#include "GDB.h"   

void printSyntax()
{
	cerr << "Convert MFR fragment table to ROSETTA fragments: " << endl;
	cerr << "File Name Settings: " << endl;	
	cerr << " -mfr                  MFR table." << endl;
	cerr << " -segLength            fragment length." << endl;
	cerr << " -angleSSDir           direcotory for the idelized angles and secondary structure table files for proteins in MFR database." << endl;	
	cerr << "Examples:" << endl;
	cerr << "   mfr2rosetta -mfr mfr.tab -angleSSDir ./ANGLESS -segLength 9" << endl ;
	cerr << "       Convert 9-residues MFR fragments with filename 'mfr.tab' to ROSETTA format, " << endl;
	cerr << "       the converted ROSETTA fragments will be printed to the screen" << endl ;

	exit(0);
}

char * ftoa( float n, char *buff, char f='g', int prec=6 )
{
    if ( !(f=='f' || f=='F' || f=='e' || f=='E' || f=='g' || f=='G') ) {
		f = 'f';
    }
    char format[20];
    char *fs = format;				// generate format string
    *fs++ = '%';					//   "%.<prec>l<f>"
    if ( prec >= 0 ) {
		if ( prec > 99 )			// buf big enough for precision?
			prec = 99;
		*fs++ = '.';
		if ( prec >= 10 ) {
			*fs++ = prec / 10 + '0';
			*fs++ = prec % 10 + '0';
		} else {
		    *fs++ = prec + '0';
		}
    }
    *fs++ = 'l';
    *fs++ = f;
    *fs = '\0';
    sprintf( buff, format, n );

    return buff;
}

char * itoa( int n, char *buff, int base=10 )
{
	sprintf(buff, "%d", n);
	return buff;
}



char * tolower( string str, char *buff )
{
	int len = str.length();
	
	for(int i = 0; i< len; i++)
	{
		char c = str[i];
		if( c >='A' && c <= 'Z')
			buff[i] = c+32;
		else buff[i] = c;
	}
	buff[len] = '\0';	
	return buff;
}


int main( int argc, char ** argv )
{
	string argList, slash_char;

	if(argc == 1) {
	 	printSyntax(); 
	}

	for(int i = 1; i < argc; i++){
		argList+= (argv[i]);
		argList+= (" ");
	}

	vector<string> fields = GDB::split("-", argList);
	GDB db;
	int len = 0;

	string temp = getenv( "PATH" );
	if(temp.find("/") != string::npos ) slash_char = "/"; // unix
	else if(temp.find("\\") != string::npos ) slash_char = "\\"; // Windows 

	string angleSSDir;
	if (getenv( "ANGLESS_DIR" ) == NULL )
		angleSSDir = "./ANGLESS";
	else
		angleSSDir = getenv( "ANGLESS_DIR" );

	for(int i = 0; i < fields.size(); i++){
		vector<string> temp;
		int pos = fields[i].find_first_of(' ');
		temp.push_back( fields[i].substr(0,pos) );
		temp.push_back( fields[i].substr(pos+1,fields[i].length()-pos-1 ));
		string arg = GDB::simplifyWhiteSpace(temp[1]);

		if (temp[0] == "mfr" )
			db.loadGDB(arg);
		else if(temp[0] == "angleSSDir" )
			angleSSDir = arg;
		else if(temp[0] == "segLength" )
			len = atoi( arg.c_str() );
		else printSyntax();  
	}

	if( len == 0 ) {
		cerr << "Fragment length '-segLength' need to be specified" << endl;
		exit(0);
	}

	char buf[100];

	map< int, map<string, string> >::iterator it, itA;
	int tag = 2, tag_miss = 4;
	float zero = 0.0;
	string ss = "L";

	map<string, int> name_his, cnt_his;

	for ( it = db.Entries.begin(); it != db.Entries.end(); it++ )
	{
		string PDB_NAME = it->second["PDB_NAME"];
		
		name_his[PDB_NAME]++;
		cnt_his[ it->second["D_RES1"] ]++;
	}
	
	map<string, int>::iterator itN;

