Added empty classes for recover tree solver

.gitignore

@@ -79,3 +79,9 @@ atlassian-ide-plugin.xml
 com_crashlytics_export_strings.xml
 
 
+### https://raw.github.com/github/gitignore/298588469ac0cb08a00eebf7b00efb5ab726daca/Global/vagrant.gitignore
+
+.vagrant/
+
+
+src/CMakeLists.txt.user

Vagrantfile

@@ -0,0 +1,122 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # All Vagrant configuration is done here. The most common configuration
+  # options are documented and commented below. For a complete reference,
+  # please see the online documentation at vagrantup.com.
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "ubuntu/trusty64"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # If true, then any SSH connections made will enable agent forwarding.
+  # Default value: false
+  # config.ssh.forward_agent = true
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Don't boot with headless mode
+  #   vb.gui = true
+  #
+  #   # Use VBoxManage to customize the VM. For example to change memory:
+  #   vb.customize ["modifyvm", :id, "--memory", "1024"]
+  # end
+  #
+  # View the documentation for the provider you're using for more
+  # information on available options.
+
+  # Enable provisioning with CFEngine. CFEngine Community packages are
+  # automatically installed. For example, configure the host as a
+  # policy server and optionally a policy file to run:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.am_policy_hub = true
+  #   # cf.run_file = "motd.cf"
+  # end
+  #
+  # You can also configure and bootstrap a client to an existing
+  # policy server:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.policy_server_address = "10.0.2.15"
+  # end
+
+  # Enable provisioning with Puppet stand alone.  Puppet manifests
+  # are contained in a directory path relative to this Vagrantfile.
+  # You will need to create the manifests directory and a manifest in
+  # the file default.pp in the manifests_path directory.
+  #
+  # config.vm.provision "puppet" do |puppet|
+  #   puppet.manifests_path = "manifests"
+  #   puppet.manifest_file  = "default.pp"
+  # end
+
+  # Enable provisioning with chef solo, specifying a cookbooks path, roles
+  # path, and data_bags path (all relative to this Vagrantfile), and adding
+  # some recipes and/or roles.
+  #
+  # config.vm.provision "chef_solo" do |chef|
+  #   chef.cookbooks_path = "../my-recipes/cookbooks"
+  #   chef.roles_path = "../my-recipes/roles"
+  #   chef.data_bags_path = "../my-recipes/data_bags"
+  #   chef.add_recipe "mysql"
+  #   chef.add_role "web"
+  #
+  #   # You may also specify custom JSON attributes:
+  #   chef.json = { mysql_password: "foo" }
+  # end
+
+  # Enable provisioning with chef server, specifying the chef server URL,
+  # and the path to the validation key (relative to this Vagrantfile).
+  #
+  # The Opscode Platform uses HTTPS. Substitute your organization for
+  # ORGNAME in the URL and validation key.
+  #
+  # If you have your own Chef Server, use the appropriate URL, which may be
+  # HTTP instead of HTTPS depending on your configuration. Also change the
+  # validation key to validation.pem.
+  #
+  # config.vm.provision "chef_client" do |chef|
+  #   chef.chef_server_url = "https://api.opscode.com/organizations/ORGNAME"
+  #   chef.validation_key_path = "ORGNAME-validator.pem"
+  # end
+  #
+  # If you're using the Opscode platform, your validator client is
+  # ORGNAME-validator, replacing ORGNAME with your organization name.
+  #
+  # If you have your own Chef Server, the default validation client name is
+  # chef-validator, unless you changed the configuration.
+  #
+  #   chef.validation_client_name = "ORGNAME-validator"
+end

examples/recover/x_chr.cfg

@@ -0,0 +1,14 @@
+[Genomes]
+M Mouse 
+R Rat
+D Dog
+Q Champanse
+H Human 
+C Cat 
+
+##[Trees]
+##(((Mouse,Rat),Dog)MRD,(Champanse,(Human,Cat)HC)HCQ)
+
+## [Target] 
+
+## [Completion]

src/include/algo/Algorithms.hpp

@@ -5,8 +5,6 @@
 
 #include "algo/Stage.hpp"
 
