pull request for pseudoknots

src/include/document_writer.hpp

@@ -106,6 +106,10 @@ class document_writer
     std::string get_rna_subtree_formatted(
                                           rna_tree::iterator root) const;
 
+    std::string find_pseudoknots(
+                                 rna_tree::pre_post_order_iterator begin,
+                                 rna_tree::pre_post_order_iterator end) const;
+
 public:
     /**
      * initialize new document_writer on document `filename`.`suffix`

src/include/rna_tree_label.hpp

@@ -39,6 +39,7 @@ struct rna_label
     std::string label;
     std::string tmp_label; //label used in the template (can be used to store information about the mapped nodes label in the template)
     point p;
+    size_t pseudoknot;
 };
 
 /**
@@ -63,6 +64,9 @@ class rna_pair_label : public node_base
     rna_pair_label() = default;
     rna_pair_label(
                    const std::string& s);
+
+    rna_pair_label(const std::string& s, size_t pseudoknot);
+
     bool operator==(
                     const rna_pair_label& other) const;
     rna_pair_label operator+(
@@ -138,9 +142,9 @@ class rna_pair_label : public node_base
 public:
     status_type status = untouched;
     std::vector<size_t> remake_ids;
+    std::vector<rna_label> labels;
 
 private:
-    std::vector<rna_label> labels;
     point parent_center;
     std::vector<rectangle> bounding_objects;
 

src/tree/rna_tree.cpp

@@ -32,6 +32,9 @@ using namespace std;
 inline static std::vector<rna_pair_label> convert(
                                                   const std::string& labels);
 
+inline static std::vector<rna_pair_label> convert(const std::string& labels, const std::string& brackets);
+
+
 inline static std::string trim(
                                std::string s);
 
@@ -41,7 +44,7 @@ rna_tree::rna_tree(
                    const std::string& _labels,
                    const std::string& _name)
 : tree_base<rna_pair_label>(
-                            trim(_brackets), convert(trim(_labels))), _name(_name)
+                            trim(_brackets), convert(trim(_labels), trim(_brackets))), _name(_name)
 {
     set_postorder_ids();
     distances = {0xBADF00D, 0xBADF00D, 0xBADF00D};
@@ -82,7 +85,34 @@ void rna_tree::set_name(
     return vec;
 }
 
-
+std::vector<rna_pair_label> convert(
+                                    const std::string& labels,
+                                    const std::string& brackets)
+{
+    vector<rna_pair_label> vec;
+    vec.reserve(labels.size());
+    size_t pseudoknot = 1;
+
+    for (size_t i = 0; i < labels.size(); ++i)
+    {
+        if(brackets[i] == '[' || brackets[i] == '{')
+        {
+            vec.emplace_back(labels.substr(i, 1), pseudoknot);
+            pseudoknot++;
+        }
+        else if(brackets[i] == ']' || brackets[i] == '}')
+        {
+            --pseudoknot;
+            vec.emplace_back(labels.substr(i, 1), pseudoknot);
+        }
+        else
+        {
+            vec.emplace_back(labels.substr(i, 1));
+        }
+    }
+
+    return vec;
+}
 
 
 void rna_tree::update_points(

src/tree/rna_tree_label.cpp

@@ -38,9 +38,15 @@ bool rna_label::operator==(
 rna_pair_label::rna_pair_label(
                                const std::string& s)
 {
-    labels.push_back({s, "", point::bad_point()});
+    labels.push_back({s, "", point::bad_point(), 0});
 }
 
+rna_pair_label::rna_pair_label(const std::string& s, size_t pseudoknot)
+{
+    labels.push_back({s, point::bad_point(), pseudoknot});
+}
+
+
 const rna_label& rna_pair_label::operator[](
                                             size_t index) const
 {

src/utils/document_writer.cpp

@@ -227,11 +227,45 @@ std::string document_writer::get_rna_background_formatted(
     return out.str();
 }
 
+std::string document_writer::find_pseudoknots(rna_tree::pre_post_order_iterator begin, rna_tree::pre_post_order_iterator end) const
+{
+    ostringstream out;
+
+    while(begin != end)
+    {
+        for(auto&& l: begin->labels)
+        {
+            if(l.pseudoknot != 0)
+            {
+                auto rest = begin;
+                ++rest;
+
+                while(rest != end)
+                {
+                    for(auto&& ll: rest->labels)
+                    {
+                        if(ll.pseudoknot == l.pseudoknot)
+                        {
+                            out << get_line_formatted(l.p, ll.p, RGB::RED);
+                        }
+                    }
+                    ++rest;
+                }
+            }
+        }
+
+        ++begin;
+    }
+
+    return out.str();
+}
+
 std::string document_writer::get_rna_formatted(
                                                rna_tree rna) const
 {
     return get_rna_subtree_formatted(rna.begin())
-    + get_rna_background_formatted(rna.begin_pre_post(), rna.end_pre_post());
+    + get_rna_background_formatted(rna.begin_pre_post(), rna.end_pre_post())
+    + find_pseudoknots(rna.begin_pre_post(), rna.end_pre_post());
 }
 
 void document_writer::init(