+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-static char *whereispairalign;
-static char *laraparams;
-static char foldalignopt[1000];
-
-static void t2u( char *seq )
-{
- while( *seq )
- {
- if ( *seq == 'A' ) *seq = 'a';
- else if( *seq == 'a' ) *seq = 'a';
- else if( *seq == 'T' ) *seq = 'u';
- else if( *seq == 't' ) *seq = 'u';
- else if( *seq == 'U' ) *seq = 'u';
- else if( *seq == 'u' ) *seq = 'u';
- else if( *seq == 'G' ) *seq = 'g';
- else if( *seq == 'g' ) *seq = 'g';
- else if( *seq == 'C' ) *seq = 'c';
- else if( *seq == 'c' ) *seq = 'c';
- else *seq = 'n';
- seq++;
- }
-}
-
-static float recallpairfoldalign( char **mseq1, char **mseq2, int m1, int m2, int *of1pt, int *of2pt, int alloclen )
-{
- static FILE *fp = NULL;
- float value;
- char *aln1;
- char *aln2;
- int of1tmp, of2tmp;
-
- if( fp == NULL )
- {
- fp = fopen( "_foldalignout", "r" );
- if( fp == NULL )
- {
- fprintf( stderr, "Cannot open _foldalignout\n" );
- exit( 1 );
- }
- }
-
- aln1 = calloc( alloclen, sizeof( char ) );
- aln2 = calloc( alloclen, sizeof( char ) );
-
- readpairfoldalign( fp, *mseq1, *mseq2, aln1, aln2, m1, m2, &of1tmp, &of2tmp, alloclen );
-
- if( strstr( foldalignopt, "-global") )
- {
- fprintf( stderr, "Calling G__align11\n" );
- value = G__align11( mseq1, mseq2, alloclen );
- *of1pt = 0;
- *of2pt = 0;
- }
- else
- {
- fprintf( stderr, "Calling L__align11\n" );
- value = L__align11( mseq1, mseq2, alloclen, of1pt, of2pt );
- }
-
-// value = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
-
- if( aln1[0] == 0 )
- {
- fprintf( stderr, "FOLDALIGN returned no alignment between %d and %d. Sequence alignment is used instead.\n", m1+1, m2+1 );
- }
- else
- {
- strcpy( *mseq1, aln1 );
- strcpy( *mseq2, aln2 );
- *of1pt = of1tmp;
- *of2pt = of2tmp;
- }
-
-// value = naivepairscore11( *mseq1, *mseq2, penalty ); // v6.511 ha kore wo tsukau, global nomi dakara.
-
-// fclose( fp ); // saigo dake yatta houga yoi.
-
-// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
-// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
-
-
- free( aln1 );
- free( aln2 );
-
- return( value );
-}
-
-static void callfoldalign( int nseq, char **mseq )
-{
- FILE *fp;
- int i;
- int res;
- static char com[10000];
-
- for( i=0; i<nseq; i++ )
- t2u( mseq[i] );
-
- fp = fopen( "_foldalignin", "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _foldalignin\n" );
- exit( 1 );
- }
- for( i=0; i<nseq; i++ )
- {
- fprintf( fp, ">%d\n", i+1 );
- fprintf( fp, "%s\n", mseq[i] );
- }
- fclose( fp );
-
- sprintf( com, "env PATH=%s foldalign210 %s _foldalignin > _foldalignout ", whereispairalign, foldalignopt );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in foldalign\n" );
- exit( 1 );
- }
-
-}
-
-static void calllara( int nseq, char **mseq, char *laraarg )
-{
- FILE *fp;
- int i;
- int res;
- static char com[10000];
-
- for( i=0; i<nseq; i++ )
-
- fp = fopen( "_larain", "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _larain\n" );
- exit( 1 );
- }
- for( i=0; i<nseq; i++ )
- {
- fprintf( fp, ">%d\n", i+1 );
- fprintf( fp, "%s\n", mseq[i] );
- }
- fclose( fp );
-
-
-// fprintf( stderr, "calling LaRA\n" );
- sprintf( com, "env PATH=%s:/bin:/usr/bin mafft_lara -i _larain -w _laraout -o _lara.params %s", whereispairalign, laraarg );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in lara\n" );
- exit( 1 );
- }
-}
-
-static float recalllara( char **mseq1, char **mseq2, int alloclen )
-{
- static FILE *fp = NULL;
- static char *ungap1;
- static char *ungap2;
- static char *ori1;
- static char *ori2;
- int res;
- static char com[10000];
- float value;
-
-
- if( fp == NULL )
- {
- fp = fopen( "_laraout", "r" );
