+++ /dev/null
-#include "mltaln.h"
-
-static int upperCase = 0;
-
-#define DEBUG 0
-#define IODEBUG 0
-
-char creverse( char f )
-{
- static char *table = NULL;
- if( table == NULL )
- {
- table = AllocateCharVec(0x80);
- table['a'] = 't';
- table['c'] = 'g';
- table['g'] = 'c';
- table['t'] = 'a';
- table['u'] = 'a';
- table['m'] = 'k';
- table['r'] = 'y';
- table['w'] = 'w';
- table['s'] = 's';
- table['y'] = 'r';
- table['k'] = 'm';
- table['v'] = 'b';
- table['h'] = 'd';
- table['d'] = 'h';
- table['b'] = 'v';
- table['n'] = 'n';
- table['-'] = '-';
- table['.'] = '.';
- table['*'] = '*';
- }
- return( table[(int)f] );
-}
-
-void sreverse( char *r, char *s )
-{
- r += strlen( s );
- *r-- = 0;
- while( *s )
- *r-- = creverse( *s++ );
-// *r-- = ( *s++ );
-}
-
-void gappick_samestring( char *seq )
-{
- char *aseq = seq;
-
- for( ; *seq != 0; seq++ )
- {
- if( *seq != '-' )
- *aseq++ = *seq;
- }
- *aseq = 0;
-}
-
-#if 0
-
-static int addlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip )
-{
- int pos1, pos2, start1, start2, end1, end2;
- char *pt1, *pt2;
- int iscore;
- int isumscore;
- int sumoverlap;
- LocalHom *tmppt;
- int st;
- int nlocalhom = 0;
- pt1 = al1; pt2 = al2;
- pos1 = off1; pos2 = off2;
-
- isumscore = 0;
- sumoverlap = 0;
-
-#if 0
- fprintf( stderr, "nlocalhom = %d in addlocalhom\n", nlocalhom );
- fprintf( stderr, "al1 = %s, al2 = %s\n", al1, al2 );
- fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
- fprintf( stderr, "localhopt = %p, skip = %d\n", localhompt, skip );
- fprintf( stderr, "pt1 = \n%s\n, pt2 = \n%s\n", pt1, pt2 );
-#endif
-
- if( skip )
- {
- while( --skip > 0 ) localhompt = localhompt->next;
- localhompt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- localhompt = localhompt->next;
-// fprintf( stderr, "tmppt = %p, localhompt = %p\n", tmppt, localhompt );
- }
- tmppt = localhompt;
-
- st = 0;
- iscore = 0;
- while( *pt1 != 0 )
- {
-// fprintf( stderr, "In in while loop\n" );
-// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
- if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
- {
- end1 = pos1 - 1;
- end2 = pos2 - 1;
-
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- isumscore += iscore;
- sumoverlap += end2-start2+1;
-#else
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = iscore * 5.8 / 600;
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "iscore (1)= %d\n", iscore );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- iscore = 0;
- st = 0;
- }
- else if( *pt1 != '-' && *pt2 != '-' )
- {
- if( st == 0 )
- {
- start1 = pos1; start2 = pos2;
- st = 1;
- }
- iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]];
-// fprintf( stderr, "%c-%c, score(0) = %d\n", *pt1, *pt2, iscore );
- }
- if( *pt1++ != '-' ) pos1++;
- if( *pt2++ != '-' ) pos2++;
- }
-
- if( st )
- {
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- end1 = pos1 - 1;
- end2 = pos2 - 1;
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- isumscore += iscore;
- sumoverlap += end2-start2+1;
-#else
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore * 5.8 / 600;
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-#if 0
- fprintf( stderr, "score (2)= %d\n", iscore );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- }
-
- for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
- {
- tmppt->overlapaa = sumoverlap;
- tmppt->opt = (double)sumscore * 5.8 / 600 / sumoverlap;
- }
- return( nlocalhom );
-}
-
-#endif
-
-
-
-static int addlocalhom_r( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip )
-{
- int pos1, pos2, start1, start2, end1, end2;
- char *pt1, *pt2;
- double score;
- double sumscore;
- int sumoverlap;
- LocalHom *tmppt = NULL; // by D.Mathog, a guess
- int st;
- int nlocalhom = 0;
- pt1 = al1; pt2 = al2;
- pos1 = off1; pos2 = off2;
-
- sumscore = 0.0;
- sumoverlap = 0;
- start1 = 0; // by D.Mathog, a guess
- start2 = 0; // by D.Mathog, a guess
-
-#if 0
- fprintf( stderr, "nlocalhom = %d in addlocalhom\n", nlocalhom );
- fprintf( stderr, "al1 = %s, al2 = %s\n", al1, al2 );
- fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
- fprintf( stderr, "localhopt = %p, skip = %d\n", localhompt, skip );
-#endif
- fprintf( stderr, "pt1 = \n%s\n, pt2 = \n%s\n", pt1, pt2 );
-
- if( skip )
- {
- while( --skip > 0 ) localhompt = localhompt->next;
- localhompt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- localhompt = localhompt->next;
- fprintf( stderr, "tmppt = %p, localhompt = %p\n", (void *)tmppt, (void *)localhompt );
- }
- tmppt = localhompt;
-
- st = 0;
- score = 0.0;
- while( *pt1 != 0 )
- {
- fprintf( stderr, "In in while loop\n" );
- fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
- if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
- {
- end1 = pos1 - 1;
- end2 = pos2 - 1;
-
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- sumscore += score;
- sumoverlap += end2-start2+1;
-#else
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score * 5.8 / 600;
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
- fprintf( stderr, "score (1)= %f\n", score );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
- score = 0.0;
- st = 0;
- }
- else if( *pt1 != '-' && *pt2 != '-' )
- {
- if( st == 0 )
- {
- start1 = pos1; start2 = pos2;
- st = 1;
- }
- score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]];
-// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
- }
- if( *pt1++ != '-' ) pos1++;
- if( *pt2++ != '-' ) pos2++;
- }
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- end1 = pos1 - 1;
- end2 = pos2 - 1;
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- sumscore += score;
- sumoverlap += end2-start2+1;
-#else
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score * 5.8 / 600;
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
- fprintf( stderr, "score (2)= %f\n", score );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-
- for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
- {
- tmppt->overlapaa = sumoverlap;
- tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
- }
- return( nlocalhom );
-}
-void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
-{
- int pos1, pos2, start1, start2, end1, end2;
- char *pt1, *pt2;
- double score;
- double sumscore;
- int sumoverlap;
- LocalHom *tmppt;
- LocalHom *subnosento;
- int st;
- int saisho;
-
- pt1 = al1; pt2 = al2;
- pos1 = off1; pos2 = off2;
-
- sumscore = 0.0;
- sumoverlap = 0;
- start1 = 0; // by Mathog, a guess
- start2 = 0; // by Mathog, a guess
-
- subnosento = localhompt;
- while( subnosento->next ) subnosento = subnosento->next;
- tmppt = subnosento;
-
- saisho = ( localhompt->nokori == 0 );
-
- fprintf( stderr, "localhompt = %p\n", (void *)localhompt );
- fprintf( stderr, "tmppt = %p\n", (void *)tmppt );
- fprintf( stderr, "subnosento = %p\n", (void *)subnosento );
-
- st = 0;
- score = 0.0;
- while( *pt1 != 0 )
- {
-// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
- if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
- {
- end1 = pos1 - 1;
- end2 = pos2 - 1;
-
- if( localhompt->nokori++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- sumscore += score;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "score (1)= %f\n", score );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- score = 0.0;
- st = 0;
- }
- else if( *pt1 != '-' && *pt2 != '-' )
- {
- if( st == 0 )
- {
- start1 = pos1; start2 = pos2;
- st = 1;
- }
- score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
-// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
- }
- if( *pt1++ != '-' ) pos1++;
- if( *pt2++ != '-' ) pos2++;
- }
- if( *(pt1-1) != '-' && *(pt2-1) != '-' )
- {
- if( localhompt->nokori++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
-
- end1 = pos1 - 1;
- end2 = pos2 - 1;
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- sumscore += score;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "score (2)= %f\n", score );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- }
-
- fprintf( stderr, "sumscore = %f\n", sumscore );
- if( !divpairscore )
- {
-
- if( !saisho ) subnosento = subnosento->next;
- for( tmppt=subnosento; tmppt; tmppt=tmppt->next )
- {
- tmppt->overlapaa = sumoverlap;
- tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
- fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
- }
- }
-}
-void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
-{
- int pos1, pos2, start1, start2, end1, end2;
- char *pt1, *pt2;
- int iscore;
- int isumscore;
- int sumoverlap;
- LocalHom *tmppt = localhompt;
- int nlocalhom = 0;
- int st;
- pt1 = al1; pt2 = al2;
- pos1 = off1; pos2 = off2;
-
-
- isumscore = 0;
- sumoverlap = 0;
- start1 = 0; // by D.Mathog, a guess
- start2 = 0; // by D.Mathog, a guess
-
- st = 0;
- iscore = 0;
- while( *pt1 != 0 )
- {
-// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
- if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
- {
- end1 = pos1 - 1;
- end2 = pos2 - 1;
-
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- isumscore += iscore;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "iscore (1)= %d\n", iscore );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- iscore = 0;
- st = 0;
- }
- else if( *pt1 != '-' && *pt2 != '-' )
- {
- if( st == 0 )
- {
- start1 = pos1; start2 = pos2;
- st = 1;
- }
- iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
-// fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
- }
- if( *pt1++ != '-' ) pos1++;
- if( *pt2++ != '-' ) pos2++;
- }
- if( *(pt1-1) != '-' && *(pt2-1) != '-' )
- {
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- end1 = pos1 - 1;
- end2 = pos2 - 1;
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- isumscore += iscore;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "iscore (2)= %d\n", iscore );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- }
-
- if( !divpairscore )
- {
- for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
- {
- tmppt->overlapaa = sumoverlap;
-// tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
- tmppt->opt = (double)600 * 5.8 / 600;
-// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
- }
- }
-}
-
-void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
-{
- int posinaln, pos1, pos2, start1, start2, end1, end2;
- char *pt1, *pt2;
- int isumscore;
- int sumoverlap;
- LocalHom *tmppt = localhompt;
- int nlocalhom = 0;
-// int st;
- pt1 = al1; pt2 = al2;
- pos1 = off1; pos2 = off2;
-
- isumscore = 0;
- sumoverlap = 0;
- start1 = 0; // by D.Mathog, a guess
- start2 = 0; // by D.Mathog, a guess
-
- posinaln = 0;
- while( *pt1 != 0 )
- {
- if( *pt1 != '-' && *pt2 != '-' && equiv[posinaln] > 0.0 )
- {
- start1 = end1 = pos1; start2 = end2 = pos2;