	int res0 = atoi( (cnt_his.begin()->first).c_str() );
	int resN = res0;
	for ( itN = cnt_his.begin(); itN != cnt_his.end(); itN++ )
	{
		int resID = atoi( (itN->first).c_str() );
		if( resID > resN ) resN = resID;
	}

	cerr << "Checking MFR Fragments Candidates ... " << endl;
	bool checked = true;
	if( res0 != 1) {
		cerr << "\t***ERROR:: Fragments not start from residue 1 " << endl;
		checked = false;
	}
	for( int i = res0; i <= resN; i++)
	{
		string temp = itoa(i, buf);
		if( cnt_his[temp] == 0 ) { 
			cerr << "\tERROR:: No fragment candidates for target fragment " << i << "-" << i+len-2 << endl;
			checked = false;
		}
		else if( cnt_his[ temp ] == 200 )
			cerr << "\t" << cnt_his[ temp ] << " fragments candidates for target fragment " << i << "-" << i+len-1 << endl;
		else cerr << "\t" << cnt_his[ temp ] << " fragments candidates for target fragment " << i << "-" << i+len-1 << " *** \n";
	}
	if(!checked) { 
		cerr << "ERRORS found in MFR fragment candidates, exit ... " << endl;
		exit(0);
	}

	map<string, map<int, string> > pdb_phi, pdb_psi, pdb_omega;
	map<string, map<int, string> > pdb_ss;
	
	cerr << "Collecting structural information ... " ;
	for ( itN = name_his.begin(); itN != name_his.end(); itN++ )
	{
		string PDB_NAME = itN->first;
		
		string fname0 = angleSSDir+slash_char+PDB_NAME.substr(0,5)+".tab"; //

		ifstream iangle_file(fname0.c_str());
		if( iangle_file.is_open() ) {
			GDB angle_tab;
			angle_tab.loadGDB(fname0);
			
			for ( it = angle_tab.Entries.begin(); it != angle_tab.Entries.end(); it++ )
			{
				int resID = atoi(it->second["RESID"].c_str());
				pdb_phi[PDB_NAME][resID] = it->second["PHI"];
				pdb_psi[PDB_NAME][resID] = it->second["PSI"];
				pdb_omega[PDB_NAME][resID] = it->second["OMEGA"];
				pdb_ss[PDB_NAME][resID] = it->second["SS"];
			}
		}
		else {
			cerr << "Angle Table " << fname0 << " not Found! Exit... \n";
			exit(0);
		}
		
	}
	cerr << "\t Done (" << name_his.size() << ")! \nCreating Rosetta fragments ..." ;
	
	for ( it = db.Entries.begin(); it != db.Entries.end(); it++ )
	{
		string PDB_NAME = it->second["PDB_NAME"];
		string temp0 = PDB_NAME.substr(0,4);
		string PDB4 = tolower(temp0, buf);
		
		string CHAIN = PDB_NAME.substr(4,1);
		if(CHAIN == "0") CHAIN = "_";
		
		string SEQ = it->second["SEQ"];
		
		int resID_1 = atoi(it->second["RES1"].c_str());
		
		int RANK = atoi(it->second["RANK"].c_str());
		int INDEX = atoi(it->second["D_RES1"].c_str());
				
		if( RANK == 1  ) // print a title for each set of fragments
			printf(" position:          %3d neighbors:           %3d\n\n", INDEX, cnt_his[ it->second["D_RES1"] ]);

		for( int i = 1; i <= len; i++)
		{
			string sequ = SEQ.substr(i-1,1);
			printf(" %4s %1s %5d %1s %1s%9s%9s%9s%9.3f%9.3f %9.3f%2d %9.3f P%3d F%3d\n",PDB4.c_str(),CHAIN.c_str(),
				resID_1+i-1,sequ.c_str(), pdb_ss[PDB_NAME][resID_1+i-1].c_str(), pdb_phi[PDB_NAME][resID_1+i-1].c_str(), 
				pdb_psi[PDB_NAME][resID_1+i-1].c_str(),pdb_omega[PDB_NAME][resID_1+i-1].c_str(),
				zero,zero,zero,tag,zero,INDEX,RANK);
		}
		cout << endl;

		continue;
	}
	
	cerr << "\tDone! \n" ;
}