modification_list.txt

Now the subparticles that belong to the same particle are choosing the same value for free parameters, so now the models that belong to the same particle are comaparable to each other.
In attachment is an example of how the summarized results look like. Results for each particle are printed in one line, where Fit_M1 is the fit value for the Mutant 1 model, and Fit_M2 is the fit for the Mutant2 model.

Now the summary output looks like this

Particle        Fit_M1          Fit_M2          K2RT            KD1             kdephos         km1             km2             kphos           
Particle_1      0               0               109.933         0.232433        49.9569         61.7505         295.042         0.015322        
Particle_2      0               0               16.0642         72.1204         0.00341         0.005356        0.122982        0.34023         
Particle_3      0               0               2.33497         0.022382        0.228324        0.460925        0.051315        0.007391        
Particle_4      0               0               315.317         0.006366        0.014037        0.036348        0.019306        0.144866        
Particle_5      0               0               0.044512        0.0019          904.756         0.003021        0.007694        0.003005        
Particle_6      0               0               0.006496        595.8           62.8584         0.261852        0.003242        68.2037         
Particle_7      0               0               0.834497        161.385         3.59374         0.01942         0.001152        1.22719         
Particle_8      0               0               0.130787        54.6434         272.242         0.001834        531.606         0.030876        
Particle_9      0               0               0.01745         15.7432         0.016618        0.142323        202.856         0.601761        
Particle_10     0               191.638         2.48236         4.62998         1.08295         0.011964        79.4543         0.012613        




In Particle

- Now BioNetFit will force the subparticles that belong to the same particle to have the same parameter values

- Added new code to the function setParam

	//Raquel: this code check with the master whether the parameter exists in model
	for (auto p = swarm_->options.models.at(mid)->getFreeParams_().begin(); p != swarm_->options.models.at(mid)->getFreeParams_().end(); ++p) {
		if(p->first == myParams.first) {
				//cout << "Raquel myParams first: " << myParams.first << " second: " << myParams.second << endl;
				simParams_.at(mid).insert(myParams);//Raquel: if it does exist, set the param value
		}//Raquel: otherwise, do nothing
	}

- Added new code to the function generateParams

#ifdef VER2
			//code for forcing the subparticles to have the same values
			for (int mid = 0; mid < models.size(); mid++){
				if (models.at(mid)){
					setParam(paramPair, mid);

				}
			}
#else


In Evaluate.cpp and Evaluate.hh: New code added, see files Evaluate.cpp and Evaluate.hh for more updates

- Added a new function for comparing results, given a list of constraints provided by the user


- Code for Evaluate.cpp:


//Raquel: added new function for comparing results given a list of constraints Frebuary 1st, 2017
#include "Evaluate.hh"



using namespace std;

//Raquel: this function splits the result line into a vector of strings
vector<string> splitResults(const string &s, char delim) {
    stringstream ss;
    ss.str(s);
    string item;
    vector<string> elems;
    while (getline(ss, item, delim)) {
        elems.push_back(item);
    }
    return elems;
}


//Raquel: this function apply the logical test based on logical operators parsed from the constraint file
int constraintFunction(double value1, string constraintOperator, double value2){

    bool result;

    if(constraintOperator == "=" || constraintOperator == "=="){
      result = (value1 == value2); return result;
    }

    if(constraintOperator == ">"){
      result = (value1 > value2); return result;
    }

    if(constraintOperator == "<"){
       result = (value1 < value2); return result;
    }

    if(constraintOperator == ">="){
      result = (value1 >= value2); return result;
    }

    if(constraintOperator == "<="){
       result = (value1 <= value2); return result;
    }

    if(constraintOperator == "!="){
       result = (value1 != value2); return result;
    }
   //0 means false
   //1 means true
   //-1 means that the logial operator was not found in this function
   return -1;