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ... (posinaln=%d)\n", posinaln );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
- tmppt->overlapaa = 1;
-// tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
- tmppt->opt = equiv[posinaln] * scale;
-// fprintf( stdout, "*pt1=%c, *pt2=%c, equiv=%f\n", *pt1, *pt2, equiv[posinaln] );
-
- }
- if( *pt1++ != '-' ) pos1++;
- if( *pt2++ != '-' ) pos2++;
- posinaln++;
- }
-}
-
-void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
-{
- int pos1, pos2, start1, start2, end1, end2;
- char *pt1, *pt2;
- int iscore;
- int isumscore;
- int sumoverlap;
- LocalHom *tmppt = localhompt;
- int nlocalhom = 0;
- int st;
- pt1 = al1; pt2 = al2;
- pos1 = off1; pos2 = off2;
-
-
- isumscore = 0;
- sumoverlap = 0;
- start1 = 0; // by D.Mathog, a guess
- start2 = 0; // by D.Mathog, a guess
-
- st = 0;
- iscore = 0;
- while( *pt1 != 0 )
- {
-// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
- if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
- {
- end1 = pos1 - 1;
- end2 = pos2 - 1;
-
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- isumscore += iscore;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "iscore (1)= %d\n", iscore );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- iscore = 0;
- st = 0;
- }
- else if( *pt1 != '-' && *pt2 != '-' )
- {
- if( st == 0 )
- {
- start1 = pos1; start2 = pos2;
- st = 1;
- }
- iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
-// fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
- }
- if( *pt1++ != '-' ) pos1++;
- if( *pt2++ != '-' ) pos2++;
- }
- if( *(pt1-1) != '-' && *(pt2-1) != '-' )
- {
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- end1 = pos1 - 1;
- end2 = pos2 - 1;
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- isumscore += iscore;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "iscore (2)= %d\n", iscore );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- }
-
- if( !divpairscore )
- {
- for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
- {
- tmppt->overlapaa = sumoverlap;
- tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
-// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
- }
- }
-}
-void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
-{
- int pos1, pos2, start1, start2, end1, end2;
- char *pt1, *pt2;
- double score;
- double sumscore;
- int sumoverlap;
- LocalHom *tmppt = localhompt;
- int nlocalhom = 0;
- int st;
- pt1 = al1; pt2 = al2;
- pos1 = off1; pos2 = off2;
-
-
- sumscore = 0.0;
- sumoverlap = 0;
- start1 = 0; // by D.Mathog, a guess
- start2 = 0; // by D.Mathog, a guess
-
- st = 0;
- score = 0.0;
- while( *pt1 != 0 )
- {
-// fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
- if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
- {
- end1 = pos1 - 1;
- end2 = pos2 - 1;
-
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- sumscore += score;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "score (1)= %f\n", score );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
- score = 0.0;
- st = 0;
- }
- else if( *pt1 != '-' && *pt2 != '-' )
- {
- if( st == 0 )
- {
- start1 = pos1; start2 = pos2;
- st = 1;
- }
- score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
-// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
- }
- if( *pt1++ != '-' ) pos1++;
- if( *pt2++ != '-' ) pos2++;
- }
- if( nlocalhom++ > 0 )
- {
-// fprintf( stderr, "reallocating ...\n" );
- tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
-// fprintf( stderr, "done\n" );
- tmppt = tmppt->next;
- tmppt->next = NULL;
- }
- end1 = pos1 - 1;
- end2 = pos2 - 1;
- tmppt->start1 = start1;
- tmppt->start2 = start2;
- tmppt->end1 = end1 ;
- tmppt->end2 = end2 ;
-
-#if 1
- if( divpairscore )
- {
- tmppt->overlapaa = end2-start2+1;
- tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
- }
- else
- {
- sumscore += score;
- sumoverlap += end2-start2+1;
- }
-#else
- tmppt->overlapaa = overlapaa;
- tmppt->opt = (double)opt;
-#endif
-
-#if 0
- fprintf( stderr, "score (2)= %f\n", score );
- fprintf( stderr, "al1: %d - %d\n", start1, end1 );
- fprintf( stderr, "al2: %d - %d\n", start2, end2 );
-#endif
-
- if( !divpairscore )
- {
- for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
- {
- tmppt->overlapaa = sumoverlap;
- tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
-// fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
- }
- }
-}
-
-char *cutal( char *al, int al_display_start, int start, int end )
-{
- int pos;
- char *pt = al;
- char *val = NULL;
-
- pos = al_display_start;
- do
- {
- if( start == pos ) val = pt;
- if( end == pos ) break;
-// fprintf( stderr, "pos=%d, *pt=%c, val=%p\n", pos, *pt, val );
- if( *pt != '-' ) pos++;
- } while( *pt++ != 0 );
- *(pt+1) = 0;
- return( val );
-}
-
-void ErrorExit( char *message )
-{
- fprintf( stderr, "%s\n", message );
- exit( 1 );
-}
-
-void strncpy_caseC( char *str1, char *str2, int len )
-{
- if( dorp == 'd' && upperCase > 0 )
- {
- while( len-- )
- *str1++ = toupper( *str2++ );
- }
- else strncpy( str1, str2, len );
-}
-
-void seqUpper( int nseq, char **seq ) /* not used */
-{
- int i, j, len;
- for( i=0; i<nseq; i++ )
- {
- len = strlen( seq[i] );
- for( j=0; j<len; j++ )
- seq[i][j] = toupper( seq[i][j] );
- }
-}
-
-void seqLower( int nseq, char **seq )
-{
- int i, j, len;
- for( i=0; i<nseq; i++ )
- {
- len = strlen( seq[i] );
- for( j=0; j<len; j++ )
- seq[i][j] = tolower( seq[i][j] );
- }
-}
-
-int getaline_fp_eof( char *s, int l, FILE *fp ) /* end of file -> return 1 */
-{
- int c, i = 0 ;
- int noteofflag = 0;
- for( i=0; i<l && ( noteofflag = ( (c=getc(fp)) != EOF ) ) && c != '\n'; i++ )
- *s++ = c;
- *s = '\0' ;
- return( !noteofflag );
-}
-
-int getaline_fp_eof_new(s, l, fp) /* end of file -> return 1 */
-char s[] ; int l ; FILE *fp ;
-{
- int c = 0, i = 0 ;
- int noteofflag = 0;
-
- if( feof( fp ) ) return( 1 );
-
- for( i=0; i<l && ( noteofflag = ( (c=getc(fp)) != EOF ) ) && c != '\n'; i++ )
- { *s++ = c ; }
- *s = '\0' ;
- if( c != '\n' && c != EOF ) while( getc(fp) != '\n' )
- ;
- return( !noteofflag );
-}
-
-int myfgets(s, l, fp) /* l°Ê¾å¤Ï¡¢¹ÔËö¤Þ¤ÇÆɤßÈô¤Ð¤¹ */
-char s[] ; int l ; FILE *fp ;
-{
- int c = 0, i = 0 ;
-
- if( feof( fp ) ) return( 1 );
-
- for( i=0; i<l && ( c=getc( fp ) ) != '\n'; i++ )
- *s++ = c;
- *s = '\0' ;
- if( c != '\n' )
- while( getc(fp) != '\n' )
- ;
- return( 0 );
-}
-
-float input_new( FILE *fp, int d )
-{
- char mojiretsu[10];
- int i, c;
-
- c = getc( fp );
- if( c != '\n' )
- ungetc( c, fp );
-
- for( i=0; i<d; i++ )
- mojiretsu[i] = getc( fp );
- mojiretsu[i] = 0;
-
- return( atof( mojiretsu ) );
-}
-
-
-void PreRead( FILE *fp, int *locnjob, int *locnlenmax )
-{
- int i, nleni;
- char b[B];
-
- fgets( b, B-1, fp ); *locnjob = atoi( b );
- *locnlenmax = 0;
- i=0;
- while( i<*locnjob )
- {
- fgets( b, B-1, fp );
- if( !strncmp( b, "=", 1 ) )
- {
- i++;
- fgets( b, B-1, fp ); nleni = atoi( b );
- if( nleni > *locnlenmax ) *locnlenmax = nleni;
- }
- }
- if( *locnlenmax > N )
- {
- fprintf( stderr, "TOO LONG SEQUENCE!\n" );
- exit( 1 );
- }
- if( njob > M )
- {
- fprintf( stderr, "TOO MANY SEQUENCE!\n" );
- fprintf( stderr, "%d > %d\n", njob, M );
- exit( 1 );
- }
-}
-
-int allSpace( char *str )
-{
- int value = 1;
- while( *str ) value *= ( !isdigit( *str++ ) );
- return( value );
-}
-
-void Read( char name[M][B], int nlen[M], char **seq )
-{
- extern void FRead( FILE *x, char y[M][B], int z[M], char **w );
- FRead( stdin, name, nlen, seq );
-}
-
-
-void FRead( FILE *fp, char name[][B], int nlen[], char **seq )
-{
- int i, j;
- char b[B];
-
- fgets( b, B-1, fp );
-#if DEBUG
- fprintf( stderr, "b = %s\n", b );
-#endif
-
- if( strstr( b, "onnet" ) ) scoremtx = 1;
- else if( strstr( b, "DnA" ) )
- {
- scoremtx = -1;
- upperCase = -1;
- }
- else if( strstr( b, "dna" ) )
- {
- scoremtx = -1;
- upperCase = 0;
- }
- else if( strstr( b, "DNA" ) )
- {
- scoremtx = -1;
- upperCase = 1;
- }
- else if( strstr( b, "M-Y" ) || strstr( b, "iyata" ) ) scoremtx = 2;
- else scoremtx = 0;
-#if DEBUG
- fprintf( stderr, " %s->scoremtx = %d\n", b, scoremtx );
-#endif
-
- geta2 = GETA2;
-
-#if 0
- if( strlen( b ) >=25 )
- {
- b[25] = 0;
- #if DEBUG
- fprintf( stderr, "kimuraR = %s\n", b+20 );
- #endif
- kimuraR = atoi( b+20 );
-
- if( kimuraR < 0 || 20 < kimuraR ) ErrorExit( "Illeagal kimuraR value.\n" );
- if( allSpace( b+20 ) ) kimuraR = NOTSPECIFIED;
- }
- else kimuraR = NOTSPECIFIED;
- #if DEBUG
- fprintf( stderr, "kimuraR = %d\n", kimuraR );
- #endif
-
- if( strlen( b ) >=20 )
- {
- b[20] = 0;
- #if DEBUG
- fprintf( stderr, "pamN = %s\n", b+15 );
- #endif
- pamN = atoi( b+15 );
- if( pamN < 0 || 400 < pamN ) ErrorExit( "Illeagal pam value.\n" );
- if( allSpace( b+15 ) ) pamN = NOTSPECIFIED;
- }
- else pamN = NOTSPECIFIED;
-
- if( strlen( b ) >= 15 )
- {
- b[15] = 0;
- #if DEBUG
- fprintf( stderr, "poffset = %s\n", b+10 );
- #endif
- poffset = atoi( b+10 );
- if( poffset > 500 ) ErrorExit( "Illegal extending gap ppenalty\n" );
- if( allSpace( b+10 ) ) poffset = NOTSPECIFIED;
- }
- else poffset = NOTSPECIFIED;
-
- if( strlen( b ) >= 10 )
- {
- b[10] = 0;
- #if DEBUG
- fprintf( stderr, "ppenalty = %s\n", b+5 );
- #endif
- ppenalty = atoi( b+5 );
- if( ppenalty > 0 ) ErrorExit( "Illegal opening gap ppenalty\n" );
- if( allSpace( b+5 ) ) ppenalty = NOTSPECIFIED;
- }
- else ppenalty = NOTSPECIFIED;
-#endif
-
- for( i=0; i<njob; i++ )
- {
- getaline_fp_eof_new( b, B-1, fp );
- strcpy( name[i], b );
-#if DEBUG
- fprintf( stderr, "name[%d] = %s\n", i, name[i] );
-#endif
- fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */
- seq[i][0] = 0;
- if( nlen[i] ) for( j=0; j <= (nlen[i]-1)/C; j++ )
- {
- getaline_fp_eof_new( b, B-1, fp );
- /* b[C] = 0; */
- strcat( seq[i], b );
- }
- seq[i][nlen[i]] = 0;
- }
- if( scoremtx == -1 && upperCase != -1 ) seqLower( njob, seq );
-}
-
-
-static int countKUorWA( FILE *fp )
-{
- int value;
- int c, b;
-
- value= 0;
- b = '\n';
- while( ( c = getc( fp ) ) != EOF )
- {
- if( b == '\n' && ( c == '>' ) )
- value++;
- b = c;
- }
- rewind( fp );
- return( value );
-}
-
-void searchKUorWA( FILE *fp )
-{
- int c, b;
- b = '\n';
- while( !( ( ( c = getc( fp ) ) == '>' || c == EOF ) && b == '\n' ) )
- b = c;
- ungetc( c, fp );
-}
-
-static int onlyGraph( char *str )
-{
- char tmp;
- char *res = str;
- char *bk = str;
-
-// while( (tmp=*str++) ) if( isgraph( tmp ) ) *res++ = tmp;
- while( (tmp=*str++) )
- {
- if( 0x20 < tmp && tmp < 0x7f ) *res++ = tmp;
- if( tmp == '>' )
- {
- fprintf( stderr, "========================================================\n" );
- fprintf( stderr, "========================================================\n" );
- fprintf( stderr, "=== \n" );
