utility.cc

#include "defs.h"
using namespace std;

std::string category;
std::string RUNPATH;

std::string currentDateTime()
{
	time_t now = time(0);
	struct tm  tstruct;
    	char buf[80];
    	tstruct = *localtime(&now);
    	strftime(buf, sizeof(buf), "%Y-%m-%d.%X", &tstruct);

    	return buf;
	
}

//modulename, option, cbp, ibp, char XY, valOption ,val mean stdev param1 param2
void fileLog(std::string moduleName, std::string opt,std::string cbp_opt, std::string ibp_opt, std::string xy_opt, std::string cbp, std::string ibp, std::string xy,std::string valOption,float val,float mean,float stdev,float param1,float param2,int mc)
{
	logfile << "[" << currentDateTime() << "]" << ": " << "<"<<moduleName<<"> " << "Options:"<<opt<<" "<< cbp_opt <<" "<< ibp_opt << " " << xy_opt <<" cbp:"<<cbp<<"  ibp:"<< ibp <<"  xy:"<<xy<<"  valOption:"<<valOption<<"  val:"<<val<<"  mean:"<<mean<<"  stdev:"<<stdev<<"  ub:"<<param1<<"  lb:"<<param2<<"   #mod="<< mc <<"\n";
	
}

void fileLog(std::string query)
{
  logfile << "[" << currentDateTime() << "]" << ": " << query <<"\n";  	  
}

void undoModule()
{
  //int21
  for(int i=0; i<LINES_INT21; i++)
    {
      for(int j=0; j<COLS_INT21; j++)
	{
	  int21[i][j] = int21_ORIG[i][j];
	}
    }
  //int22
  for(int i=0; i<LINES_INT22; i++)
    {
      for(int j=0; j<COLS_INT22; j++)
	{
	  int22[i][j] = int22_ORIG[i][j];
	}
    }
  //dangle
  for(int i=0; i<LINES_DANGLE; i++)
    {
      for(int j=0; j<COLS_DANGLE; j++)
	{
	  dangle[i][j] = dangle_ORIG[i][j];
	}
    }
  //int21
  for(int i=0; i<LINES_INT11; i++)
    {
      for(int j=0; j<COLS_INT11; j++)
	{
	  int11[i][j] = int11_ORIG[i][j];
	}
    }
  //loop
  for(int i=0; i<LINES_LOOP; i++)
    {
      for(int j=0; j<COLS_LOOP; j++)
	{
	  loop[i][j] = loop_ORIG[i][j];
	}
    }	
  //stack
  for(int i=0; i<LINES_STACK; i++)
    {
      for(int j=0; j<COLS_STACK; j++)
	{
	  stack[i][j] = stack_ORIG[i][j];
	}
    }
  //tloop
  for(int i=0; i<LINES_TLOOP; i++)
    {
      tloop[i] = tloop_ORIG[i];
    }
  //tstackh
  for(int i=0; i<LINES_TSTACKH; i++)
    {
      for(int j=0; j<COLS_TSTACKH; j++)
	{
	  tstackh[i][j] = tstackh_ORIG[i][j];
	}
    }
  //tstacki
  for(int i=0; i<LINES_TSTACKI; i++)
    {
      for(int j=0; j<COLS_TSTACKI; j++)
	{
	  tstacki[i][j] = tstacki_ORIG[i][j];
	}
    }
  fileLog("UNDO OPERATION");
  cout<<"\n>>Latest Query Undone!";
  return;
}

string getCurrentWorkingDir()
{
  char cwd[1000];
  string retval="";
  if(getcwd(cwd, sizeof(cwd)) == NULL)
    return retval;
  else
    retval = cwd;
  
  return retval;
}

string findRunPath()
{
  char *val;
  val = getenv("GTMODIFYRUNPATH");
  string retval = "";
  if(val != NULL)
    retval = val;
  return retval;
}

void computeFunction()
{
  //implement integration with gtfold
  string retval = findRunPath();	
  if(retval == "")
    {
      cout<<"\n>>Environment variable GTMODIFYRUNPATH not set";
      return;
    }
  