}

//Raquel: this function will parse the results, apply the logical operations for testing for constraints
//Raquel: this function will write TRUE or FALSE in the output, depending on whether the constraints are fulfilled
int evaluateResults(string inputFile1, string inputFile2, string consFile) {
  ifstream simResult1;
  ifstream simResult2;
  ifstream constraintFile;

  /*
  if(argc != 4){
     cout << endl << endl;
     cout << "Usage: ./evaluate_results result_file1.txt result_file2.txt constraint_file.cons";
     cout << endl << endl;
     return 1;
  }
*/

  simResult1.open (inputFile1);
  simResult2.open (inputFilefile2);
  constraintFile.open (consFile);

  int count = 0;
  vector<string> constraintValue1;
  vector<string> constraintValue2;
  vector<string> constraintOp;
  vector<string> variableNames;
  vector<string> variableValues;
  string constraintItem;


  map< string, map <int, double> > namesValues;

  string constraints("<>=!");
  size_t pos = 0;
  size_t newpos;
  size_t newpos2;

  string line;

  string tmpStr;

//just to test if the constraing function works
//int test = constraintFunction(0, "=", 0);
//cout << "test result is: " << test << endl; //the result should be 1

  //tests if input files exist
  if (!simResult1.is_open()){cout << "Error! Can't find simulation result file 1.\n"; return 1;}
  if (!simResult2.is_open()){cout << "Error! Can't find simulation result file 2.\n"; return 1;}
  if (!constraintFile.is_open()){cout << "Error! Can't find test file.\n"; return 1; }

  //reads test constraints file
  cout << "Reading constraints file..." << endl;

  while ( getline (constraintFile,line) ){

      //parse constraints using a logical expression parser
      //continue here
      //constraintValue1[0] = line.substr(0, line.find(constraints));

        newpos = line.find_first_of(constraints, pos);
        constraintValue1.push_back(line.substr(pos, newpos));

        newpos2 = line.find_last_of(constraints);
        constraintValue2.push_back(line.substr(newpos2+1));

        //cout << "newpos " << newpos << " newpos2 " << newpos2 << endl;

        if(newpos == newpos2){
	constraintOp.push_back(line.substr(newpos,1));

        }else{constraintOp.push_back(line.substr(newpos,newpos2-newpos+1));}

        //cout << constraintValue1[count] << "\t" <<  constraintOp[count] << "\t" << constraintValue2[count] << endl;


        count++;


  }

  constraintFile.close();


  cout << "Done reading constraints file." << endl;







  //get variable/collumn names
  cout << "Reading Result File 1..." << endl;
  getline (simResult1,line);
  variableNames = splitResults(line, ' ');

  for (int i = 0; i < variableNames.size(); i++){
      if (variableNames[i].empty() || variableNames[i]=="#"){
         //cout << "Found empty string at " << i << endl;
         variableNames.erase(variableNames.begin()+i);
         i--;
      }
   }

/*
  //debug
  for(int i = 0; i < variableNames.size(); i++){
      cout << i << ": !!!!" << variableNames[i] << "@@@@" << endl;

  }
*/

  //get variable values
  count = 0;
  while ( getline (simResult1,line) ){

      //cout << line << '\n';

      variableValues =  splitResults(line, ' ');

      for(int i = 0; i < variableValues.size(); i++){
          if (variableValues[i].empty()){
             //cout << "Found empty string at " << i << endl;
             variableValues.erase(variableValues.begin()+i);
             i--;
          }

       }

       //start making the map here
       //make a map with the variable names (string) vs their index (int), pointing to values (double)
       //example map[variableNames[i]][count] = variableValues[i];
       for(int i = 0; i < variableNames.size(); i++){

          if(variableNames[i] != "Iteration" || variableNames[i] != "iteration" || variableNames[i] != "time" || variableNames[i] != "Time"){
             tmpStr = static_cast<string>(variableValues[i]);
             namesValues[variableNames[i]][count] = atof(tmpStr.c_str());
             //cout << "tmpStr: " << tmpStr << endl;
             //cout << "name: " << variableNames[i] << "; value at " << count << ": " << namesValues[variableNames[i]][count]  << endl;
          }