- fprintf( stderr, "=== ERROR!! \n" );
- fprintf( stderr, "=== In the '--anysymbol' and '--preservecase' modes, \n" );
- fprintf( stderr, "=== '>' in sequence is unacceptable.\n" );
- fprintf( stderr, "=== \n" );
- fprintf( stderr, "========================================================\n" );
- fprintf( stderr, "========================================================\n" );
- exit( 1 );
- }
- }
- *res = 0;
- return( res - bk );
-}
-
-static int onlyAlpha_lower( char *str )
-{
- char tmp;
- char *res = str;
- char *bk = str;
-
- while( (tmp=*str++) )
- if( isalpha( tmp ) || tmp == '-' || tmp == '*' || tmp == '.' )
- *res++ = tolower( tmp );
- *res = 0;
- return( res - bk );
-}
-static int onlyAlpha_upper( char *str )
-{
- char tmp;
- char *res = str;
- char *bk = str;
-
- while( (tmp=*str++) )
- if( isalpha( tmp ) || tmp == '-' || tmp == '*' || tmp == '.' )
- *res++ = toupper( tmp );
- *res = 0;
- return( res - bk );
-}
-
-void kake2hiku( char *str )
-{
- do
- if( *str == '*' ) *str = '-';
- while( *str++ );
-}
-
-char *load1SeqWithoutName_realloc_casepreserve( FILE *fpp )
-{
- int c, b;
- char *cbuf;
- int size = N;
- char *val;
-
- val = malloc( (size+1) * sizeof( char ) );
- cbuf = val;
-
- b = '\n';
- while( ( c = getc( fpp ) ) != EOF &&
- !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
- {
- *cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
- if( cbuf - val == size )
- {
- size += N;
- fprintf( stderr, "reallocating...\n" );
- val = (char *)realloc( val, (size+1) * sizeof( char ) );
- if( !val )
- {
- fprintf( stderr, "Allocation error in load1SeqWithoutName_realloc \n" );
- exit( 1 );
- }
- fprintf( stderr, "done.\n" );
- cbuf = val + size-N;
- }
- b = c;
- }
- ungetc( c, fpp );
- *cbuf = 0;
- onlyGraph( val );
-// kake2hiku( val );
- return( val );
-}
-
-char *load1SeqWithoutName_realloc( FILE *fpp )
-{
- int c, b;
- char *cbuf;
- int size = N;
- char *val;
-
- val = malloc( (size+1) * sizeof( char ) );
- cbuf = val;
-
- b = '\n';
- while( ( c = getc( fpp ) ) != EOF &&
- !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
- {
- *cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
- if( cbuf - val == size )
- {
- size += N;
- fprintf( stderr, "reallocating...\n" );
- val = (char *)realloc( val, (size+1) * sizeof( char ) );
- if( !val )
- {
- fprintf( stderr, "Allocation error in load1SeqWithoutName_realloc \n" );
- exit( 1 );
- }
- fprintf( stderr, "done.\n" );
- cbuf = val + size-N;
- }
- b = c;
- }
- ungetc( c, fpp );
- *cbuf = 0;
- if( dorp == 'd' )
- onlyAlpha_lower( val );
- else
- onlyAlpha_upper( val );
- kake2hiku( val );
- return( val );
-}
-
-int load1SeqWithoutName_new( FILE *fpp, char *cbuf )
-{
- int c, b;
- char *bk = cbuf;
-
- b = '\n';
- while( ( c = getc( fpp ) ) != EOF && /* by T. Nishiyama */
- !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
- {
- *cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
- b = c;
- }
- ungetc( c, fpp );
- *cbuf = 0;
- if( dorp == 'd' )
- onlyAlpha_lower( bk );
- else
- onlyAlpha_upper( bk );
- kake2hiku( bk );
- return( 0 );
-}
-
-
-void readDataforgaln( FILE *fp, char **name, int *nlen, char **seq )
-{
- int i;
- static char *tmpseq = NULL;
-
-#if 0
- if( !tmpseq )
- {
- tmpseq = AllocateCharVec( N );
- }
-#endif
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<njob; i++ )
- {
- name[i][0] = '='; getc( fp );
-#if 0
- fgets( name[i]+1, B-2, fp );
- j = strlen( name[i] );
- if( name[i][j-1] != '\n' )
- ErrorExit( "Too long name\n" );
- name[i][j-1] = 0;
-#else
- myfgets( name[i]+1, B-2, fp );
-#endif
-#if 0
- fprintf( stderr, "name[%d] = %s\n", i, name[i] );
-#endif
- tmpseq = load1SeqWithoutName_realloc( fp );
- strcpy( seq[i], tmpseq );
- nlen[i] = strlen( seq[i] );
- free( tmpseq );
- }
- if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
-#if 0
- free( tmpseq );
-#endif
-}
-
-void readData_varlen( FILE *fp, char **name, int *nlen, char **seq )
-{
- int i;
- static char *tmpseq = NULL;
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<njob; i++ )
- {
- name[i][0] = '='; getc( fp );
-#if 0
- fgets( name[i]+1, B-2, fp );
- j = strlen( name[i] );
- if( name[i][j-1] != '\n' )
- ErrorExit( "Too long name\n" );
- name[i][j-1] = 0;
-#else
- myfgets( name[i]+1, B-2, fp );
-#endif
-#if 0
- fprintf( stderr, "name[%d] = %s\n", i, name[i] );
-#endif
- tmpseq = load1SeqWithoutName_realloc( fp );
- nlen[i] = strlen( tmpseq );
-// fprintf( stderr, "nlen[%d] = %d\n", i+1, nlen[i] );
- seq[i] = calloc( nlen[i]+1, sizeof( char ) );
- strcpy( seq[i], tmpseq );
- free( tmpseq );
- }
- if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
-#if 0
- free( tmpseq );
-#endif
-}
-
-void readData_pointer2( FILE *fp, int nseq, char **name, int *nlen, char **seq )
-{
- int i;
- static char *tmpseq = NULL;
-
-#if 0
- if( !tmpseq )
- {
- tmpseq = AllocateCharVec( N );
- }
-#endif
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<nseq; i++ )
- {
- name[i][0] = '='; getc( fp );
-#if 0
- fgets( name[i]+1, B-2, fp );
- j = strlen( name[i] );
- if( name[i][j-1] != '\n' )
- ErrorExit( "Too long name\n" );
- name[i][j-1] = 0;
-#else
- myfgets( name[i]+1, B-2, fp );
-#endif
-#if 0
- fprintf( stderr, "name[%d] = %s\n", i, name[i] );
-#endif
- tmpseq = load1SeqWithoutName_realloc( fp );
- strcpy( seq[i], tmpseq );
- free( tmpseq );
- nlen[i] = strlen( seq[i] );
- }
- if( dorp == 'd' && upperCase != -1 ) seqLower( nseq, seq );
-#if 0
- free( tmpseq );
-#endif
- if( outnumber )
- {
- char *namebuf;
- char *cptr;
- namebuf = calloc( B+100, sizeof( char ) );
- for( i=0; i<nseq; i++ )
- {
- namebuf[0] = '=';
- cptr = strstr( name[i], "_numo_e_" );
- if( cptr )
- sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
- else
- sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
- strncpy( name[i], namebuf, B );
- name[i][B-1] = 0;
- }
- free( namebuf );
-// exit( 1 );
- }
-}
-
-
-void readData_pointer_casepreserve( FILE *fp, char **name, int *nlen, char **seq )
-{
- int i;
- static char *tmpseq = NULL;
-
-#if 0
- if( !tmpseq )
- {
- tmpseq = AllocateCharVec( N );
- }
-#endif
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<njob; i++ )
- {
- name[i][0] = '='; getc( fp );
-#if 0
- fgets( name[i]+1, B-2, fp );
- j = strlen( name[i] );
- if( name[i][j-1] != '\n' )
- ErrorExit( "Too long name\n" );
- name[i][j-1] = 0;
-#else
- myfgets( name[i]+1, B-2, fp );
-#endif
-#if 0
- fprintf( stderr, "name[%d] = %s\n", i, name[i] );
-#endif
- tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
- strcpy( seq[i], tmpseq );
- free( tmpseq );
- nlen[i] = strlen( seq[i] );
- }
-}
-
-
-void readData_pointer( FILE *fp, char **name, int *nlen, char **seq )
-{
- int i;
- static char *tmpseq = NULL;
-
-#if 0
- if( !tmpseq )
- {
- tmpseq = AllocateCharVec( N );
- }
-#endif
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<njob; i++ )
- {
- name[i][0] = '='; getc( fp );
-#if 0
- fgets( name[i]+1, B-2, fp );
- j = strlen( name[i] );
- if( name[i][j-1] != '\n' )
- ErrorExit( "Too long name\n" );
- name[i][j-1] = 0;
-#else
- myfgets( name[i]+1, B-2, fp );
-#endif
-#if 0
- fprintf( stderr, "name[%d] = %s\n", i, name[i] );
-#endif
- tmpseq = load1SeqWithoutName_realloc( fp );
- strcpy( seq[i], tmpseq );
- free( tmpseq );
- nlen[i] = strlen( seq[i] );
- }
- if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
-#if 0
- free( tmpseq );
-#endif
- if( outnumber )
- {
- char *namebuf;
- char *cptr;
- namebuf = calloc( B+100, sizeof( char ) );
- for( i=0; i<njob; i++ )
- {
- namebuf[0] = '=';
- cptr = strstr( name[i], "_numo_e_" );
- if( cptr )
- sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
- else
- sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
- strncpy( name[i], namebuf, B );
- name[i][B-1] = 0;
- }
- free( namebuf );
-// exit( 1 );
- }
-}
-
-void readData( FILE *fp, char name[][B], int nlen[], char **seq )
-{
- int i;
- static char *tmpseq = NULL;
-
-#if 0
- if( !tmpseq )
- {
- tmpseq = AllocateCharVec( N );
- }
-#endif
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<njob; i++ )
- {
- name[i][0] = '='; getc( fp );
-#if 0
- fgets( name[i]+1, B-2, fp );
- j = strlen( name[i] );
- if( name[i][j-1] != '\n' )
- ErrorExit( "Too long name\n" );
- name[i][j-1] = 0;
-#else
- myfgets( name[i]+1, B-2, fp );
-#endif
-#if 0
- fprintf( stderr, "name[%d] = %s\n", i, name[i] );
-#endif
- tmpseq = load1SeqWithoutName_realloc( fp );
- strcpy( seq[i], tmpseq );
- nlen[i] = strlen( seq[i] );
- free( tmpseq );
- }
- if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
-#if 0
- free( tmpseq );
-#endif
-}
-
-void cutAlignment( FILE *fp, int **regtable, char **revtable, int *outtable, char **name, char **outseq )
-{
- int i, j;
- int outlen;
- static char *tmpseq = NULL;
- static char *dumname = NULL;
- char *fs, *rs;
- int npos, lpos;
- int startpos, endpos, seqlen;
-
- if( dumname == NULL )
- {
- dumname = AllocateCharVec( N );
- }
-
- rewind( fp );
- searchKUorWA( fp );
-
-
- npos = 0;
- for( i=0; i<njob; i++ )
- {
- dumname[0] = '>'; getc( fp );
- myfgets( dumname+1, B-1, fp );
- tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
-
- if( outtable[i] )
- {
-// putc( '>', stdout );
-// puts( dumname+1 );
-
-
- strncat( name[npos], dumname, B-1 );
- name[npos][B-1] = 0;
-
- if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
- seqlen = strlen( tmpseq );
- lpos = 0;
- for( j=0; j<5; j++ )
- {
- if( regtable[0][j*2] == -1 && regtable[0][j*2+1] == -1 ) continue;
-
- startpos = regtable[0][j*2];
- endpos = regtable[0][j*2+1];
- if( startpos > endpos )
- {
- endpos = regtable[0][j*2];
- startpos = regtable[0][j*2+1];
- }
-
- if( startpos < 0 ) startpos = 0;
- if( endpos < 0 ) endpos = 0;
- if( endpos >= seqlen ) endpos = seqlen-1;
- if( startpos >= seqlen ) startpos = seqlen-1;
-
-// fprintf( stderr, "startpos = %d, endpos = %d\n", startpos, endpos );
-
- outlen = endpos - startpos+1;
- if( revtable[0][j] == 'f' )
- {
-// fprintf( stderr, "regtable[%d][st] = %d\n", i, regtable[0][j*2+0] );
-// fprintf( stderr, "regtable[%d][en] = %d\n", i, regtable[0][j*2+1] );
-// fprintf( stderr, "outlen = %d\n", outlen );
-// fprintf( stdout, "%.*s\n", outlen, tmpseq+regtable[0][j*2] );
- strncpy( outseq[npos] + lpos, tmpseq+startpos, outlen );
- lpos += outlen;
- }
- else
- {
- fs = AllocateCharVec( outlen+1 );
- rs = AllocateCharVec( outlen+1 );
-
- fs[outlen] = 0;
- strncpy( fs, tmpseq+startpos, outlen );
- sreverse( rs, fs );
-// fprintf( stdout, "%s\n", rs );
- strncpy( outseq[npos] + lpos, rs, outlen );
- lpos += outlen;
- free( fs );
- free( rs );
- }
- outseq[npos][lpos] = 0;
- }
- npos++;
- }
- free( tmpseq );
- }
-}
-
-void cutData( FILE *fp, int **regtable, char **revtable, int *outtable )
-{
- int i, j;
