#include "mltaln.h"

#define DEBUG 0
#define IODEBUG 0
#define SCOREOUT 0



void arguments( int argc, char *argv[] )
{
    int c;

	inputfile = NULL;
	fftkeika = 0;
	pslocal = -1000.0;
	constraint = 0;
	nblosum = 62;
	fmodel = 0;
	calledByXced = 0;
	devide = 0;
	use_fft = 0;
	fftscore = 1;
	fftRepeatStop = 0;
	fftNoAnchStop = 0;
    weight = 3;
    utree = 1;
	tbutree = 1;
    refine = 0;
    check = 1;
    cut = 0.0;
    disp = 0;
    outgap = 1;
    alg = 'A';
    mix = 0;
	tbitr = 0;
	scmtd = 5;
	tbweight = 0;
	tbrweight = 3;
	checkC = 0;
	treemethod = 'x';
	contin = 0;
	scoremtx = 1;
	kobetsubunkatsu = 0;
	divpairscore = 0;
	dorp = NOTSPECIFIED;
	ppenalty = NOTSPECIFIED;
	ppenalty_OP = NOTSPECIFIED;
	ppenalty_ex = NOTSPECIFIED;
	ppenalty_EX = NOTSPECIFIED;
	poffset = NOTSPECIFIED;
	kimuraR = NOTSPECIFIED;
	pamN = NOTSPECIFIED;
	geta2 = GETA2;
	fftWinSize = NOTSPECIFIED;
	fftThreshold = NOTSPECIFIED;
	RNAppenalty = NOTSPECIFIED;
	RNApthr = NOTSPECIFIED;

    while( --argc > 0 && (*++argv)[0] == '-' )
	{
        while ( ( c = *++argv[0] ) )
		{
            switch( c )
            {
				case 'i':
					inputfile = *++argv;
					fprintf( stderr, "inputfile = %s\n", inputfile );
					--argc;
					goto nextoption;
				case 'o':
					RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
					--argc;
					goto nextoption;
				case 'f':
					ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
					--argc;
					goto nextoption;
				case 'g':
					ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
					--argc;
					goto nextoption;
				case 'O':
					ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
					--argc;
					goto nextoption;
				case 'E':
					ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
					--argc;
					goto nextoption;
				case 'h':
					poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
					--argc;
					goto nextoption;
				case 'k':
					kimuraR = atoi( *++argv );
//					fprintf( stderr, "kimuraR = %d\n", kimuraR );
					--argc;
					goto nextoption;
				case 'b':
					nblosum = atoi( *++argv );
					scoremtx = 1;
					fprintf( stderr, "blosum %d\n", nblosum );
					--argc;
					goto nextoption;
				case 'j':
					pamN = atoi( *++argv );
					scoremtx = 0;
					TMorJTT = JTT;
					fprintf( stderr, "jtt %d\n", pamN );
					--argc;
					goto nextoption;
				case 'm':
					pamN = atoi( *++argv );
					scoremtx = 0;
					TMorJTT = TM;
					fprintf( stderr, "TM %d\n", pamN );
					--argc;
					goto nextoption;
				case 'l':
					ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );
					pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);
//					fprintf( stderr, "ppslocal = %d\n", ppslocal );
//					fprintf( stderr, "pslocal = %d\n", pslocal );
					--argc;
					goto nextoption;
#if 1
				case 'a':
					fmodel = 1;
					break;
#endif
				case 'r':
					fmodel = -1;
					break;
				case 'D':
					dorp = 'd';
					break;
				case 'P':
					dorp = 'p';
					break;
#if 0
				case 'e':
					fftscore = 0;
					break;
				case 'O':
					fftNoAnchStop = 1;
					break;
				case 'R':
					fftRepeatStop = 1;
					break;
#endif
				case 'Q':
					calledByXced = 1;
					break;
				case 's':
					treemethod = 's';
					break;
				case 'x':
					disp = 1;
					break;
				case 'p':
					treemethod = 'p';
					break;
#if 0
				case 'a':
					alg = 'a';
					break;
#endif
				case 'S':
					alg = 'S';
					break;
				case 'L':
					alg = 'L';
					break;
				case 'M':
					alg = 'M';
					break;
				case 'R':
					alg = 'R';
					break;
				case 'N':
					alg = 'N';
					break;
				case 'A':
					alg = 'A';
					break;
				case 'V':
					alg = 'V';
					break;
				case 'C':
					alg = 'C';
					break;
				case 'F':
					use_fft = 1;
					break;
				case 'v':
					tbrweight = 3;
					break;
				case 'd':
					divpairscore = 1;
					break;
/* Modified 01/08/27, default: user tree */
				case 'J':
					tbutree = 0;
					break;
/* modification end. */
				case 'z':
					fftThreshold = atoi( *++argv );
					--argc; 
					goto nextoption;
				case 'w':
					fftWinSize = atoi( *++argv );
					--argc;
					goto nextoption;
				case 'Z':
					checkC = 1;
					break;
                default:
                    fprintf( stderr, "illegal option %c\n", c );
                    argc = 0;
                    break;
            }
		}
		nextoption:
			;
	}
    if( argc == 1 )
    {
        cut = atof( (*argv) );
        argc--;
    }
    if( argc != 0 ) 
    {
        fprintf( stderr, "options: Check source file !\n" );
        exit( 1 );
    }
	if( tbitr == 1 && outgap == 0 )
	{
		fprintf( stderr, "conflicting options : o, m or u\n" );
		exit( 1 );
	}
	if( alg == 'C' && outgap == 0 )
	{
		fprintf( stderr, "conflicting options : C, o\n" );
		exit( 1 );
	}
}