       }


  count++;

  }


  simResult1.close();


  cout << "Done reading Result File 1." << endl;








  //get variable/collumn names
  cout << "Reading Result File 2..." << endl;
  getline (simResult2,line);
  variableNames = splitResults(line, ' ');

  for (int i = 0; i < variableNames.size(); i++){
      if (variableNames[i].empty() || variableNames[i]=="#"){
         //cout << "Found empty string at " << i << endl;
         variableNames.erase(variableNames.begin()+i);
         i--;
      }
   }

/*//debug
  for(int i = 0; i < variableNames.size(); i++){
      cout << i << ": !!!!" << variableNames[i] << "@@@@" << endl;

  }
*/
  //get variable values
  count = 0;
  while ( getline (simResult2,line) ){

      //cout << line << '\n';

      variableValues =  splitResults(line, ' ');

      for(int i = 0; i < variableValues.size(); i++){
          if (variableValues[i].empty()){
             //cout << "Found empty string at " << i << endl;
             variableValues.erase(variableValues.begin()+i);
             i--;
          }

       }

       //start making the map here
       //make a map with the variable names (string) vs their index (int), pointing to values (double)
       //example map[variableNames[i]][count] = variableValues[i];

      for(int i = 0; i < variableNames.size(); i++){

          if(variableNames[i] != "Iteration"){

             tmpStr = static_cast<string>(variableValues[i]);
             namesValues[variableNames[i]][count] = atof(tmpStr.c_str());
            // cout << "tmpStr: " << tmpStr << endl;
            // cout << "name: " << variableNames[i] << "; value at " << count << ": " << namesValues[variableNames[i]][count]  << endl;
          }


      }


  count++;

  }


  simResult2.close();


  cout << "Done reading Result File 2." << endl;


int result;

 //Now test if the constraints are fulfilled
 //And return a list of iterations where they were fulfilled
 cout << "Iteration" << "\t" << "Constraint" << "\t" << "Result(0=FALSE;1=TRUE)" << endl;

 for(int i = 0; i < constraintValue1.size(); i++){
     //constraintFunction(0, "=", 0);
     //cout << "@@@" << constraintValue1[i] << "@@@map size" << namesValues[constraintValue1[i]].size() << endl;
     //cout << constraintValue1[i] << "\t" <<  constraintOp[i] << "\t" << constraintValue2[i] << endl;

     for (int j = 0; j < namesValues[constraintValue1[i]].size(); j++){
         //cout << namesValues[constraintValue1[i]][j] << " " << constraintOp[i] << " " << namesValues[constraintValue2[i]][j];
         result = constraintFunction(namesValues[constraintValue1[i]][j], constraintOp[i], namesValues[constraintValue2[i]][j]);
         //cout << " = " << result << "; iteration = " << j << " constraints = " << constraintValue1[i] << constraintOp[i] << constraintValue2[i] << endl;


         cout << j+1 << "\t";
         cout << constraintValue1[i] << constraintOp[i] << constraintValue2[i] << "\t";
         cout << result << endl;
     }


 }






//namesValues[variableNames[i]][count]

  return 0;
}


- New code added in Evaluate.hh

//Raquel: added new file
//Name: evaluateResults.hh
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <sstream>
#include <map>
#include <stdlib.h>

using namespace std;

int constraintFunction(double value1, string constraintOperator, double value2);

void evaluateResults(string);

vector<string> splitResults(const string &s, char delim);




In Utils

-	Fixed Linux compatibility issue that was caused by wrong absolute file path.