- int outlen, seqlen, startpos, endpos;
- static char *tmpseq = NULL;
- static char *dumname = NULL;
- char *fs, *rs;
-
- if( dumname == NULL )
- {
- dumname = AllocateCharVec( N );
- }
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<njob; i++ )
- {
- dumname[0] = '='; getc( fp );
- myfgets( dumname+1, B-2, fp );
- tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
-
- if( outtable[i] )
- {
- gappick_samestring( tmpseq );
- putc( '>', stdout );
- puts( dumname+1 );
-
- seqlen = strlen( tmpseq );
-
- if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
- for( j=0; j<5; j++ )
- {
- if( regtable[i][j*2] == -1 && regtable[i][j*2+1] == -1 ) continue;
-
- startpos = regtable[i][j*2];
- endpos = regtable[i][j*2+1];
-
- if( startpos > endpos )
- {
- endpos = regtable[i][j*2];
- startpos = regtable[i][j*2+1];
- }
-
- if( startpos < 0 ) startpos = 0;
- if( endpos < 0 ) endpos = 0;
- if( endpos >= seqlen ) endpos = seqlen-1;
- if( startpos >= seqlen ) startpos = seqlen-1;
-
- outlen = endpos - startpos + 1;
- if( revtable[i][j] == 'f' )
- {
- fprintf( stderr, "startpos = %d\n", startpos );
- fprintf( stderr, "endpos = %d\n", endpos );
- fprintf( stderr, "outlen = %d\n", outlen );
- fprintf( stdout, "%.*s\n", outlen, tmpseq+startpos );
- }
- else
- {
- fs = AllocateCharVec( outlen+1 );
- rs = AllocateCharVec( outlen+1 );
-
- fs[outlen] = 0;
- strncpy( fs, tmpseq+startpos, outlen );
- sreverse( rs, fs );
- fprintf( stdout, "%s\n", rs );
- free( fs );
- free( rs );
- }
- }
- }
- free( tmpseq );
- }
-}
-
-void catData( FILE *fp )
-{
- int i;
- static char *tmpseq = NULL;
- static char *dumname = NULL;
-// char *cptr;
-
- if( dumname == NULL )
- {
- dumname = AllocateCharVec( N );
- }
-
- rewind( fp );
- searchKUorWA( fp );
-
- for( i=0; i<njob; i++ )
- {
- dumname[0] = '='; getc( fp );
- myfgets( dumname+1, B-2, fp );
- if( outnumber )
- {
- fprintf( stdout, ">_numo_s_%08d_numo_e_", i+1 );
- }
- else
- {
- putc( '>', stdout );
- }
- puts( dumname+1 );
- tmpseq = load1SeqWithoutName_realloc( fp );
- if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
- puts( tmpseq );
- free( tmpseq );
- }
-}
-
-int countATGC( char *s, int *total )
-{
- int nATGC;
- int nChar;
- char c;
- nATGC = nChar = 0;
-
- if( *s == 0 )
- {
- total = 0;
- return( 0 );
- }
-
- do
- {
- c = tolower( *s );
- if( isalpha( c ) )
- {
- nChar++;
- if( c == 'a' || c == 't' || c == 'g' || c == 'c' || c == 'u' || c == 'n' )
- nATGC++;
- }
- }
- while( *++s );
-
- *total = nChar;
- return( nATGC );
-}
-
-double countATGCbk( char *s )
-{
- int nATGC;
- int nChar;
- char c;
- nATGC = nChar = 0;
-
- do
- {
- c = tolower( *s );
- if( isalpha( c ) )
- {
- nChar++;
- if( c == 'a' || c == 't' || c == 'g' || c == 'c' || c == 'u' || c == 'n' )
- nATGC++;
- }
- }
- while( *++s );
- return( (double)nATGC / nChar );
-}
-
-
-int countnogaplen( char *seq )
-{
- int val = 0;
- while( *seq )
- if( *seq++ != '-' ) val++;
- return( val );
-}
-
-void getnumlen_casepreserve( FILE *fp, int *nlenminpt )
-{
- int total;
- int nsite = 0;
- int atgcnum;
- int i, tmp;
- char *tmpseq, *tmpname;
- double atgcfreq;
- tmpname = AllocateCharVec( N );
- njob = countKUorWA( fp );
- searchKUorWA( fp );
- nlenmax = 0;
- *nlenminpt = 99999999;
- atgcnum = 0;
- total = 0;
- for( i=0; i<njob; i++ )
- {
- myfgets( tmpname, N-1, fp );
- tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
- tmp = strlen( tmpseq );
- if( tmp > nlenmax ) nlenmax = tmp;
- if( tmp < *nlenminpt ) *nlenminpt = tmp;
- atgcnum += countATGC( tmpseq, &nsite );
- total += nsite;
- free( tmpseq );
- }
- free( tmpname );
- atgcfreq = (double)atgcnum / total;
-// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
- if( dorp == NOTSPECIFIED )
- {
- if( atgcfreq > 0.75 )
- {
- dorp = 'd';
- upperCase = -1;
- }
- else
- {
- dorp = 'p';
- upperCase = 0;
- }
- }
-}
-
-void getnumlen_nogap( FILE *fp, int *nlenminpt )
-{
- int total;
- int nsite = 0;
- int atgcnum;
- int i, tmp;
- char *tmpseq, *tmpname;
- double atgcfreq;
- tmpname = AllocateCharVec( N );
- njob = countKUorWA( fp );
- searchKUorWA( fp );
- nlenmax = 0;
- *nlenminpt = 99999999;
- atgcnum = 0;
- total = 0;
- for( i=0; i<njob; i++ )
- {
- myfgets( tmpname, N-1, fp );
- tmpseq = load1SeqWithoutName_realloc( fp );
- tmp = countnogaplen( tmpseq );
- if( tmp > nlenmax ) nlenmax = tmp;
- if( tmp < *nlenminpt ) *nlenminpt = tmp;
- atgcnum += countATGC( tmpseq, &nsite );
- total += nsite;
- free( tmpseq );
- }
- free( tmpname );
- atgcfreq = (double)atgcnum / total;
- fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
- if( dorp == NOTSPECIFIED )
- {
- if( atgcfreq > 0.75 )
- {
- dorp = 'd';
- upperCase = -1;
- }
- else
- {
- dorp = 'p';
- upperCase = 0;
- }
- }
-}
-
-
-void getnumlen_nogap_outallreg( FILE *fp, int *nlenminpt )
-{
- int total;
- int nsite = 0;
- int atgcnum;
- int i, tmp;
- char *tmpseq, *tmpname;
- double atgcfreq;
- tmpname = AllocateCharVec( N );
- njob = countKUorWA( fp );
- searchKUorWA( fp );
- nlenmax = 0;
- *nlenminpt = 99999999;
- atgcnum = 0;
- total = 0;
- for( i=0; i<njob; i++ )
- {
- myfgets( tmpname, N-1, fp );
- fprintf( stdout, "%s\n", tmpname );
- tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
- tmp = countnogaplen( tmpseq );
- fprintf( stdout, "%d\n", tmp );
- if( tmp > nlenmax ) nlenmax = tmp;
- if( tmp < *nlenminpt ) *nlenminpt = tmp;
- atgcnum += countATGC( tmpseq, &nsite );
- total += nsite;
- free( tmpseq );
- }
- free( tmpname );
- atgcfreq = (double)atgcnum / total;
- fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
- if( dorp == NOTSPECIFIED )
- {
- if( atgcfreq > 0.75 )
- {
- dorp = 'd';
- upperCase = -1;
- }
- else
- {
- dorp = 'p';
- upperCase = 0;
- }
- }
-}
-
-void getnumlen_nogap_outallreg_web( FILE *fp, FILE *ofp, int *nlenminpt, int *isalignedpt )
-{
- int total;
- int nsite = 0;
- int atgcnum;
- int alnlen = 0, alnlen_prev;
- int i, tmp;
- char *tmpseq, *tmpname;
- double atgcfreq;
- tmpname = AllocateCharVec( N );
- njob = countKUorWA( fp );
- searchKUorWA( fp );
- nlenmax = 0;
- *nlenminpt = 99999999;
- atgcnum = 0;
- total = 0;
- alnlen_prev = -1;
- *isalignedpt = 1;
- for( i=0; i<njob; i++ )
- {
- myfgets( tmpname, N-1, fp );
-// fprintf( stdout, "%s\n", tmpname );
- tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
- tmp = countnogaplen( tmpseq );
-// fprintf( stdout, "%d\n", tmp );
- if( tmp > nlenmax ) nlenmax = tmp;
- if( tmp < *nlenminpt ) *nlenminpt = tmp;
- atgcnum += countATGC( tmpseq, &nsite );
- total += nsite;
-
- alnlen = strlen( tmpseq );
-// fprintf( stdout, "##### alnlen, alnlen_prev = %d, %d\n", alnlen, alnlen_prev );
- if( i>0 && alnlen_prev != alnlen ) *isalignedpt = 0;
- alnlen_prev = alnlen;
-
- free( tmpseq );
- atgcfreq = (double)atgcnum / total;
-// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
-// if( dorp == NOTSPECIFIED ) // you kentou
- {
- if( atgcfreq > 0.75 )
- {
- dorp = 'd';
- upperCase = -1;
- }
- else
- {
- dorp = 'p';
- upperCase = 0;
- }
- }
-
-
-
-
- fprintf( ofp, " <label for='s%d'><input type='checkbox' id='s%d' name='s%d' checked>%s</label>\n", i, i, i, tmpname );
- fprintf( ofp, "<span id='t%d-0' style='display:none'>", i );
- fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"t%d\")'>+reg</a>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-0' size='8' value='1'> End:<input type='text' name='e%d-0' size='8' value='%d'>", i, i, tmp );
- if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-0'><input type='checkbox' name='r%d-0' id='r%d-0'>Reverse</label>", i, i, i );
- fprintf( ofp, " Sequence Length:<input type='text' name='l%d' size='8' value='%d' readonly='readonly'>", i, tmp );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='t%d-1' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-1' size='8' value=''> End:<input type='text' name='e%d-1' size='8' value=''>", i, i );
- if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-1'><input type='checkbox' name='r%d-1' id='r%d-1'>Reverse</label>", i, i, i );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='t%d-2' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-2' size='8' value=''> End:<input type='text' name='e%d-2' size='8' value=''>", i, i );
- if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-2'><input type='checkbox' name='r%d-2' id='r%d-2'>Reverse</label>", i, i, i );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='t%d-3' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-3' size='8' value=''> End:<input type='text' name='e%d-3' size='8' value=''>", i, i );
- if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-3'><input type='checkbox' name='r%d-3' id='r%d-3'>Reverse</label>", i, i, i );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='t%d-4' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-4' size='8' value=''> End:<input type='text' name='e%d-4' size='8' value=''>", i, i );
- if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-4'><input type='checkbox' name='r%d-4' id='r%d-4'>Reverse</label>", i, i, i );
- fprintf( ofp, "\n</span>" );
- }
- free( tmpname );
- atgcfreq = (double)atgcnum / total;
- fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
-// if( dorp == NOTSPECIFIED ) // you kentou
- {
- if( atgcfreq > 0.75 )
- {
- dorp = 'd';
- upperCase = -1;
- }
- else
- {
- dorp = 'p';
- upperCase = 0;
- }
- }
- if( *isalignedpt )
- {
- fprintf( ofp, "\n" );
- fprintf( ofp, "<span id='tall-0' style='display:none'>" );
- fprintf( ofp, "Cut the alignment\n" );
- fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"tall\")'>+reg</a>" );
- fprintf( ofp, " Begin:<input type='text' name='ball-0' size='8' value='1'> End:<input type='text' name='eall-0' size='8' value='%d'>", alnlen );
- if( dorp == 'd' ) fprintf( ofp, " <label for='rall-0'><input type='checkbox' name='rall-0' id='rall-0'>Reverse</label>" );
- fprintf( ofp, " Alignment length:<input type='text' name='lall' size='8' value='%d' readonly='readonly'>", alnlen );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='tall-1' style='display:none'>" );
- fprintf( ofp, " Begin:<input type='text' name='ball-1' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
- if( dorp == 'd' ) fprintf( ofp, " <label for='rall-1'><input type='checkbox' name='rall-1' id='rall-1'>Reverse</label>" );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='tall-2' style='display:none'>" );
- fprintf( ofp, " Begin:<input type='text' name='ball-2' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
- if( dorp == 'd' ) fprintf( ofp, " <label for='rall-2'><input type='checkbox' name='rall-2' id='rall-2'>Reverse</label>" );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='tall-3' style='display:none'>" );