int countamino( char *s, int end )
{
	int val = 0;
	while( end-- )
		if( *s++ != '-' ) val++;
	return( val );
}


static void WriteOptions( FILE *fp )
{

	if( dorp == 'd' ) fprintf( fp, "DNA\n" );
	else
	{
		if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
		else if( scoremtx ==  1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
		else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
	}
    fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
    if( use_fft ) fprintf( fp, "FFT on\n" );

	fprintf( fp, "tree-base method\n" );
	if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
	else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
	if( tbitr || tbweight ) 
	{
		fprintf( fp, "iterate at each step\n" );
		if( tbitr && tbrweight == 0 ) fprintf( fp, "  unweighted\n" ); 
		if( tbitr && tbrweight == 3 ) fprintf( fp, "  reversely weighted\n" ); 
		if( tbweight ) fprintf( fp, "  weighted\n" ); 
		fprintf( fp, "\n" );
	}

   	 fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );

	if( alg == 'a' )
		fprintf( fp, "Algorithm A\n" );
	else if( alg == 'A' ) 
		fprintf( fp, "Algorithm A+\n" );
	else if( alg == 'S' ) 
		fprintf( fp, "Apgorithm S\n" );
	else if( alg == 'C' ) 
		fprintf( fp, "Apgorithm A+/C\n" );
	else
		fprintf( fp, "Unknown algorithm\n" );

	if( treemethod == 'x' )
		fprintf( fp, "Tree = UPGMA (3).\n" );
	else if( treemethod == 's' )
		fprintf( fp, "Tree = UPGMA (2).\n" );
	else if( treemethod == 'p' )
		fprintf( fp, "Tree = UPGMA (1).\n" );
	else
		fprintf( fp, "Unknown tree.\n" );

    if( use_fft )
    {
        fprintf( fp, "FFT on\n" );
        if( dorp == 'd' )
            fprintf( fp, "Basis : 4 nucleotides\n" );
        else
        {
            if( fftscore )
                fprintf( fp, "Basis : Polarity and Volume\n" );
            else
                fprintf( fp, "Basis : 20 amino acids\n" );
        }
        fprintf( fp, "Threshold   of anchors = %d%%\n", fftThreshold );
        fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
    }
	else
        fprintf( fp, "FFT off\n" );
	fflush( fp );
}
	 

int main( int argc, char *argv[] )
{
	static int  *nlen;	
	static char **name, **seq, **useq;
	static char **mseq1, **mseq2;
	static char **aseq;
	static char **bseq;
	static double *eff;
	int i;
	FILE *infp;
	char c;
	int alloclen;
	RNApair **pair1;
	RNApair **pair2;
	float **map;

