last commit

src/analysis/site.cpp

@@ -368,7 +368,7 @@ static uint backtrackingDataflow(std::map<sptrBipartite, bool>* graph_nodes1,std
 /* Returns true if there is a path from source 's' to sink
   't' in residual graph. Also fills parent[] to store the
   path */
-bool beadth_first_search(boost::multi_array<int, 2> rGraph, int s, int t, int parent[])
+bool beadth_first_search(int *rGraph[], int s, int t, int parent[])
 {
     // Create a visited array and mark all vertices as not
     // visited
@@ -450,8 +450,10 @@ static int ford_fulkersonDataFlow(std::map<sptrBipartite, uint> graph_index1,std
   }
 
   // Ford Fulkerson algorithm, with BFS
-  boost::multi_array <int, 2>::extent_gen extents;
-  boost::multi_array <int, 2> rGraph(extents[index + 1][index + 1]);
+  int *rGraph[index + 1];
+    for(int i = 0; i < index + 1; i++){
+        rGraph[i] = new int[index + 1];
+    }
   // Create a residual graph and fill the residual graph with given capacities in the original graph as residual capacities in residual graph
   // Residual graph where rGraph[i][j] indicates residual capacity of edge from i to j (if there is an edge. If rGraph[i][j] is 0, then there is not)
   for (uint u = 0; u < index + 1; u++){
@@ -510,7 +512,6 @@ static std::unordered_set<sptrBipartite> getMatchesOfDF(sptrBipartite DF_graph,
 float Site::computeDataflowSimilarity(const std::shared_ptr<Site> site2, std::shared_ptr<spdlog::logger> log, const std::string similarity_method) const{
 	SPDLOG_LOGGER_TRACE(log, "computeDataflowSimilarity with {}", similarity_method); 
 	float score=0;
-
   if (similarity_method == "ford-fulkerson"){
     std::unordered_set<sptrBipartite> matches;
 		std::map<sptrBipartite, std::unordered_set<sptrBipartite>> graph_matches; // key: site1's DF, value: this DF's matches in site2

src/analysis/site.hpp

@@ -8,7 +8,6 @@
 #include <limits.h>
 #include <queue>
 #include <string.h>
-#include "boost/multi_array.hpp"
 
 namespace boa{
 
@@ -55,7 +54,7 @@ public:
     std::vector<sptrBipartite> getSiteDataflow() const;
     bool isDataflowEqual(std::shared_ptr<Site> site2, std::shared_ptr<spdlog::logger> log) const;
     bool isDataflowEqualV2( std::shared_ptr<Site> site2) const;
-    bool beadth_first_search(boost::multi_array<int, 2> rGraph, int s, int t, int parent[]);
+    bool beadth_first_search(int *rGraph[], int s, int t, int parent[]);
     float computeDataflowSimilarity(const std::shared_ptr<Site> site2, std::shared_ptr<spdlog::logger> log, const std::string similarity_method) const;
 
 

src/config.cpp

@@ -624,7 +624,7 @@ Config::Config(int argc, char* argv[])
     throw std::runtime_error("No mode is selected. Please select one.");
   }
 	std::unordered_set<std::string> authorized_site_sim_methods ({"backtracking", "sum", "ford-fulkerson", "sum_general_reg"});
-  if(authorized_site_sim_methods.find(m_config_global.site_sim_method)==0){
+  if(authorized_site_sim_methods.count(m_config_global.site_sim_method)==0){
   	throw std::runtime_error("Please select a valid site similarity computation method: backtracking, sum, sum_general_reg, or ford-fulkerson");
 	}
 	if(!std::filesystem::exists(std::filesystem::path(m_config_global.log_output).parent_path())){

src/main.cpp

@@ -238,7 +238,6 @@ void handleResultsLearn(Config *config, std::shared_ptr<AnalysisEngine> analysis
 }
 
 void handleResultsCorrelation(Config *config, std::shared_ptr<ClassificationEngine> classification_engine,std::shared_ptr<spdlog::logger> log){
-
   classification_engine->sortCorrelFunctions();
 
 
@@ -319,7 +318,6 @@ void handleResultsCorrelation(Config *config, std::shared_ptr<ClassificationEngi
   }
 
   log->info("Done\n", config->getConfigGlobal().log_output);
-
   return;
 }