- fprintf( ofp, " Begin:<input type='text' name='ball-3' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
- if( dorp == 'd' ) fprintf( ofp, " <label for='rall-3'><input type='checkbox' name='rall-3' id='rall-3'>Reverse</label>" );
- fprintf( ofp, "\n</span>" );
- fprintf( ofp, "<span id='tall-4' style='display:none'>" );
- fprintf( ofp, " Begin:<input type='text' name='ball-4' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
- if( dorp == 'd' ) fprintf( ofp, " <label for='rall-4'><input type='checkbox' name='rall-4' id='rall-4'>Reverse</label>" );
- fprintf( ofp, "\n</span>" );
- }
-
-}
-
-void getnumlen( FILE *fp )
-{
- int total;
- int nsite = 0;
- int atgcnum;
- int i, tmp;
- char *tmpseq;
- char *tmpname;
- double atgcfreq;
- tmpname = AllocateCharVec( N );
- njob = countKUorWA( fp );
- searchKUorWA( fp );
- nlenmax = 0;
- atgcnum = 0;
- total = 0;
- for( i=0; i<njob; i++ )
- {
- myfgets( tmpname, N-1, fp );
- tmpseq = load1SeqWithoutName_realloc( fp );
- tmp = strlen( tmpseq );
- if( tmp > nlenmax ) nlenmax = tmp;
- atgcnum += countATGC( tmpseq, &nsite );
- total += nsite;
-// fprintf( stderr, "##### total = %d\n", total );
- free( tmpseq );
- }
-
- atgcfreq = (double)atgcnum / total;
-// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
- if( dorp == NOTSPECIFIED )
- {
- if( atgcfreq > 0.75 )
- {
- dorp = 'd';
- upperCase = -1;
- }
- else
- {
- dorp = 'p';
- upperCase = 0;
- }
- }
- free( tmpname );
-}
-
-
-
-void WriteGapFill( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq )
-{
- static char b[N];
- int i, j;
- int nalen[M];
- static char gap[N];
- static char buff[N];
-
-#if IODEBUG
- fprintf( stderr, "IMAKARA KAKU\n" );
-#endif
- nlenmax = 0;
- for( i=0; i<locnjob; i++ )
- {
- int len = strlen( aseq[i] );
- if( nlenmax < len ) nlenmax = len;
- }
-
- for( i=0; i<nlenmax; i++ ) gap[i] = '-';
- gap[nlenmax] = 0;
-
- fprintf( fp, "%5d", locnjob );
- fprintf( fp, "\n" );
-
- for( i=0; i<locnjob; i++ )
- {
- strcpy( buff, aseq[i] );
- strncat( buff, gap, nlenmax-strlen( aseq[i] ) );
- buff[nlenmax] = 0;
- nalen[i] = strlen( buff );
- fprintf( fp, "%s\n", name[i] );
- fprintf( fp, "%5d\n", nalen[i] );
- for( j=0; j<nalen[i]; j=j+C )
- {
- strncpy_caseC( b, buff+j, C ); b[C] = 0;
- fprintf( fp, "%s\n",b );
- }
- }
-#if DEBUG
- fprintf( stderr, "nalen[0] = %d\n", nalen[0] );
-#endif
-#if IODEBUG
- fprintf( stderr, "KAKIOWATTA\n" );
-#endif
-}
-
-void writeDataforgaln( FILE *fp, int locnjob, char **name, int *nlen, char **aseq )
-{
- int i, j;
- int nalen;
-
- for( i=0; i<locnjob; i++ )
- {
- nalen = strlen( aseq[i] );
- fprintf( fp, ">%s\n", name[i]+1 );
- for( j=0; j<nalen; j=j+C )
- {
-#if 0
- strncpy( b, aseq[i]+j, C ); b[C] = 0;
- fprintf( fp, "%s\n",b );
-#else
- fprintf( fp, "%.*s\n", C, aseq[i]+j );
-#endif
- }
- }
-}
-
-void writeData_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq )
-{
- int i, j;
- int nalen;
-
- for( i=0; i<locnjob; i++ )
- {
-#if DEBUG
- fprintf( stderr, "i = %d in writeData\n", i );
-#endif
- nalen = strlen( aseq[i] );
- fprintf( fp, ">%s\n", name[i]+1 );
- for( j=0; j<nalen; j=j+C )
- {
-#if 0
- strncpy( b, aseq[i]+j, C ); b[C] = 0;
- fprintf( fp, "%s\n",b );
-#else
- fprintf( fp, "%.*s\n", C, aseq[i]+j );
-#endif
- }
- }
-}
-
-void writeData( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq )
-{
- int i, j;
- int nalen;
-
- for( i=0; i<locnjob; i++ )
- {
-#if DEBUG
- fprintf( stderr, "i = %d in writeData\n", i );
-#endif
- nalen = strlen( aseq[i] );
- fprintf( fp, ">%s\n", name[i]+1 );
- for( j=0; j<nalen; j=j+C )
- {
-#if 0
- strncpy( b, aseq[i]+j, C ); b[C] = 0;
- fprintf( fp, "%s\n",b );
-#else
- fprintf( fp, "%.*s\n", C, aseq[i]+j );
-#endif
- }
- }
-}
-
-
-void write1seq( FILE *fp, char *aseq )
-{
- int j;
- int nalen;
-
- nalen = strlen( aseq );
- for( j=0; j<nalen; j=j+C )
- fprintf( fp, "%.*s\n", C, aseq+j );
-}
-
-
-
-void readhat2_floathalf_pointer( FILE *fp, int nseq, char **name, float **mtx )
-{
- int i, j, nseq0;
- char b[B];
-
- fgets( b, B, fp );
- fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
- fgets( b, B, fp );
- for( i=0; i<nseq; i++ )
- {
-#if 0
- getaline_fp_eof( b, B, fp );
-#else
- myfgets( b, B-2, fp );
-#endif
-#if 0
- j = MIN( strlen( b+6 ), 10 );
- if( strncmp( name[i], b+6 , j ) )
- {
- fprintf( stderr, "Error in hat2\n" );
- fprintf( stderr, "%s != %s\n", b, name[i] );
- exit( 1 );
- }
-#endif
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- mtx[i][j-i] = ( input_new( fp, D ) );
- }
-}
-void readhat2_floathalf( FILE *fp, int nseq, char name[M][B], float **mtx )
-{
- int i, j, nseq0;
- char b[B];
-
- fgets( b, B, fp );
- fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
- fgets( b, B, fp );
- for( i=0; i<nseq; i++ )
- {
-#if 0
- getaline_fp_eof( b, B, fp );
-#else
- myfgets( b, B-2, fp );
-#endif
-#if 0
- j = MIN( strlen( b+6 ), 10 );
- if( strncmp( name[i], b+6 , j ) )
- {
- fprintf( stderr, "Error in hat2\n" );
- fprintf( stderr, "%s != %s\n", b, name[i] );
- exit( 1 );
- }
-#endif
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- mtx[i][j-i] = ( input_new( fp, D ) );
- }
-}
-void readhat2_float( FILE *fp, int nseq, char name[M][B], float **mtx )
-{
- int i, j, nseq0;
- char b[B];
-
- fgets( b, B, fp );
- fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
- fgets( b, B, fp );
- for( i=0; i<nseq; i++ )
- {
-#if 0
- getaline_fp_eof( b, B, fp );
-#else
- myfgets( b, B-2, fp );
-#endif
-#if 0
- j = MIN( strlen( b+6 ), 10 );
- if( strncmp( name[i], b+6 , j ) )
- {
- fprintf( stderr, "Error in hat2\n" );
- fprintf( stderr, "%s != %s\n", b, name[i] );
- exit( 1 );
- }
-#endif
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- mtx[i][j] = ( input_new( fp, D ) );
- }
-}
-void readhat2_int( FILE *fp, int nseq, char name[M][B], int **mtx )
-{
- int i, j, nseq0;
- char b[B];
-
- fgets( b, B, fp );
- fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
- fgets( b, B, fp );
- for( i=0; i<nseq; i++ )
- {
-#if 0
- getaline_fp_eof( b, B, fp );
-#else
- myfgets( b, B-2, fp );
-#endif
-#if 0
- j = MIN( strlen( b+6 ), 10 );
- if( strncmp( name[i], b+6 , j ) )
- {
- fprintf( stderr, "Error in hat2\n" );
- fprintf( stderr, "%s != %s\n", b, name[i] );
- exit( 1 );
- }
-#endif
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- mtx[i][j] = (int)( input_new( fp, D ) * INTMTXSCALE + 0.5 );
- }
-}
-
-void readhat2_pointer( FILE *fp, int nseq, char **name, double **mtx )
-{
- int i, j, nseq0;
- char b[B];
-
- fgets( b, B, fp );
- fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
- fgets( b, B, fp );
- for( i=0; i<nseq; i++ )
- {
-#if 0
- getaline_fp_eof( b, B, fp );
-#else
- myfgets( b, B-2, fp );
-#endif
-#if 0
- j = MIN( strlen( b+6 ), 10 );
- if( strncmp( name[i], b+6 , j ) )
- {
- fprintf( stderr, "Error in hat2\n" );
- fprintf( stderr, "%s != %s\n", b, name[i] );
- exit( 1 );
- }
-#endif
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- mtx[i][j] = (double)input_new( fp, D);
- }
-}
-void readhat2( FILE *fp, int nseq, char name[M][B], double **mtx )
-{
- int i, j, nseq0;
- char b[B];
-
- fgets( b, B, fp );
- fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
- fgets( b, B, fp );
- for( i=0; i<nseq; i++ )
- {
-#if 0
- getaline_fp_eof( b, B, fp );
-#else
- myfgets( b, B-2, fp );
-#endif
-#if 0
- j = MIN( strlen( b+6 ), 10 );
- if( strncmp( name[i], b+6 , j ) )
- {
- fprintf( stderr, "Error in hat2\n" );
- fprintf( stderr, "%s != %s\n", b, name[i] );
- exit( 1 );
- }
-#endif
- }
- for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
- {
- mtx[i][j] = (double)input_new( fp, D);
- }
-}
-
-void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, float **mtx )
-{
- int i, j, ijsa;
- double max = 0.0;
- for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
-
- fprintf( hat2p, "%5d\n", 1 );
- fprintf( hat2p, "%5d\n", locnjob );
- fprintf( hat2p, " %#6.3f\n", max * 2.5 );
-
- for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
- for( i=0; i<locnjob; i++ )
- {
- for( j=i+1; j<njob; j++ )
- {
- fprintf( hat2p, "%#6.3f", mtx[i][j-i] );
- ijsa = j-i;
- if( ijsa % 12 == 0 || ijsa == locnjob-i-1 ) fprintf( hat2p, "\n" );
- }
- }
-}
-
-void WriteFloatHat2_pointer( FILE *hat2p, int locnjob, char **name, float **mtx )
-{
- int i, j;
- double max = 0.0;
- for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
-
- fprintf( hat2p, "%5d\n", 1 );
- fprintf( hat2p, "%5d\n", locnjob );
- fprintf( hat2p, " %#6.3f\n", max * 2.5 );
-
- for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
- for( i=0; i<locnjob; i++ )
- {
- for( j=1; j<locnjob-i; j++ )
- {
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
- if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
- }
- }
-}
-
-void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], float **mtx )
-{
- int i, j;
- double max = 0.0;
- for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
-
- fprintf( hat2p, "%5d\n", 1 );
- fprintf( hat2p, "%5d\n", locnjob );
- fprintf( hat2p, " %#6.3f\n", max * 2.5 );
-
- for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
- for( i=0; i<locnjob; i++ )
- {
- for( j=1; j<locnjob-i; j++ )
- {
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
- if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
- }
- }
-}
-
-void WriteHat2_int( FILE *hat2p, int locnjob, char name[M][B], int **mtx )
-{
- int i, j;
- double max = 0.0;
- for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
- max /= INTMTXSCALE;
-
- fprintf( hat2p, "%5d\n", 1 );
- fprintf( hat2p, "%5d\n", locnjob );
- fprintf( hat2p, " %#6.3f\n", max * 2.5 );
-
- for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
- for( i=0; i<locnjob-1; i++ )
- {
- for( j=i+1; j<locnjob; j++ )
- {
- fprintf( hat2p, "%#6.3f", (float)mtx[i][j] / INTMTXSCALE );
- if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
- }
- }
-}
-void WriteHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx )
-{
- int i, j;
- double max = 0.0;
- for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
-
- fprintf( hat2p, "%5d\n", 1 );
- fprintf( hat2p, "%5d\n", locnjob );
- fprintf( hat2p, " %#6.3f\n", max * 2.5 );
-
- for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
- for( i=0; i<locnjob-1; i++ )
- {
- for( j=i+1; j<locnjob; j++ )
- {
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
- if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
- }
- }
-}
-void WriteHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx )
-{
- int i, j;
- double max = 0.0;
- for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
-
- fprintf( hat2p, "%5d\n", 1 );
- fprintf( hat2p, "%5d\n", locnjob );
- fprintf( hat2p, " %#6.3f\n", max * 2.5 );
-
- for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