	arguments( argc, argv );

	if( inputfile )
	{
		infp = fopen( inputfile, "r" );
		if( !infp )
		{
			fprintf( stderr, "Cannot open %s\n", inputfile );
			exit( 1 );
		}
	}
	else
		infp = stdin;

	getnumlen( infp );
	rewind( infp );

	if( njob > M )
	{
		fprintf( stderr, "The number of sequences must be < %d\n", M );
		fprintf( stderr, "Please try the splittbfast program for such large data.\n" );
		exit( 1 );
	}

    name = AllocateCharMtx( njob, B+1 );
    nlen = AllocateIntVec( njob ); 

	seq = AllocateCharMtx( njob, nlenmax*5+1 );
	useq = AllocateCharMtx( njob, nlenmax*5+1 );
	aseq = AllocateCharMtx( njob, nlenmax*5+1 );
	bseq = AllocateCharMtx( njob, nlenmax*5+1 );
	mseq1 = AllocateCharMtx( njob, 0 );
	mseq2 = AllocateCharMtx( njob, 0 );
	alloclen = nlenmax*5;

	pair1 = calloc( nlenmax*5+1, sizeof( RNApair *) );
	pair2 = calloc( nlenmax*5+1, sizeof( RNApair *) );
	map = AllocateFloatMtx( nlenmax+1, nlenmax );

	eff = AllocateDoubleVec( njob );

	readData_pointer( infp, name, nlen, seq );
	fclose( infp );

	for( i=0; i<njob; i++ ) strcpy( useq[i], seq[i] );

	constants( njob, seq );

#if 0
	fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
#endif

	initSignalSM();

	initFiles();

	WriteOptions( trap_g );

	c = seqcheck( seq );
	if( c )
	{
		fprintf( stderr, "Illeagal character %c\n", c );
		exit( 1 );
	}

//	writePre( njob, name, nlen, seq, 0 );

	for( i=0; i<njob; i++ ) eff[i] = 1.0;

//	for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );


	fprintf( stderr, "folding group1\n" );
//	rnalocal( seq, useq, eff, eff, njob, njob, alloclen, pair1 );
	rnaalifoldcall( seq, njob, pair1 );
	exit( 1 );

#if 0
	fprintf( stderr, "folding group1\n" );
	rnalocal( seq+1, useq+1, eff+1, eff+1, 1, 1, alloclen, pair2 );
	fprintf( stderr, "aligning 1 and 2, phase 1\n" );
	Lalignmm_hmout( seq, seq+1, eff, eff+1, 1, 1, alloclen, NULL, NULL, NULL, NULL, map );


#if 0
	lgth1 = strlen( seq[0] );
	for( i=0; i<lgth1; i++ )
	{
		fprintf( stderr, "\n" );
		if( pair1[i].pos == -1 ) continue;
		fprintf( stderr, "i=%d (%c):%d", i, seq[0][i], pair1[i].pos );
		if( map12[pair1[i].pos].pos == -1 ) continue;
		fprintf( stderr, "%c -> %c ", seq[0][pair1[i].pos], seq[1][map12[pair1[i].pos].pos] );
		if( pair2[map12[pair1[i].pos].pos].pos == -1 ) continue;
		fprintf( stderr, "%d:%d (%c)", map12[pair1[i].pos].pos, pair2[map12[pair1[i].pos].pos].pos, seq[1][pair2[map12[pair1[i].pos].pos].pos] );
	}
#endif


	exit( 1 );


	pairalign( name, nlen, bseq, aseq, mseq1, mseq2, eff, alloclen ); 
	fprintf( trap_g, "done.\n" );
#if DEBUG
	fprintf( stderr, "closing trap_g\n" );
#endif
	fclose( trap_g );

//	writePre( njob, name, nlen, aseq, !contin );
#if 0
	writeData( stdout, njob, name, nlen, aseq );
#endif
#if IODEBUG
	fprintf( stderr, "OSHIMAI\n" );
#endif
	SHOWVERSION;
	return( 0 );
#endif
}