-//#include "algo/recover_tree/RecoveredTree.hpp"
-
 #include "algo/main/Balance.hpp"
 #include "algo/main/SimplePath.hpp"
 #include "algo/main/FourCycles.hpp"
@@ -20,102 +18,101 @@
 
 //#include "algo/linearization/Linearization.hpp"
 
-namespace algo { 
-
-template<class graph_pack_t> 
-void StageManager<graph_pack_t>::add_stage(kind_stage stage) { 
-  if (stage == balance_k) { 
-    add_stage(new Balance<graph_pack_t>(1));
-  } else if (stage == simple_path_k) {
-    add_stage(new ProcessSimplePath<graph_pack_t>(3));
-  } else if (stage == four_cycles_k) {
-    add_stage(new ProcessFourCycles<graph_pack_t>(1));
-  } else if (stage == fair_edge_k) {
-    add_stage(new ProcessFairEdge<graph_pack_t>(3));
-  } else if (stage == clone_k) {
-    add_stage(new ProcessClone<graph_pack_t>(3));
-  } else if (stage == fair_clone_edge_k) {
-    add_stage(new ProcessTwoBreakAndClone<graph_pack_t>(3));
-  } else if (stage == components_k) {
-    add_stage(new IncreaseNumberComponents<graph_pack_t>(1));
-  } else if (stage == change_canform_k) {
-    add_stage(new ChangeCanformInfinity<graph_pack_t>());
-  } else if (stage == bruteforce_k) { 
-    add_stage(new BruteForce<graph_pack_t>(cfg::get().size_component_in_bruteforce));
-  } else if (stage == blossomv_k) {
-    add_stage(new ProcessWithBlossomV<graph_pack_t>());
-  } else if (stage == completion_k) {
-    add_stage(new ProcessComplection<graph_pack_t>(cfg::get().completion));
-  } 
-}
-
+namespace algo {
+
+  template<class graph_pack_t>
+  void StageManager<graph_pack_t>::add_stage(kind_stage stage) {
+    if (stage == balance_k) {
+      add_stage(new Balance<graph_pack_t>(1));
+    } else if (stage == simple_path_k) {
+      add_stage(new ProcessSimplePath<graph_pack_t>(3));
+    } else if (stage == four_cycles_k) {
+      add_stage(new ProcessFourCycles<graph_pack_t>(1));
+    } else if (stage == fair_edge_k) {
+      add_stage(new ProcessFairEdge<graph_pack_t>(3));
+    } else if (stage == clone_k) {
+      add_stage(new ProcessClone<graph_pack_t>(3));
+    } else if (stage == fair_clone_edge_k) {
+      add_stage(new ProcessTwoBreakAndClone<graph_pack_t>(3));
+    } else if (stage == components_k) {
+      add_stage(new IncreaseNumberComponents<graph_pack_t>(1));
+    } else if (stage == change_canform_k) {
+      add_stage(new ChangeCanformInfinity<graph_pack_t>());
+    } else if (stage == bruteforce_k) {
+      add_stage(new BruteForce<graph_pack_t>(cfg::get().size_component_in_bruteforce));
+    } else if (stage == blossomv_k) {
+      add_stage(new ProcessWithBlossomV<graph_pack_t>());
+    } else if (stage == completion_k) {
+      add_stage(new ProcessComplection<graph_pack_t>(cfg::get().completion));
+    }
+  }
 }
 
 /**
- * This pipeline uses in main converter, when avaliable
- * full phylogenetic tree and genomes doesn't need to scaffold
- */
-template<class graph_pack_t> 
-bool main_algorithm(graph_pack_t & graph_pack) {
-  assert(cfg::get().how_build == default_algo); 
+* This pipeline uses in main converter, when avaliable
+* full phylogenetic tree and genomes doesn't need to scaffold
+*/
+template<class graph_pack_t>
+bool main_algorithm(graph_pack_t &graph_pack) {
+  assert(cfg::get().how_build == default_algo);
 
   INFO("Start algorithm for convert from breakpoint graph to identity breakpoint graph");
 
-  using namespace algo; 
+  using namespace algo;
   StageManager<graph_pack_t> algorithm(cfg::get().rounds, {cfg::get().is_debug, cfg::get().out_path_to_debug_dir});
 