- for( i=0; i<locnjob-1; i++ )
- {
- for( j=i+1; j<locnjob; j++ )
- {
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
- if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
- }
- }
-}
-
-#if 0
-void WriteHat2plain( FILE *hat2p, int locnjob, double **mtx )
-{
- int i, j, ilim;
-
- ilim = locnjob-1;
- for( i=0; i<ilim; i++ )
- {
- fprintf( hat2p, "%d-%d d=%.3f\n", i+1, i+1, 0.0 );
- for( j=i+1; j<locnjob; j++ )
- {
- fprintf( hat2p, "%d-%d d=%.3f\n", i+1, j+1, mtx[i][j] );
- }
- }
-}
-#endif
-
-int ReadFasta_sub( FILE *fp, double *dis, int nseq, char name[M][B] )
-{
- int i, count=0;
- char b[B];
- int junban[M];
-
- count = 0;
- for( i=0; i<10000000 && count<nseq; i++ )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
- count++;
- }
- }
-
- for( i=0; i<nseq; i++ ) dis[i] = 0.0;
- count = 0;
- for( i=0; i<100000 && count<nseq; i++ )
- {
- if( fgets( b, B-1, fp ) ) break;
- if( !strncmp( name[junban[count]], b, 20 ) )
- {
- fgets( b, B-1, fp );
- dis[junban[count]] = atof( b );
- count++;
- }
- }
- return 0;
-}
-
-
-int ReadSsearch( FILE *fp, double *dis, int nseq, char name[M][B] )
-{
- int i, count=0;
- char b[B];
- int junban[M];
- int opt;
-
- count = 0;
- for( i=0; i<10000000 && count<nseq; i++ )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
- sscanf( b+75, "%d", &opt );
- dis[junban[count]] = (double)opt;
- count++;
- }
- }
-
-/*
- count = 0;
- for( i=0; i<100000 && count<nseq; i++ )
- {
- fgets( b, B-1, fp );
- if( !strncmp( name[junban[count]], b, 20 ) )
- {
- dis[junban[count]] = atof( b+65 );
- count++;
- }
- }
-*/
- return 0;
-}
-
-int ReadBlastm7_avscore( FILE *fp, double *dis, int nin )
-{
- int count=0;
- char b[B];
- char *pt;
- int *junban;
- double score, sumscore;
- double len, sumlen;
- int qstart, qend, tstart, tend;
- double scorepersite;
- static char qal[N], tal[N], al[N];
- int nlocalhom;
-
- junban = calloc( nin, sizeof( int ) );
-
- count = 0;
- sumscore = 0.0;
- sumlen = 0.0;
- score = 0.0;
- len = 0.0;
- scorepersite = 0.0; // by D.Mathog, a guess
- while( 1 )
- {
-
- if( feof( fp ) ) break;
-
- while( fgets( b, B-1, fp ) )
- {
- if( !strncmp( " <Hit_def>", b, 19 ) || !strncmp( " <Hsp_num>", b, 23 ) ) break;
- }
-
- if( !strncmp( " <Hit_def>", b, 19 ) )
- {
- junban[count] = atoi( b+31 );
- nlocalhom = 0;
- }
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_score>", b, 25 ) ) break;
- pt = b + 25;
- score = atof( pt );
- sumscore += score;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_query-from>", b, 30 ) ) break;
- pt = b + 30;
- qstart = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_query-to>", b, 28 ) ) break;
- pt = b + 28;
- qend = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_hit-from>", b, 28 ) ) break;
- pt = b + 28;
- tstart = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_hit-to>", b, 26 ) ) break;
- pt = b + 26;
- tend = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_align-len>", b, 29 ) ) break;
- pt = b + 29;
- len = atoi( pt );
- sumlen += len;
-
-
- while( fgets( al, N-100, fp ) )
- if( !strncmp( " <Hsp_qseq>", al, 24 ) ) break;
-
- strcpy( qal, al+24 );
- pt = qal;
- while( *++pt != '<' )
- ;
- *pt = 0;
-
-
- while( fgets( al, N-100, fp ) )
- if( !strncmp( " <Hsp_hseq>", al, 24 ) ) break;
-
- strcpy( tal, al+24 );
- pt = tal;
- while( *++pt != '<' )
- ;
- *pt = 0;
-
-
-// fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " </Hsp>:", b, 18 ) ) break;
-
-
- fgets( b, B-1, fp );
-
-
- if( !strncmp( " </Hit_hsps>", b, 21 ) )
- {
- dis[junban[count++]] = sumscore;
- sumscore = 0.0;
- fgets( b, B-1, fp );
- fgets( b, B-1, fp );
- scorepersite = sumscore / sumlen;
- if( scorepersite != (int)scorepersite )
- {
- fprintf( stderr, "ERROR! sumscore=%f, sumlen=%f, and scorepersite=%f\n", sumscore, sumlen, scorepersite );
- exit( 1 );
- }
-
- if( !strncmp( " </Iteration_hits>", b, 23 ) ) break;
- }
- }
-
- free( junban );
-
- return (int)scorepersite;
-}
-int ReadBlastm7_scoreonly( FILE *fp, double *dis, int nin )
-{
- int count=0;
- char b[B];
- char *pt;
- int *junban;
- int overlapaa;
- double score, sumscore;
- int qstart, qend, tstart, tend;
- static char qal[N], tal[N], al[N];
- int nlocalhom;
-
- junban = calloc( nin, sizeof( int ) );
-
- count = 0;
- sumscore = 0.0;
- score = 0.0;
- while( 1 )
- {
-
- if( feof( fp ) ) break;
-
- while( fgets( b, B-1, fp ) )
- {
- if( !strncmp( " <Hit_def>", b, 19 ) || !strncmp( " <Hsp_num>", b, 23 ) ) break;
- }
-
- if( !strncmp( " <Hit_def>", b, 19 ) )
- {
- junban[count] = atoi( b+31 );
- nlocalhom = 0;
- }
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_score>", b, 25 ) ) break;
- pt = b + 25;
- score = atof( pt );
- sumscore += score;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_query-from>", b, 30 ) ) break;
- pt = b + 30;
- qstart = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_query-to>", b, 28 ) ) break;
- pt = b + 28;
- qend = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_hit-from>", b, 28 ) ) break;
- pt = b + 28;
- tstart = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_hit-to>", b, 26 ) ) break;
- pt = b + 26;
- tend = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_align-len>", b, 29 ) ) break;
- pt = b + 29;
- overlapaa = atoi( pt );
-
-
- while( fgets( al, N-100, fp ) )
- if( !strncmp( " <Hsp_qseq>", al, 24 ) ) break;
-
- strcpy( qal, al+24 );
- pt = qal;
- while( *++pt != '<' )
- ;
- *pt = 0;
-
-
- while( fgets( al, N-100, fp ) )
- if( !strncmp( " <Hsp_hseq>", al, 24 ) ) break;
-
- strcpy( tal, al+24 );
- pt = tal;
- while( *++pt != '<' )
- ;
- *pt = 0;
-
-
-// fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
-
-// nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom );
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " </Hsp>:", b, 18 ) ) break;
-
-
- fgets( b, B-1, fp );
-
-
- if( !strncmp( " </Hit_hsps>", b, 21 ) )
- {
- dis[junban[count++]] = sumscore;
- sumscore = 0.0;
- fgets( b, B-1, fp );
- fgets( b, B-1, fp );
- if( !strncmp( " </Iteration_hits>", b, 23 ) ) break;
- }
- }
-
- free( junban );
-
- return count;
-}
-
-int ReadBlastm7( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
-{
- int count=0;
- char b[B];
- char *pt;
- static int junban[M];
- int overlapaa;
- double score, sumscore;
- int qstart, qend, tstart, tend;
- static char qal[N], tal[N], al[N];
- int nlocalhom;
-
-
-
- count = 0;
- sumscore = 0.0;
- score = 0.0;
- nlocalhom = 0;
- while( 1 )
- {
-
- if( feof( fp ) ) break;
-
- while( fgets( b, B-1, fp ) )
- {
- if( !strncmp( " <Hit_def>", b, 19 ) || !strncmp( " <Hsp_num>", b, 23 ) ) break;
- }
-
- if( !strncmp( " <Hit_def>", b, 19 ) )
- {
- junban[count] = atoi( b+31 );
- nlocalhom = 0;
- }
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_score>", b, 25 ) ) break;
- pt = b + 25;
- score = atof( pt );
- sumscore += score;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_query-from>", b, 30 ) ) break;
- pt = b + 30;
- qstart = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_query-to>", b, 28 ) ) break;
- pt = b + 28;
- qend = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_hit-from>", b, 28 ) ) break;
- pt = b + 28;
- tstart = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_hit-to>", b, 26 ) ) break;
- pt = b + 26;
- tend = atoi( pt ) - 1;
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " <Hsp_align-len>", b, 29 ) ) break;
- pt = b + 29;
- overlapaa = atoi( pt );
-
-
- while( fgets( al, N-100, fp ) )
- if( !strncmp( " <Hsp_qseq>", al, 24 ) ) break;
-
- strcpy( qal, al+24 );
- pt = qal;
- while( *++pt != '<' )
- ;
- *pt = 0;
-
-
- while( fgets( al, N-100, fp ) )
- if( !strncmp( " <Hsp_hseq>", al, 24 ) ) break;
-
- strcpy( tal, al+24 );
- pt = tal;
- while( *++pt != '<' )
- ;
- *pt = 0;
-
-
-// fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
-
- nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom );
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( " </Hsp>:", b, 18 ) ) break;
-
-
- fgets( b, B-1, fp );
-
-
- if( !strncmp( " </Hit_hsps>", b, 21 ) )
- {
- dis[junban[count++]] = sumscore;
- sumscore = 0.0;
- fgets( b, B-1, fp );
- fgets( b, B-1, fp );
- if( !strncmp( " </Iteration_hits>", b, 23 ) ) break;
- }
- }
- return count;
-}
-
-int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
-{
- int count=0;
- char b[B];
- char *pt;
- static int junban[M];
- int opt;
- double z, bits;
-
-
- count = 0;
-#if 0
- for( i=0; i<10000000 && count<nseq; i++ )
-#else
- while( !feof( fp ) )
-#endif
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
-
- pt = strchr( b, ')' ) + 1;
- sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
- dis[junban[count]] = (double)opt;
- count++;
-
- }
- }
-
- return count;
-}
-int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
-{
- int count=0;
- char b[B];
- char *pt;
- static int junban[M];
- int overlapaa;
- int opt, qstart, qend, tstart, tend;
- double z, bits;
- int qal_display_start, tal_display_start;
- static char qal[N], tal[N];
- char *qal2, *tal2;
- int c;
-
-
- count = 0;
-#if 0
- for( i=0; i<10000000 && count<nseq; i++ )
-#else
- while( !feof( fp ) )
-#endif
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
-
- if( strchr( b, 'r' ) ) continue;
-
- pt = strchr( b, ']' ) + 1;
- sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
- dis[junban[count]] = (double)opt;
- count++;
-
- }
- else if( 0 == strncmp( ">>+==========+", b, 14 ) )
- {
- break;
- }
-
- }
- if( !count ) return -1;
-
- count = 0;
- while( 1 )
- {
- if( strncmp( ">>+==========+", b, 14 ) )
- {
- fgets( b, B-1, fp );
- if( feof( fp ) ) break;
- continue;
- }
- junban[count++] = atoi( b+14 );
-// fprintf( stderr, "t = %d\n", atoi( b+14 ) );
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "; fa_opt:", b, 9 ) || !strncmp( "; sw_s-w opt:", b, 13 ) ) break;
- pt = strstr( b, ":" ) +1;
- opt = atoi( pt );
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_overlap:", b+4, 9 ) ) break;
- pt = strstr( b, ":" ) +1;
- overlapaa = atoi( pt );
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_start:", b+4, 7 ) ) break;
- pt = strstr( b, ":" ) +1;
- qstart = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_stop:", b+4, 6 ) ) break;
- pt = strstr( b, ":" ) +1;
- qend = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_display_start:", b+4, 15 ) ) break;
- pt = strstr( b, ":" ) +1;
- qal_display_start = atoi( pt ) - 1;
-
- pt = qal;
- while( (c = fgetc( fp )) )
- {
- if( c == '>' )
- {
- ungetc( c, fp );
- break;
- }
- if( isalpha( c ) || c == '-' )
- *pt++ = c;
- }
- *pt = 0;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_start:", b+4, 7 ) ) break;
- pt = strstr( b, ":" ) + 1;
- tstart = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_stop:", b+4, 6 ) ) break;