  //saving arrays to default temp dir which will be used to feed parameter values to gtfold
  saveArraysToPath(CURRENT_WORKING_DIR+"/temp");	 
  
  //making the runpath and integrating with gtfold
  string gtfoldFileName;
  cout<<"\n>>Enter File Name: ";
  cin >> gtfoldFileName;
  RUNPATH = retval+"/gtmfe "+"-p "+ CURRENT_WORKING_DIR +"/temp " +"./"+gtfoldFileName;
  //cout<<"\n------"<<RUNPATH;
  system(RUNPATH.c_str());
  
  return;
}

void readCategory()
{
  cout<< ">>Categories:\n>>(length) : modify hairpin/bulge/internal energies based on length of loop\n>>(misc) : modify tetraloop and other miscellaneous energies\n>>(internal) : modify 1x1 2x1 2x2 internal loop energies\n>>(stack) : modify stack energies\n>>(terminal) : modify terminal mismatch energies for hairpin and internal loops\n>>(dangle) : modify dangling energies\n\n";
  cout<<">>Enter category to Modify: ";
  cin >> category;
  
  if (category == "length")
    {
      lengthBasedModule();
      return;
    }
  
  else if (category == "misc")
    {
      miscModule();
      return;
    }
  
  else if (category == "dangle")
    {
      dangleModule();
      return;
    }
  
  else if(category == "stack")
    {
      stackModule();
      return;
    }
  
  else if(category == "terminal")
    {
      terminalModule();
      return;
    }
  
  if(category == "internal")
    {
      internalModule();
      return;
    }
  
  else if (category == "exit")
    {
      exitFunction();
    }
  
  else
    {
      cout<<">>Wrong Input Format\n";
      return;
    }
  
}

void saveModule()
{
  string savePath;
  cout<<"\n>>Enter Full Path where you wish to save: ";
  cin >> savePath;
  
  if(savePath == "0")
    return;
  
  if(saveArraysToPath(savePath))
    {
      cout << ">>Files saved to :" << savePath << "\n";
      fileLog("SAVE OPERATION to : "+savePath);
    }
  else
    cout << "ERROR Saving to :" << savePath << "\n";
  
}

int saveArraysToPath(string savePath)
{
	
	//try to make dir if not exists
  string makeTheDir = "mkdir "+ savePath;
  system(makeTheDir.c_str());
  
  string fileSavePath;
  FILE *fp;
  
  //save int22
  fileSavePath = savePath+"/int22.DAT";
  fp = fopen(fileSavePath.c_str(),"w");
  for(int i=0; i<LINES_INT22; i++)
    {
      for(int j=0; j<COLS_INT22; j++)
	{	
	  fprintf(fp, "%f  ",int22[i][j]);
	}
      fprintf(fp,"\n");
    }
  fclose(fp);
  
  //save int21
  fileSavePath = savePath+"/int21.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_INT21; i++)
    {
      for(int j=0; j<COLS_INT21; j++)
	{
	  fprintf(fp, "%f\t",int21[i][j]);
	}
      fprintf(fp, "\n");
    }
  fclose(fp);
  
  //save dangle
  fileSavePath = savePath +"/dangle.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_DANGLE; i++)
    {
      for(int j=0; j<COLS_DANGLE; j++)
	{
	  fprintf(fp,"%f \t",dangle[i][j]);
	}
      fprintf(fp,"\n");
    }
  fclose(fp);
  
  //save int11
  fileSavePath = savePath +"/int11.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_INT11; i++)
    {
      for(int j=0; j<COLS_INT11; j++)
	{
	  fprintf(fp, "%f\t",int11[i][j]);
	}
      fprintf(fp, "\n");
    }
  fclose(fp);
  