- if( fp == NULL )
- {
- fprintf( stderr, "Cannot open _laraout\n" );
- exit( 1 );
- }
- ungap1 = AllocateCharVec( alloclen );
- ungap2 = AllocateCharVec( alloclen );
- ori1 = AllocateCharVec( alloclen );
- ori2 = AllocateCharVec( alloclen );
- }
-
-
- strcpy( ori1, *mseq1 );
- strcpy( ori2, *mseq2 );
-
- fgets( com, 999, fp );
- myfgets( com, 9999, fp );
- strcpy( *mseq1, com );
- myfgets( com, 9999, fp );
- strcpy( *mseq2, com );
-
- gappick0( ungap1, *mseq1 );
- gappick0( ungap2, *mseq2 );
- t2u( ungap1 );
- t2u( ungap2 );
-
- if( strcmp( ungap1, ori1 ) || strcmp( ungap2, ori2 ) )
- {
- fprintf( stderr, "SEQUENCE CHANGED!!\n" );
- fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
- fprintf( stderr, "ungap1 = %s\n", ungap1 );
- fprintf( stderr, "ori1 = %s\n", ori1 );
- fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
- fprintf( stderr, "ungap2 = %s\n", ungap2 );
- fprintf( stderr, "ori2 = %s\n", ori2 );
- exit( 1 );
- }
-
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
-
-// fclose( fp ); // saigo dake yatta houga yoi.
-
- return( value );
-}
-
-static float callmxscarna( char **mseq1, char **mseq2, int alloclen )
-{
- FILE *fp;
- int res;
- static char com[10000];
- float value;
-
-
- t2u( *mseq1 );
- t2u( *mseq2 );
- fp = fopen( "_mxscarnain", "w" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _mxscarnain\n" );
- exit( 1 );
- }
- fprintf( fp, ">1\n" );
- fprintf( fp, "%s\n", *mseq1 );
- fprintf( fp, ">2\n" );
- fprintf( fp, "%s\n", *mseq2 );
- fclose( fp );
-
- sprintf( com, "env PATH=%s mxscarna _mxscarnain > _mxscarnaout 2>/dev/null", whereispairalign );
- res = system( com );
- if( res )
- {
- fprintf( stderr, "Error in mxscarna\n" );
- exit( 1 );
- }
-
- fp = fopen( "_mxscarnaout", "r" );
- if( !fp )
- {
- fprintf( stderr, "Cannot open _mxscarnaout\n" );
- exit( 1 );
- }
-
- fgets( com, 999, fp );
- load1SeqWithoutName_new( fp, *mseq1 );
- fgets( com, 999, fp );
- load1SeqWithoutName_new( fp, *mseq2 );
-
- fclose( fp );
-
-// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
-// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
-
- value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
-
- return( value );
-}
-
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- foldalignopt[0] = 0;
- laraparams = NULL;
- 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 '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;
- case 'd':
- whereispairalign = *++argv;
- fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
- --argc;
- goto nextoption;
- case 'p':
- laraparams = *++argv;
- fprintf( stderr, "laraparams = %s\n", laraparams );
- --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;
- case 'e':
- fftscore = 0;
- break;
-#if 0
- case 'O':
- fftNoAnchStop = 1;
- break;
-#endif
- case 'Q':
- calledByXced = 1;
- break;
- case 'x':
- disp = 1;
- break;
-#if 0
- case 'a':
- alg = 'a';
- break;
-#endif
- case 'S':
- alg = 'S';
- break;
- case 'L':
- alg = 'L';
- break;
- case 's':
- alg = 's';
- break;
- case 'B':
- alg = 'B';
- break;
- case 'T':
- alg = 'T';
- break;
- case 'H':
- alg = 'H';
- 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 'y':
- divpairscore = 1;
- break;
-/* Modified 01/08/27, default: user tree */
- case 'J':
- tbutree = 0;
- break;
-/* modification end. */
- case 'o':
-// foldalignopt = *++argv;
- strcat( foldalignopt, " " );
- strcat( foldalignopt, *++argv );
- fprintf( stderr, "foldalignopt = %s\n", foldalignopt );
- --argc;
- goto nextoption;
- 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 pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, int alloclen )
-{
- int i, j, ilim;
- int clus1, clus2;
- int off1, off2;