- pt = strstr( b, ":" ) + 1;
- tend = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_display_start:", b+4, 15 ) ) break;
- pt = strstr( b, ":" ) + 1;
- tal_display_start = atoi( pt ) - 1;
-
- pt = tal;
- while( ( c = fgetc( fp ) ) )
- {
- if( c == '>' )
- {
- ungetc( c, fp );
- break;
- }
- if( isalpha( c ) || c == '-' )
- *pt++ = c;
- }
- *pt = 0;
-
-// fprintf( stderr, "(%d-%d:%d-%d)\n", qstart, qend, tstart, tend );
-// fprintf( stderr, "qal_display_start = %d, tal_display_start = %d\n", qal_display_start, tal_display_start );
-
-// fprintf( stderr, "qal = %s\n", qal );
-// fprintf( stderr, "tal = %s\n", tal );
-
- qal2 = cutal( qal, qal_display_start, qstart, qend );
- tal2 = cutal( tal, tal_display_start, tstart, tend );
-
-// fprintf( stderr, "qal2 = %s\n", qal2 );
-// fprintf( stderr, "tal2 = %s\n", tal2 );
-
-// fprintf( stderr, "putting %d - %d, opt = %d\n", qmem, junban[count-1], opt );
- putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
- }
-// fprintf( stderr, "count = %d\n", count );
- return count;
-}
-int ReadFasta34m10( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
-{
- int count=0;
- char b[B];
- char *pt;
- static int junban[M];
- int overlapaa;
- int opt, qstart, qend, tstart, tend;
- double z, bits;
- int qal_display_start, tal_display_start;
- static char qal[N], tal[N];
- char *qal2, *tal2;
- int c;
-
-
- count = 0;
-#if 0
- for( i=0; i<10000000 && count<nseq; i++ )
-#else
- while( !feof( fp ) )
-#endif
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
-
- pt = strchr( b, ')' ) + 1;
- sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
- dis[junban[count]] = (double)opt;
- count++;
-
- }
- else if( 0 == strncmp( ">>+==========+", b, 14 ) )
- {
- break;
- }
-
- }
- if( !count ) return -1;
-
- count = 0;
- while( 1 )
- {
- if( strncmp( ">>+==========+", b, 14 ) )
- {
- fgets( b, B-1, fp );
- if( feof( fp ) ) break;
- continue;
- }
- junban[count++] = atoi( b+14 );
-// fprintf( stderr, "t = %d\n", atoi( b+14 ) );
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "; fa_opt:", b, 9 ) || !strncmp( "; sw_s-w opt:", b, 13 ) ) break;
- pt = strstr( b, ":" ) +1;
- opt = atoi( pt );
-
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_overlap:", b+4, 9 ) ) break;
- pt = strstr( b, ":" ) +1;
- overlapaa = atoi( pt );
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_start:", b+4, 7 ) ) break;
- pt = strstr( b, ":" ) +1;
- qstart = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_stop:", b+4, 6 ) ) break;
- pt = strstr( b, ":" ) +1;
- qend = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_display_start:", b+4, 15 ) ) break;
- pt = strstr( b, ":" ) +1;
- qal_display_start = atoi( pt ) - 1;
-
- pt = qal;
- while( (c = fgetc( fp )) )
- {
- if( c == '>' )
- {
- ungetc( c, fp );
- break;
- }
- if( isalpha( c ) || c == '-' )
- *pt++ = c;
- }
- *pt = 0;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_start:", b+4, 7 ) ) break;
- pt = strstr( b, ":" ) + 1;
- tstart = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_stop:", b+4, 6 ) ) break;
- pt = strstr( b, ":" ) + 1;
- tend = atoi( pt ) - 1;
-
- while( fgets( b, B-1, fp ) )
- if( !strncmp( "_display_start:", b+4, 15 ) ) break;
- pt = strstr( b, ":" ) + 1;
- tal_display_start = atoi( pt ) - 1;
-
- pt = tal;
- while( ( c = fgetc( fp ) ) )
- {
- if( c == '>' )
- {
- ungetc( c, fp );
- break;
- }
- if( isalpha( c ) || c == '-' )
- *pt++ = c;
- }
- *pt = 0;
-
-// fprintf( stderr, "(%d-%d:%d-%d)\n", qstart, qend, tstart, tend );
-// fprintf( stderr, "qal_display_start = %d, tal_display_start = %d\n", qal_display_start, tal_display_start );
-
-// fprintf( stderr, "qal = %s\n", qal );
-// fprintf( stderr, "tal = %s\n", tal );
-
- qal2 = cutal( qal, qal_display_start, qstart, qend );
- tal2 = cutal( tal, tal_display_start, tstart, tend );
-
-// fprintf( stderr, "qal2 = %s\n", qal2 );
-// fprintf( stderr, "tal2 = %s\n", tal2 );
-
-// fprintf( stderr, "putting %d - %d, opt = %d\n", qmem, junban[count-1], opt );
- putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
- }
-// fprintf( stderr, "count = %d\n", count );
- return count;
-}
-int ReadFasta34m10_scoreonly_nucbk( FILE *fp, double *dis, int nin )
-{
- int count=0;
- char b[B];
- char *pt;
- int pos;
- int opt;
- double z, bits;
-
- count = 0;
- while( !feof( fp ) )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+===========+", b, 13 ) )
- {
- pos = atoi( b+13 );
-
- if( strchr( b, 'r' ) ) continue;
-
-// pt = strchr( b, ')' ) + 1;
- pt = strchr( b, ']' ) + 1;
- sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
- dis[pos] += (double)opt;
- count++;
-#if 0
- fprintf( stderr, "b=%s\n", b );
- fprintf( stderr, "opt=%d\n", opt );
- fprintf( stderr, "pos=%d\n", pos );
- fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
-#endif
-
- }
- else if( 0 == strncmp( ">>><<<", b, 6 ) )
- {
- break;
- }
-
- }
- if( !count ) return -1;
-
- return count;
-}
-
-int ReadFasta34m10_scoreonly_nuc( FILE *fp, double *dis, int nin )
-{
- int count=0;
- char b[B];
- char *pt;
- int pos;
- int opt;
- double z, bits;
- int c;
- int *yonda;
-
-
- yonda = AllocateIntVec( nin );
- for( c=0; c<nin; c++ ) yonda[c] = 0;
- for( c=0; c<nin; c++ ) dis[c] = 0.0;
-
- count = 0;
- while( !feof( fp ) )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+===========+", b, 13 ) )
- {
- pos = atoi( b+13 );
-
- if( strchr( b, 'r' ) ) continue;
-
-// pt = strchr( b, ')' ) + 1;
- pt = strchr( b, ']' ) + 1;
- sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
- if( yonda[pos] == 0 )
- {
- dis[pos] += (double)opt;
- yonda[pos] = 1;
- }
- count++;
-#if 0
- fprintf( stderr, "b=%s\n", b );
- fprintf( stderr, "opt=%d\n", opt );
- fprintf( stderr, "pos=%d\n", pos );
- fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
-#endif
-
- }
- else if( !strncmp( ">>>", b, 3 ) )
- {
- for( c=0; c<nin; c++ ) yonda[c] = 0;
- }
- else if( 0 == strncmp( ">>><<<", b, 6 ) )
- {
- break;
- }
-
- }
-
- free( yonda );
-
- if( !count ) return -1;
-
- return count;
-}
-
-int ReadFasta34m10_scoreonly( FILE *fp, double *dis, int nin )
-{
- int count=0;
- char b[B];
- char *pt;
- int pos;
- int opt;
- double z, bits;
- int c;
- int *yonda;
-
-
- yonda = AllocateIntVec( nin );
- for( c=0; c<nin; c++ ) yonda[c] = 0;
- for( c=0; c<nin; c++ ) dis[c] = 0.0;
-
- count = 0;
- while( !feof( fp ) )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+===========+", b, 13 ) )
- {
- pos = atoi( b+13 );
-
- pt = strchr( b, ')' ) + 1;
- sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
- if( yonda[pos] == 0 )
- {
- dis[pos] += (double)opt;
- yonda[pos] = 1;
- }
- count++;
-#if 0
- fprintf( stderr, "b=%s\n", b );
- fprintf( stderr, "opt=%d\n", opt );
- fprintf( stderr, "pos=%d\n", pos );
- fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
-#endif
-
- }
- else if( !strncmp( ">>>", b, 3 ) )
- {
- for( c=0; c<nin; c++ ) yonda[c] = 0;
- }
- else if( 0 == strncmp( ">>><<<", b, 6 ) )
- {
- break;
- }
-
- }
-
- free( yonda );
-
- if( !count ) return -1;
-
- return count;
-}
-int ReadFasta34( FILE *fp, double *dis, int nseq, char name[M][B], LocalHom *localhomlist )
-{
- int count=0;
- char b[B];
- char *pt;
- static int junban[M];
- int overlapaa;
- int opt, qstart, qend, tstart, tend;
- double z, bits;
-
-
- count = 0;
-#if 0
- for( i=0; i<10000000 && count<nseq; i++ )
-#else
- while( !feof( fp ) )
-#endif
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
-
- pt = strchr( b, ')' ) + 1;
- sscanf( pt, "%d %lf %lf", &opt, &bits, &z );
- dis[junban[count]] = (double)opt;
- count++;
-
- }
- else if( 0 == strncmp( ">>+==========+", b, 14 ) )
- {
- break;
- }
-
- }
- if( !count ) return -1;
-
- count = 0;
- while( !feof( fp ) )
- {
- if( !strncmp(">>+==========+", b, 14 ) )
- {
- junban[count] = atoi( b+14 );
- count++;
- fgets( b, B-1, fp ); // initn:
- pt = strstr( b, "opt: " ) + 5;
- localhomlist[junban[count-1]].opt = atof( pt );
- fgets( b, B-1, fp ); // Smith-Waterman score
- pt = strstr( b, "ungapped) in " ) + 13;
- sscanf( pt, "%d", &overlapaa );
- fprintf( stderr, "pt = %s, overlapaa = %d\n", pt, overlapaa );
- pt = strstr( b, "overlap (" ) + 8;
- sscanf( pt, "(%d-%d:%d-%d)", &qstart, &qend, &tstart, &tend );
- localhomlist[junban[count-1]].overlapaa = overlapaa;
- localhomlist[junban[count-1]].start1 = qstart-1;
- localhomlist[junban[count-1]].end1 = qend-1;
- localhomlist[junban[count-1]].start2 = tstart-1;
- localhomlist[junban[count-1]].end2 = tend-1;
- }
- fgets( b, B-1, fp );
- }
- fprintf( stderr, "count = %d\n", count );
- return count;
-}
-
-int ReadFasta3( FILE *fp, double *dis, int nseq, char name[M][B] )
-{
- int count=0;
- char b[B];
- char *pt;
- int junban[M];
- int initn, init1, opt;
- double z;
-
- count = 0;
-#if 0
- for( i=0; i<10000000 && count<nseq; i++ )
-#else
- while( !feof( fp ) )
-#endif
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
-
- pt = strchr( b, ')' ) + 1;
- sscanf( pt, "%d %d %d %lf", &initn, &init1, &opt, &z );
- dis[junban[count]] = (double)opt;
- count++;
- }
- }
- return 0;
-}
-
-int ReadFasta( FILE *fp, double *dis, int nseq, char name[M][B] )
-{
- int i, count=0;
- char b[B];
- int junban[M];
- int initn, init1, opt;
-
- count = 0;
- for( i=0; i<nseq; i++ ) dis[i] = 0.0;
- for( i=0; !feof( fp ) && count<nseq; i++ )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
-
- sscanf( b+50, "%d %d %d", &initn, &init1, &opt );
- dis[junban[count]] = (double)opt;
- count++;
- }
- }
-
-/*
- count = 0;
- for( i=0; i<100000 && count<nseq; i++ )
- {
- fgets( b, B-1, fp );
- if( !strncmp( name[junban[count]], b, 20 ) )
- {
- dis[junban[count]] = atof( b+65 );
- count++;
- }
- }
-*/
- return 0;
-}
-
-
-int ReadOpt( FILE *fp, int opt[M], int nseq, char name[M][B] )
-{
- int i, count=0;
- char b[B];
- int junban[M];
- int optt, initn, init1;
-
- count = 0;
- for( i=0; i<10000000 && count<nseq; i++ )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
- sscanf( b+50, "%d %d %d", &initn, &init1, &optt );
- opt[junban[count]] = (double)optt;
- count++;
- }
- }
- return 0;
-}
-
-int ReadOpt2( FILE *fp, int opt[M], int nseq, char name[M][B] )
-{
- int i, count=0;
- char b[B];
- int junban[M];
-
- count = 0;
- for( i=0; i<10000000 && count<nseq; i++ )
- {
- fgets( b, B-1, fp );
- if( !strncmp( "+==========+", b, 12 ) )
- {
- junban[count] = atoi( b+12 );
- opt[junban[count]] = atoi( b+65 );
- count++;
- }
- }
- return 0;
-}
-
-
-
-int writePre( int nseq, char **name, int nlen[M], char **aseq, int force )
-{
-#if USE_XCED
- int i, value;
- if( !signalSM )
- {
- if( force )
- {
- rewind( prep_g );
- if( devide ) dvWrite( prep_g, nseq, name, nlen, aseq );
-#if 0