-	Added the following code to the Utils.cpp code, mainpath function:

		#ifndef WIN_VER //Raquel: added this block to solve compatibility issues with Linux
			path p = canonical("./"); //gets full path with linux sintax
			curdirstr = p.string(); //convert it to string
		#endif

-	Added the following line to the Utils.cpp code, function convertToAbsPath:

		#ifndef WIN_VER //Raquel: added this block to solve compatibility issues with Linux
			path fullPath2 = canonical(relPath); //Raquel: retrieves full path for relative directory
			fullPath = fullPath2.string(); //Raquel: converts path to string
		#endif
	





In Swarm



- Added new code to fix the alignment problem with the parameter values, maping associations between parameters and their values for each particle, and reorganizing them based on their associations

- New code added to outputRunSummary function:

//Raquel: new set of variables
	int counter; //Raquel: this will count the index of the parameter value for a given parameter
	int particleCounter; //Raquel: This will count the total number of particles
	vector<string> paramList; //Raquel: This is the global list of parameters
	int paramCounter; //Raquel: this is the index of the parameter name

	map<unsigned int, map<unsigned int, map<string, double>>> alignedResults;   //Raquel: Particle -> Model -> Parameter -> value


//Raquel: starting new code that I made to fix the alignment problem
//Raquel: this loop will go through all models, particles, parameters, and parameter values, associating them correctly in a new map
		paramCounter = 0;
		 for (unsigned int i=0; i< options.models.size(); i++ ){//loops through models
			 cout<<" Model ["<<i<<"]: " << options.models.at(i)->getName()<<endl<<"              ";
			 counter = 0;
		 	 for (auto it1 = options.models.at(i)->freeParams_.begin(); it1 != options.models.at(i)->freeParams_.end(); ++it1){//loop through parameters

		 		    cout<<" Free Parameter: " << it1->first << endl;

		 		    if((find(paramList.begin(), paramList.end(), it1->first)) == paramList.end()){
		 		    	paramList.insert(paramList.end(), it1->first);
		 		    	paramCounter++;

		 		    }
		 		    particleCounter = 0;

		 		    for(auto it2 = subparticleCurrParamSets_.begin(); it2!=subparticleCurrParamSets_.end(); ++it2){//loops through subparticle IDs
		 		    	particleCounter++;
		 		      	for(auto it3 = it2->second.begin(); it3 != it2->second.end(); ++it3){//loops through model IDs
		 		    		if(it3->first==i){
		 		    			if (options.verbosity >=3){
		 		    				cout << "parameter for index " <<  counter  << " : "  << it3->second[counter] << endl;
		 		    			}
		 		    			alignedResults[it2->first][i][it1->first] = it3->second[counter];
		 		    			// Particle -> Model -> Parameter -> value
		 		    		}
		 		    	}

		 		    }
					counter++; //free param counter
		 	 }
			 cout << endl;
		 }


 		 cout << left << setw(16) << "Particle" << left << setw(16) << "Model";

		 for(int i = 0; i < paramList.size(); i++){
			 cout << left << setw(16) << paramList[i];

		 }
		 cout << endl;

		 int foundModel;

int foundParam;

//Raquel: this will print the output in the correct order, aligned
//Raquel TODO: save this printed output to the output file, and calculate overall fit, merging the fits for each parameter
		 for(auto ri1 = alignedResults.begin(); ri1 != alignedResults.end(); ++ri1){//loop through particles

			 for (auto ri2 = ri1->second.begin(); ri2 != ri1->second.end(); ++ri2){//loop through models
				 //str =
				 //str = ;
				 cout << "Model_";
				 cout << left << setw(10) << +ri2->first;

				 cout << "Particle_";
				 cout << left << setw(7) << ri1->first;

				 for(int i = 0; i < paramList.size(); i++){
					 foundParam = 0;
					 for(auto ri3 = ri2->second.begin(); ri3 != ri2->second.end(); ++ri3){//loop through parameters

						 if(paramList[i] == ri3->first){
							 cout << left << setw(16) << ri3->second;
							 foundParam = 1;
						 }

					 }
					 if(foundParam == 0){
						 cout << left << setw(16) << "NA";
					 }
				 }

				 cout << endl;

			 }

		 }

//Raquel: here ends the block of code to fiz the alignment problem with the parameter values