-tree that stores interval starts
 # and ends directly in the tree, like bxinterval did.
 
-import rbtree
+# Fifth version is back to modified bxintersect...
+
+import bxintersect
 
 class IntervalError(Exception):
     """Error due to interval overlap, etc"""
@@ -128,7 +130,7 @@ class IntervalSet(object):
         """
         'source' is an Interval or IntervalSet to add.
         """
-        self.tree = rbtree.RBTree()
+        self.tree = bxinterval.IntervalTree()
         if source is not None:
             self += source
 
@@ -210,7 +212,7 @@ class IntervalSet(object):
             if self.intersects(other):
                 raise IntervalError("Tried to add overlapping interval "
                                     "to this set")
-            self.tree.insert(rbtree.RBNode(other))
+            self.tree.insert_interval(other)
         else:
             for x in other:
                 self.__iadd__(x)