- float pscore = 0.0; // by D.Mathog
- static char *indication1, *indication2;
- FILE *hat2p, *hat3p;
- static double **distancemtx;
- static double *effarr1 = NULL;
- static double *effarr2 = NULL;
- char *pt;
- char *hat2file = "hat2";
- LocalHom **localhomtable, *tmpptr;
- static char **pair;
- int intdum;
- double bunbo;
-
- localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
- for( i=0; i<njob; i++)
- {
- localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
- for( j=0; j<njob; j++)
- {
- localhomtable[i][j].start1 = -1;
- localhomtable[i][j].end1 = -1;
- localhomtable[i][j].start2 = -1;
- localhomtable[i][j].end2 = -1;
- localhomtable[i][j].opt = -1.0;
- localhomtable[i][j].next = NULL;
- localhomtable[i][j].nokori = 0;
- }
- }
-
- if( effarr1 == NULL )
- {
- distancemtx = AllocateDoubleMtx( njob, njob );
- effarr1 = AllocateDoubleVec( njob );
- effarr2 = AllocateDoubleVec( njob );
- indication1 = AllocateCharVec( 150 );
- indication2 = AllocateCharVec( 150 );
-#if 0
-#else
- pair = AllocateCharMtx( njob, njob );
-#endif
- }
-
-#if 0
- fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
-#endif
-
-#if 0
- for( i=0; i<njob; i++ )
- fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
-#endif
-
-
-// writePre( njob, name, nlen, aseq, 0 );
-
- for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
- for( i=0; i<njob; i++ ) pair[i][i] = 1;
-
- if( alg == 'H' )
- {
- fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt );
- callfoldalign( njob, seq );
- fprintf( stderr, "done.\n" );
- }
- if( alg == 'B' )
- {
- fprintf( stderr, "Calling LARA\n" );
- calllara( njob, seq, "" );
- fprintf( stderr, "done.\n" );
- }
- if( alg == 'T' )
- {
- fprintf( stderr, "Calling SLARA\n" );
- calllara( njob, seq, "-s" );
- fprintf( stderr, "done.\n" );
- }
-
- ilim = njob - 1;
- for( i=0; i<ilim; i++ )
- {
- fprintf( stderr, "% 5d / %d\r", i, njob );
- for( j=i+1; j<njob; j++ )
- {
-
- if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
- {
- distancemtx[i][j] = pscore;
- continue;
- }
-
- strcpy( aseq[i], seq[i] );
- strcpy( aseq[j], seq[j] );
- clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
- clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
- // fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
- // fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
-
-#if 0
- fprintf( stderr, "group1 = %.66s", indication1 );
- fprintf( stderr, "\n" );
- fprintf( stderr, "group2 = %.66s", indication2 );
- fprintf( stderr, "\n" );
-#endif
- // for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
-
-#if 1
- if( use_fft )
- {
- pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
- off1 = off2 = 0;
- }
- else
-#endif
- {
- switch( alg )
- {
- case( 'a' ):
- pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
- off1 = off2 = 0;
- break;
- case( 'A' ):
- pscore = G__align11( mseq1, mseq2, alloclen, NULL, 0, NULL );
- off1 = off2 = 0;
- break;
-#if 0
- case( 'V' ):
- pscore = VAalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
- fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
- break;
- case( 'S' ):
- fprintf( stderr, "aligning %d-%d\n", i, j );
- pscore = suboptalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
- fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
- break;
-#endif
- case( 'N' ):
- pscore = genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
-// fprintf( stderr, "pscore = %f\n", pscore );
- break;
- case( 'L' ):
- pscore = L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
-// fprintf( stderr, "pscore (1) = %f\n", pscore );
-// pscore = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
-// fprintf( stderr, "pscore (2) = %f\n\n", pscore );
