Merge pull request #195 from vgteam/zip-clustering

Zipcode support

bdsg/include/bdsg/snarl_distance_index.hpp

@@ -232,6 +232,13 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
     //Distance limit is the distance after which we give up if we're doing a traversal.
     size_t distance_in_parent(const net_handle_t& parent, const net_handle_t& child1, const net_handle_t& child2, const HandleGraph* graph=nullptr, size_t distance_limit = std::numeric_limits<size_t>::max()) const;
 
+    //Distance_in_parent for distances in a snarl given the rank and orientation instead of a handle
+    //You should use distance in parent unless you're sure the ranks are correct - this shouldn't
+    //be exposed to the public interface but I needed it
+    size_t distance_in_snarl(const net_handle_t& parent, const size_t& rank1, const bool& right_side1, 
+            const size_t& rank2, const bool& right_side2, const HandleGraph* graph=nullptr, 
+            size_t distance_limit = std::numeric_limits<size_t>::max()) const;
+
     ///Find the maximum distance between two children in the parent. 
     ///This is the same as distance_in_parent for everything except children of chains
     size_t max_distance_in_parent(const net_handle_t& parent, const net_handle_t& child1, const net_handle_t& child2, const HandleGraph* graph=nullptr, size_t distance_limit = std::numeric_limits<size_t>::max()) const;
@@ -257,6 +264,7 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
     bool is_externally_start_start_connected(const net_handle_t net) const {return is_externally_start_start_connected(snarl_tree_records->at(get_record_offset(net)));}
     bool is_externally_end_end_connected(const net_handle_t net) const {return is_externally_end_end_connected(snarl_tree_records->at(get_record_offset(net)));}
 
+
     ///For two net handles, get a net handle lowest common ancestor.
     ///If the lowest common ancestor is the root, then the two handles may be in
     ///different connected components. In this case, return false.
@@ -325,21 +333,25 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
 
     ///Get the prefix sum value for a node in a chain.
     ///Fails if the parent of net is not a chain
-    size_t get_prefix_sum_value(const net_handle_t net) const;
+    size_t get_prefix_sum_value(const net_handle_t& net) const;
 
-    ///Get the prefix sum value for a node in a chain.
+    ///Get the maximum prefix sum value for a node in a chain.
     ///Fails if the parent of net is not a chain
-    size_t get_forward_loop_value(const net_handle_t net) const;
+    size_t get_max_prefix_sum_value(const net_handle_t& net) const;
 
-    ///Get the prefix sum value for a node in a chain.
+    ///Get the forward loop value for a node in a chain.
+    ///Fails if the parent of net is not a chain
+    size_t get_forward_loop_value(const net_handle_t& net) const;
+
+    ///Get the reverse value for a node in a chain.
     ///Fails if the parent of net is not a chain
-    size_t get_reverse_loop_value(const net_handle_t net) const;
+    size_t get_reverse_loop_value(const net_handle_t& net) const;
 
     //If get_end is true, then get the second component of the last node in a looping chain.
     //If the chain loops, then the first and last node are the same.
     //If it is also a multicomponent, chain, then it is in two different components.
     //If get_end is true, then get the larger of the two components.
-    size_t get_chain_component(const net_handle_t net, bool get_end = false) const;
+    size_t get_chain_component(const net_handle_t& net, bool get_end = false) const;
 
 
 
@@ -363,11 +375,26 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
     ///Returns true if the given net handle refers to (a traversal of) a snarl.
     bool is_snarl(const net_handle_t& net) const;
 
+    ///Return true if the given snarl is a DAG and false otherwise
+    ///Returns true if the given net_handle_t is not a snarl
+    bool is_dag(const net_handle_t& snarl) const;
+
+    ///Given a snarl, return the number of non-dag edges it contains
+    ///0 for a dag
+    size_t non_dag_edge_count(const net_handle_t& snarl, const HandleGraph* graph) const;
+
     ///Returns true if the given net handle refers to (a traversal of) a simple snarl
     ///A simple snarl is a bubble where each child node can only reach the boundary nodes,
     ///and each side of a node reaches a different boundary node
+    ///There may also be an edge connecting the two boundary nodes but no additional 
+    ///edges are allowed
     bool is_simple_snarl(const net_handle_t& net) const;
 
+    ///Returns true if the given net handle refers to (a traversal of) a regular snarl
+    ///A regular snarl is the same as a simple snarl, except that the children may be
+    ///nested chains, rather than being restricted to nodes 
+    bool is_regular_snarl(const net_handle_t& net) const;
+
     ///Returns true if the given net handle refers to (a traversal of) a chain.
     bool is_chain(const net_handle_t& net) const;
     ///Returns true if the given net handle refers to (a traversal of) a chain that is not start-end connected
@@ -471,6 +498,11 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
     ///number of nodes in the top-level snarl 
     size_t connected_component_count() const;
 
+    ///Get the child of a snarl from its rank. This shouldn't be exposed to the public interface but I need it
+    ///Please don't use it
+    ///For 0 or 1, returns the sentinel facing in. Otherwise return the child as a chain going START_END
+    net_handle_t get_snarl_child_from_rank(const net_handle_t& snarl, const size_t& rank) const;
+
 protected:
     ///Internal implementation for for_each_child.
     bool for_each_child_impl(const net_handle_t& traversal, const std::function<bool(const net_handle_t&)>& iteratee) const;
@@ -1165,6 +1197,7 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
 
         size_t get_node_count() const;
 
+        //Get the offset of the list of children
         size_t get_child_record_pointer() const;
 
         bool for_each_child(const std::function<bool(const net_handle_t&)>& iteratee) const;
@@ -1223,6 +1256,8 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
         size_t get_node_length(size_t rank = std::numeric_limits<size_t>::max()) const;
         bool get_node_is_reversed(size_t rank = std::numeric_limits<size_t>::max()) const;
 
+
+        net_handle_t get_child_from_rank(const size_t& rank) const;
         bool for_each_child(const std::function<bool(const net_handle_t&)>& iteratee) const;
 
     };