#3

Author: mikejiang

inst/include/cytolib/GatingHierarchy.hpp

@@ -89,6 +89,8 @@ struct OurVertexPropertyWriterR {
 
 class GatingHierarchy{
 private:
+	unsigned short g_loglevel;// debug print is turned off by default
+
 	compensation comp; /*< compensation object */
 
 	/* compensation is currently done in R due to the linear Algebra
@@ -104,7 +106,7 @@ class GatingHierarchy{
 
 public:
 
-
+	void set_loglevel(unsigned short _g_loglevel){g_loglevel = _g_loglevel;};
 
 	/**
 	 * load the in-memory copy of frm
@@ -338,7 +340,7 @@ class GatingHierarchy{
 		 * , customized copy and assignment constructor is required
 		 *
 		 */
-	GatingHierarchy(const GatingHierarchy & _gh)
+	GatingHierarchy(const GatingHierarchy & _gh):g_loglevel(NO_LOG)
 	{
 		comp = _gh.comp;
 
@@ -365,8 +367,8 @@ class GatingHierarchy{
 	 * 	GatingHierarchy *curGh=new GatingHierarchy();
 	 * \endcode
 	 */
-	GatingHierarchy(){}
-	GatingHierarchy(compensation _comp, PARAM_VEC _transFlag, trans_local _trans):comp(_comp), transFlag(_transFlag),trans(_trans) {};
+	GatingHierarchy():g_loglevel(NO_LOG){}
+	GatingHierarchy(compensation _comp, PARAM_VEC _transFlag, trans_local _trans):g_loglevel(NO_LOG),comp(_comp), transFlag(_transFlag),trans(_trans) {};
 	void convertToPb(pb::GatingHierarchy & gh_pb){
 		pb::populationTree * ptree = gh_pb.mutable_tree();
 		/*
@@ -402,7 +404,7 @@ class GatingHierarchy{
 
 	}
 
-	GatingHierarchy(pb::GatingHierarchy & pb_gh, map<intptr_t, transformation *> & trans_tbl){
+	GatingHierarchy(pb::GatingHierarchy & pb_gh, map<intptr_t, transformation *> & trans_tbl):g_loglevel(NO_LOG){
 		const pb::populationTree & tree_pb =  pb_gh.tree();
 		int nNodes = tree_pb.node_size();
 

inst/include/cytolib/GatingSet.hpp

@@ -31,6 +31,7 @@ using namespace std;
  *
  */
 class GatingSet{
+	unsigned short g_loglevel;// debug print is turned off by default
 
 	biexpTrans globalBiExpTrans; //default bi-exponential transformation functions
 	linTrans globalLinTrans;
@@ -52,6 +53,13 @@ class GatingSet{
 			 return ghs.find(sampleName);
 	 }
 	 size_t erase ( const string& k ){return ghs.erase(k);}
+
+	 void set_loglevel(unsigned short _g_loglevel){
+		 g_loglevel = _g_loglevel;
+		 for(auto & it :ghs)
+			 it.second.set_loglevel(_g_loglevel);
+	 };
+	 unsigned short get_loglevel(){return g_loglevel;};
 	 /**
 	  * insert
 	  * @param sampleName
@@ -122,7 +130,7 @@ class GatingSet{
 
 	}
 
-	GatingSet(){};
+	GatingSet():g_loglevel(NO_LOG){};
 
 	/**
 	 * separate filename from dir to avoid to deal with path parsing in c++
@@ -204,7 +212,7 @@ class GatingSet{
 	 * @param format
 	 * @param isPB
 	 */
-	GatingSet(string filename)
+	GatingSet(string filename):g_loglevel(NO_LOG)
 	{
 		GOOGLE_PROTOBUF_VERIFY_VERSION;
 		ifstream input(filename.c_str(), ios::in | ios::binary);
@@ -423,7 +431,7 @@ class GatingSet{
 	 * compensation and transformation,more options can be allowed in future like providing different
 	 * comp and trans
 	 */
-	GatingSet(const GatingHierarchy & gh_template,vector<string> sampleNames){
+	GatingSet(const GatingHierarchy & gh_template,vector<string> sampleNames):g_loglevel(NO_LOG){
 
 
 
@@ -458,7 +466,7 @@ class GatingSet{
 		}
 	}
 
-	GatingSet(vector<string> sampleNames){
+	GatingSet(vector<string> sampleNames):g_loglevel(NO_LOG){
 		vector<string>::iterator it;
 		for(it=sampleNames.begin();it!=sampleNames.end();it++)
 		{

inst/include/cytolib/global.hpp

@@ -8,13 +8,13 @@
 #ifndef GLOBAL_HPP_
 #define GLOBAL_HPP_
 
-#define GATING_SET_LEVEL 1
-#define GATING_HIERARCHY_LEVEL 2
-#define POPULATION_LEVEL 3
-#define GATE_LEVEL 4
-
-extern unsigned short g_loglevel;
-extern bool my_throw_on_error;
+enum loglevel_t{
+	NO_LOG = 0,
+	GATING_SET_LEVEL = 1,
+	GATING_HIERARCHY_LEVEL = 2,
+	POPULATION_LEVEL = 3,
+	GATE_LEVEL = 4
+	};
 
 #ifdef ROUT
 #include <R_ext/Print.h>
@@ -27,8 +27,6 @@ extern bool my_throw_on_error;
 #include <vector>
 using namespace std;
 
-extern unsigned short g_loglevel;// debug print is turned off by default
-extern bool my_throw_on_error;//can be toggle off to get a partially parsed gating tree for debugging purpose
 
 inline void PRINT(string a){
 #ifdef ROUT