-  for (auto const & name_stage : cfg::get().pipeline) { 
-    algorithm.add_stage(name_stage); 
+  for (auto const &name_stage : cfg::get().pipeline) {
+    algorithm.add_stage(name_stage);
   }
 
   INFO("Run algorithms stages")
   algorithm.run(graph_pack);
-    
-  if (!graph_pack.graph.is_identity()) { 
+
+  if (!graph_pack.graph.is_identity()) {
     INFO("T-transformation is not complete. Cannot reconstruct genomes.")
-    return false; 
-  } 
-  
+    return false;
+  }
+
   if (!graph_pack.is_consistency_graph()) {
     INFO("We have problem with edges, corresponding postponed deletions.")
     INFO("If you have indentity breakpoint graph after stages, please contact us.")
     return false;
-  } 
+  }
 
   INFO("Start to replace cloning to 2-breaks")
   graph_pack.history.change_history();
   INFO("Finish to replace cloning to 2-breaks")
-   
+
   return true;
 }
 
-template<class graph_pack_t> 
-bool wgd_algorithm(graph_pack_t & graph_pack) {
-  assert(cfg::get().how_build == default_algo); 
+template<class graph_pack_t>
+bool wgd_algorithm(graph_pack_t &graph_pack) {
+  assert(cfg::get().how_build == default_algo);
 
   INFO("Start wgd algorithm for convert from breakpoint graph to identity breakpoint graph");
 
-  using namespace algo; 
+  using namespace algo;
   StageManager<graph_pack_t> algorithm(cfg::get().rounds, {cfg::get().is_debug, cfg::get().out_path_to_debug_dir});
 
   INFO("Run algorithms stages")
   algorithm.run(graph_pack);
-    
-  if (!graph_pack.graph.is_identity()) { 
+
+  if (!graph_pack.graph.is_identity()) {
     INFO("T-transformation is not complete. Cannot reconstruct genomes.")
-    return false; 
-  } 
-  
+    return false;
+  }
+
   if (!graph_pack.is_consistency_graph()) {
     INFO("We have problem with edges, corresponding postponed deletions.")
     INFO("If you have indentity breakpoint graph after stages, please contact us.")
     return false;
-  } 
+  }
 
   INFO("Start to replace cloning to 2-breaks")
   graph_pack.history.change_history();
   INFO("Finish to replace cloning to 2-breaks")
-   
+
   return true;
 }
 

src/include/algo/recover_tree/bruteforce_recover_tree_algorithm.hpp

@@ -0,0 +1,25 @@
+#ifndef BRUTEFORCE_RECOVER_TREE_ALGORITHM_HPP__
+#define BRUTEFORCE_RECOVER_TREE_ALGORITHM_HPP__
+
+#include "recover_tree_algorithm.hpp"
+#include "../../graph/graph_pack.hpp"
+
+namespace algo {
+
+  template<class mcolor_t>
+  class BruteforceRecoverTreeAlgorithm : public RecoverTreeAlgorithm<mcolor_t> {
+  public:
+    using graph_pack_t = GraphPack<mcolor_t>;
+
+    BruteforceRecoverTreeAlgorithm(graph_pack_t &breakpoint_graph) : m_graph(breakpoint_graph) {}
+
+    typename RecoverTreeAlgorithm<mcolor_t>::tree_ptr recover_tree() {
+      return std::make_shared<typename structure::BinaryTree<mcolor_t> >(nullptr);
+    }
+
+  private:
+    graph_pack_t& m_graph;
+  };
+}
+
+#endif

src/include/algo/recover_tree/recover_tree_algorithm.hpp

@@ -0,0 +1,23 @@
+#ifndef RECOVER_TREE_ALGORITHM_HPP__
+#define RECOVER_TREE_ALGORITHM_HPP__
+
+#include <memory>
+#include "../../structures/tree.hpp"
+
+namespace algo {
+
+  template<class mcolor_t>
+  class RecoverTreeAlgorithm {
+  public:
+    using algo_ptr = std::shared_ptr<RecoverTreeAlgorithm>;
+    using tree_t = structure::BinaryTree<mcolor_t>;
+    using tree_ptr = std::shared_ptr<tree_t>;
+
+    virtual tree_ptr recover_tree() = 0;
+
+    virtual ~RecoverTreeAlgorithm() {
+    }
+  };
+}
+
+#endif