- break;
- case( 'H' ):
- pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
- break;
- case( 'B' ):
- case( 'T' ):
- pscore = recalllara( mseq1, mseq2, alloclen );
- off1 = off2 = 0;
-// fprintf( stderr, "lara, pscore = %f\n", pscore );
- break;
- case( 's' ):
- pscore = callmxscarna( mseq1, mseq2, alloclen );
- off1 = off2 = 0;
-// fprintf( stderr, "scarna, pscore = %f\n", pscore );
- break;
- case( 'M' ):
-// pscore = MSalign11( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
- pscore = MSalign11( mseq1, mseq2, alloclen );
-// fprintf( stderr, "pscore = %f\n", pscore );
- break;
- ErrorExit( "ERROR IN SOURCE FILE" );
- }
- }
- distancemtx[i][j] = pscore;
-#if SCOREOUT
- fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
-#endif
-// fprintf( stderr, "pslocal = %d\n", pslocal );
-// offset = makelocal( *mseq1, *mseq2, pslocal );
-#if 0
- fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
- fprintf( stderr, ">%d\n%s\n>%d\n%s\n>\n", i, mseq1[0], j, mseq2[0] );
-#endif
-
-// putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, countamino( *mseq1, off1 ), countamino( *mseq2, off2 ), pscore, strlen( mseq1[0] ) );
-// fprintf( stderr, "pscore = %f\n", pscore );
- if( alg == 'H' )
-// if( alg == 'H' || alg == 's' || alg == 'B' ) // next version
- putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
- else if( alg != 'S' && alg != 'V' )
- putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
- }
- }
- for( i=0; i<njob; i++ )
- {
- pscore = 0.0;
- for( pt=seq[i]; *pt; pt++ )
- pscore += amino_dis[(int)*pt][(int)*pt];
- distancemtx[i][i] = pscore;
-
- }
-
- ilim = njob-1;
- for( i=0; i<ilim; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
- if( bunbo == 0.0 )
- distancemtx[i][j] = 2.0;
- else
- distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
- }
- }
-
- hat2p = fopen( hat2file, "w" );
- if( !hat2p ) ErrorExit( "Cannot open hat2." );
- WriteHat2( hat2p, njob, name, distancemtx );
- fclose( hat2p );
-
- fprintf( stderr, "##### writing hat3\n" );
- hat3p = fopen( "hat3", "w" );
- if( !hat3p ) ErrorExit( "Cannot open hat3." );
- ilim = njob-1;
- for( i=0; i<ilim; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
- {
- if( tmpptr->opt == -1.0 ) continue;
- fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
- }
- }
- }
- fclose( hat3p );
-#if DEBUG
- fprintf( stderr, "calling FreeLocalHomTable\n" );
-#endif
- FreeLocalHomTable( localhomtable, njob );
-#if DEBUG
- fprintf( stderr, "done. FreeLocalHomTable\n" );
-#endif
-}
-
-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( 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[M];
- static char name[M][B], **seq;
- static char **mseq1, **mseq2;
- static char **aseq;
- static char **bseq;
- static double *eff;
- int i;
- FILE *infp;
- char c;
- int alloclen;
-
- 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 < 2 )
- {
- fprintf( stderr, "At least 2 sequences should be input!\n"
- "Only %d sequence found.\n", njob );
- exit( 1 );
- }
- 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 );
- }
-
- seq = AllocateCharMtx( njob, nlenmax*9+1 );
- aseq = AllocateCharMtx( njob, nlenmax*9+1 );
- bseq = AllocateCharMtx( njob, nlenmax*9+1 );
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
- alloclen = nlenmax*9;
-
- eff = AllocateDoubleVec( njob );
-
-#if 0
- Read( name, nlen, seq );
-#else
- readData( infp, name, nlen, seq );
-#endif
- fclose( infp );
-
- 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, "Illegal 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] );
-
- 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 );
-}
git://source.jalview.org / jabaws.git / blobdiff