  
  //save loop
  fileSavePath = savePath +"/loop.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_LOOP; i++)
    {
      for(int j=0; j<COLS_LOOP; j++)
	{
	  if(j == 0)
	    fprintf(fp, "%d\t", (i+1));
	  else
	    //cout<<"---------------- "<<loop[i][j]<<"\n";
	    fprintf(fp, "%f\t",loop[i][j]);
	  //fprintf(fp, "Hello\t");
	}
      fprintf(fp, "\n");
    }
  fclose(fp);
  
  //save stack
  fileSavePath = savePath +"/stack.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_STACK; i++)
    {
      for(int j=0; j<COLS_STACK; j++)
	{
	  fprintf(fp, "%f\t",stack[i][j]);
	}
      fprintf(fp, "\n");
    }
  fclose(fp);
  
  
  //save tloop has string values as well
  fileSavePath = savePath + "/tloop.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_TLOOP; i++)
    {
      fprintf(fp,"%s\t%f",stringTloop[i].c_str(), tloop[i]);
      fprintf(fp, "\n");
    }
  fclose(fp);
  
  //save tstackh
  fileSavePath = savePath +"/tstackh.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_TSTACKH; i++)
    {
      for(int j=0; j<COLS_TSTACKH; j++)
	{
	  fprintf(fp, "%f\t",tstackh[i][j]);
	}
      fprintf(fp, "\n");
    }
  fclose(fp);
  
  
  //save tstacki
  fileSavePath = savePath +"/tstacki.DAT";
  fp = fopen(fileSavePath.c_str(), "w");
  for(int i=0; i<LINES_TSTACKI; i++)
    {
      for(int j=0; j<COLS_TSTACKI; j++)
	{
	  fprintf(fp, "%f\t",tstacki[i][j]);
	}
      fprintf(fp, "\n");
    }
  fclose(fp);
  
  //copy miscloop.DAT, tstacke.DAT and tstackm.DAT to savePath
  string copyCommand;
  
  //copy miscloop.DAT
  copyCommand = "cp miscloop.DAT "+savePath; 
  system(copyCommand.c_str());
  
  //copy tstacke.DAT
  copyCommand = "cp tstacke.DAT "+savePath; 
  system(copyCommand.c_str());
  
  //copy tstackm.DAT
  copyCommand = "cp tstackm.DAT "+savePath; 
  system(copyCommand.c_str());
  
  return 1;
}

void loadModule()
{
	string loadPath;
	cout<<"\n>>Enter the full Path to Load Data files: ";
	cin >> loadPath;
	if(loadPath == "0")
		return;
	if(loadArraysFromPath(loadPath))
	{
		cout<< ">>Files loaded from : "<< loadPath <<"\n";
		fileLog("LOAD OPERATION to : "+loadPath);
	}
	else
		cout << "ERROR Loading from : "<< loadPath <<"\n";
}

int loadArraysFromPath(string loadPath)
{
	//implement function here
	
	string pathInt22 = loadPath+"/int22.DAT";
	string pathInt21 = loadPath+"/int21.DAT";
	string pathDangle = loadPath+"/dangle.DAT";
	string pathInt11 = loadPath+"/int11.DAT";
	string pathLoop = loadPath+"/loop.DAT";
	string pathStack = loadPath+"/stack.DAT";
	string pathTloop = loadPath+"/tloop.DAT";
	string pathTstackh = loadPath+"/tstackh.DAT";
	string pathTstacki = loadPath+"/tstacki.DAT";

	loadInt22(pathInt22);
	loadInt21(pathInt21);	
	loadDangle(pathDangle);
	loadInt11(pathInt11);
	loadLoop(pathLoop);
	loadStack(pathStack);	
	loadTloop(pathTloop);
	loadTstackh(pathTstackh);
	loadTstacki(pathTstacki);

	return 1;
}

void exitFunction()
{
	logfile << "\n-------------------- SESSION END ---------------------\n";
	logfile.close();	
	exit(0);
}