- else WriteGapFill( prep_g, nseq, name, nlen, aseq );
-#else
- else writeData( prep_g, nseq, name, nlen, aseq );
-#endif
- }
- return( 0 );
- }
- for( i=0; i<10; i++ )
- {
-#if IODEBUG
- fprintf( stderr, "SEMAPHORE = %d\n", signalSM[SEMAPHORE] );
-#endif
- if( signalSM[SEMAPHORE]-- > 0 )
- {
-#if 0 /* /tmp/pre ¤Î´Ø·¸¤Ç¤Ï¤º¤·¤¿ */
- if( ferror( prep_g ) ) prep_g = fopen( "pre", "w" );
- if( !prep_g ) ErrorExit( "Cannot re-open pre." );
-#endif
- rewind( prep_g );
- signalSM[STATUS] = IMA_KAITERU;
-#if IODEBUG
- if( force ) fprintf( stderr, "FINAL " );
-#endif
- if( devide ) dvWrite( prep_g, nseq, name, nlen, aseq );
- else WriteGapFill( prep_g, nseq, name, nlen, aseq );
- /*
- fprintf( prep_g, '\EOF' );
- */
- fflush( prep_g );
- if( force ) signalSM[STATUS] = OSHIMAI;
- else signalSM[STATUS] = KAKIOWATTA;
- value = 1;
- signalSM[SEMAPHORE]++;
-#if IODEBUG
- fprintf( stderr, "signalSM[STATUS] = %c\n", signalSM[STATUS] );
-#endif
- break;
- }
- else
- {
-#if IODEBUG
- fprintf( stderr, "YONDERUKARA_AKIRAMERU\n" );
-#endif
- value = 0;
- signalSM[SEMAPHORE]++;
- if( !force ) break;
-#if IODEBUG
- fprintf( stderr, "MATSU\n" );
-#endif
- sleep( 1 );
- }
- }
- if( force && !value ) ErrorExit( "xced ga pre wo hanasanai \n" );
- return( value );
-#else
- if( force )
- {
- rewind( prep_g );
- writeData_pointer( prep_g, nseq, name, nlen, aseq );
- }
-#endif
- return( 0 );
-}
-
-
-void readOtherOptions( int *ppidptr, int *fftThresholdptr, int *fftWinSizeptr )
-{
- if( calledByXced )
- {
- FILE *fp = fopen( "pre", "r" );
- char b[B];
- if( !fp ) ErrorExit( "Cannot open pre.\n" );
- fgets( b, B-1, fp );
- sscanf( b, "%d %d %d", ppidptr, fftThresholdptr, fftWinSizeptr );
- fclose( fp );
-#if IODEBUG
- fprintf( stderr, "b = %s\n", b );
- fprintf( stderr, "ppid = %d\n", ppid );
- fprintf( stderr, "fftThreshold = %d\n", fftThreshold );
- fprintf( stderr, "fftWinSize = %d\n", fftWinSize );
-#endif
- }
- else
- {
- *ppidptr = 0;
- *fftThresholdptr = FFT_THRESHOLD;
- if( dorp == 'd' )
- *fftWinSizeptr = FFT_WINSIZE_D;
- else
- *fftWinSizeptr = FFT_WINSIZE_P;
- }
-#if 0
- fprintf( stderr, "fftThresholdptr=%d\n", *fftThresholdptr );
- fprintf( stderr, "fftWinSizeptr=%d\n", *fftWinSizeptr );
-#endif
-}
-
-void initSignalSM( void )
-{
-// int signalsmid;
-
-#if IODEBUG
- if( ppid ) fprintf( stderr, "PID of xced = %d\n", ppid );
-#endif
- if( !ppid )
- {
- signalSM = NULL;
- return;
- }
-
-#if 0
- signalsmid = shmget( (key_t)ppid, 3, IPC_ALLOC | 0666 );
- if( signalsmid == -1 ) ErrorExit( "Cannot get Shared memory for signal.\n" );
- signalSM = shmat( signalsmid, 0, 0 );
- if( (int)signalSM == -1 ) ErrorExit( "Cannot attatch Shared Memory for signal!\n" );
- signalSM[STATUS] = IMA_KAITERU;
- signalSM[SEMAPHORE] = 1;
-#endif
-}
-
-void initFiles( void )
-{
- char pname[100];
- if( ppid )
- sprintf( pname, "/tmp/pre.%d", ppid );
- else
- sprintf( pname, "pre" );
- prep_g = fopen( pname, "w" );
- if( !prep_g ) ErrorExit( "Cannot open pre" );
-
- trap_g = fopen( "trace", "w" );
- if( !trap_g ) ErrorExit( "cannot open trace" );
- fprintf( trap_g, "PID = %d\n", getpid() );
- fflush( trap_g );
-}
-
-
-void WriteForFasta( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq )
-{
- static char b[N];
- int i, j;
- int nalen[M];
-
- for( i=0; i<locnjob; i++ )
- {
- nalen[i] = strlen( aseq[i] );
- fprintf( fp, ">%s\n", name[i] );
- for( j=0; j<nalen[i]; j=j+C )
- {
- strncpy( b, aseq[i]+j, C ); b[C] = 0;
- fprintf( fp, "%s\n",b );
- }
- }
-}
-
-void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
-{
- double opt;
- static char buff[B];
- char infor[100];
- int i, j, overlapaa, start1, end1, start2, end2;
- LocalHom *tmpptr1, *tmpptr2;
-
-// for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
-
- while ( NULL != fgets( buff, B-1, fp ) )
- {
-// fprintf( stderr, "\n" );
- sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
- if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
-
-#if 0
- if( start1 == end1 || start2 == end2 ) continue; //mondai ari
-#endif
-
-// if( i < j )
- {
- if( localhomtable[i][j].nokori++ > 0 )
- {
- tmpptr1 = localhomtable[i][j].last;
-// fprintf( stderr, "reallocating, localhomtable[%d][%d].nokori = %d\n", i, j, localhomtable[i][j].nokori );
- tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- tmpptr1 = tmpptr1->next;
- tmpptr1->extended = -1;
- tmpptr1->next = NULL;
- localhomtable[i][j].last = tmpptr1;
-// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
- }
- else
- {
- tmpptr1 = localhomtable[i]+j;
-// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
- }
-
- tmpptr1->start1 = start1;
- tmpptr1->start2 = start2;
- tmpptr1->end1 = end1;
- tmpptr1->end2 = end2;
-// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
-// tmpptr1->opt = opt;
- tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
- tmpptr1->overlapaa = overlapaa;
- tmpptr1->korh = *infor;
- }
-// else
- {
- if( localhomtable[j][i].nokori++ > 0 )
- {
- tmpptr2 = localhomtable[j][i].last;
- tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- tmpptr2 = tmpptr2->next;
- tmpptr2->extended = -1;
- tmpptr2->next = NULL;
- localhomtable[j][i].last = tmpptr2;
-// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
- }
- else
- {
- tmpptr2 = localhomtable[j]+i;
-// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
- }
-
- tmpptr2->start2 = start1;
- tmpptr2->start1 = start2;
- tmpptr2->end2 = end1;
- tmpptr2->end1 = end2;
-// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
-// tmpptr2->opt = opt;
- tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
- tmpptr2->overlapaa = overlapaa;
- tmpptr2->korh = *infor;
-
-// fprintf( stderr, "i=%d, j=%d, st1=%d, en1=%d, opt = %f\n", i, j, tmpptr1->start1, tmpptr1->end1, opt );
- }
-
- }
-}
-void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
-{
- double opt;
- static char buff[B];
- char infor[100];
- int i, j, overlapaa, start1, end1, start2, end2;
- int **nlocalhom = NULL;
- LocalHom *tmpptr1=NULL, *tmpptr2=NULL; // by D.Mathog, a guess
-
- nlocalhom = AllocateIntMtx( njob, njob );
- for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
-
- while ( NULL != fgets( buff, B-1, fp ) )
- {
-// fprintf( stderr, "\n" );
- sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
- if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
-
-#if 0
- if( start1 == end1 || start2 == end2 ) continue; //mondai ari
-#endif
-
-
-// if( i < j )
- {
- if( nlocalhom[i][j]++ > 0 )
- {
-// fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
- tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- tmpptr1 = tmpptr1->next;
- tmpptr1->next = NULL;
- }
- else
- {
- tmpptr1 = localhomtable[i]+j;
-// fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
- }
-
- tmpptr1->start1 = start1;
- tmpptr1->start2 = start2;
- tmpptr1->end1 = end1;
- tmpptr1->end2 = end2;
-// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
-// tmpptr1->opt = opt;
- tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
- tmpptr1->overlapaa = overlapaa;
- tmpptr1->korh = *infor;
-
-// fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
- }
-// else
- {
- if( nlocalhom[j][i]++ > 0 )
- {
- tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- tmpptr2 = tmpptr2->next;
- tmpptr2->next = NULL;
- }
- else
- tmpptr2 = localhomtable[j]+i;
-
- tmpptr2->start2 = start1;
- tmpptr2->start1 = start2;
- tmpptr2->end2 = end1;
- tmpptr2->end1 = end2;
-// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
-// tmpptr2->opt = opt;
- tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
- tmpptr2->overlapaa = overlapaa;
- tmpptr2->korh = *infor;
- }
-
- }
- FreeIntMtx( nlocalhom );
-}
-
-void outlocalhom( LocalHom **localhom, int nseq )
-{
- int i, j;
- LocalHom *tmpptr;
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
- {
- tmpptr = localhom[i]+j;
- fprintf( stderr, "%d-%d\n", i, j );
- do
- {
- fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt );
- }
- while( (tmpptr=tmpptr->next) );
- }
-}
-
-void outlocalhompt( LocalHom ***localhom, int n1, int n2 )
-{
- int i, j;
- LocalHom *tmpptr;
- for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
- {
- tmpptr = localhom[i][j];
- fprintf( stderr, "%d-%d\n", i, j );
- do
- {
- fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f, wimp=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt, tmpptr->wimportance );
- }
- while( (tmpptr=tmpptr->next) );
- }
-}
-
-void FreeLocalHomTable( LocalHom **localhomtable, int n )
-{
- int i, j;
- LocalHom *ppp, *tmpptr;
- for( i=0; i<n; i++ )
- {
- for( j=0; j<n; j++ )
- {
- tmpptr=localhomtable[i]+j;
- ppp = tmpptr->next;
- for( ; tmpptr; tmpptr=ppp )
- {
-#if DEBUG
- fprintf( stderr, "i=%d, j=%d\n", i, j );
-#endif
- ppp = tmpptr->next;
- if( tmpptr!=localhomtable[i]+j )
- {
-#if DEBUG
- fprintf( stderr, "freeing %p\n", tmpptr );
-#endif
- free( tmpptr );
- }
- }
- }
-#if DEBUG
- fprintf( stderr, "freeing localhomtable[%d]\n", i );
-#endif
- free( localhomtable[i] );
- }
-#if DEBUG
- fprintf( stderr, "freeing localhomtable\n" );
-#endif
- free( localhomtable );
-#if DEBUG
- fprintf( stderr, "freed\n" );
-#endif
-}
-
-char *progName( char *str )
-{
- char *value;
- if( ( value = strrchr( str, '/' ) ) != NULL )
- return( value+1 );
- else
- return( str );
-}
-
-static void tabtospace( char *str )
-{
- char *p;
-// fprintf( stderr, "before = %s\n", str );
- while( NULL != ( p = strchr( str , '\t' ) ) )
- {
- *p = ' ';
- }
-// fprintf( stderr, "after = %s\n", str );
-}
-
-static char *extractfirstword( char *str )
-{
- char *val = str;
-
- tabtospace( str );
- while( *str )
- {
- if( val == str && *str == ' ' )
- {
- val++; str++;
- }
- else if( *str != ' ' )
- {
- str++;
- }
- else if( *str == ' ' )
- {
- *str = 0;
- }
- }
- return( val );
-}
-
-void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order )
-{
- int pos, pos2, j;
- pos = 0;
-
- fprintf( fp, " %d %d\n", nseq, maxlen );
-
- while( pos < maxlen )
- {
- for( j=0; j<nseq; j++ )
- {
- if( pos == 0 )
- fprintf( fp, "%-10.10s", extractfirstword( name[order[j]]+1 ) );
- else
- fprintf( fp, " " );
-
- pos2 = pos;
- while( pos2 < pos+41 && pos2 < maxlen )
- {
- fprintf( fp, " %.10s", seq[order[j]]+pos2 );
- pos2 += 10;
- }
- fprintf( fp, "\n" );
- }
- fprintf( fp, "\n" );
- pos += 50;
- }
-}
-
-void clustalout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, char *mark, char *comment, int *order, int namelen )
-{
- int pos, j;
- pos = 0;
- if( comment == NULL )
- fprintf( fp, "CLUSTAL format alignment by MAFFT (v%s)\n\n", VERSION );
- else
- fprintf( fp, "CLUSTAL format alignment by MAFFT %s (v%s)\n\n", comment, VERSION );
-
- while( pos < maxlen )
- {
- fprintf( fp, "\n" );
- for( j=0; j<nseq; j++ )
- {
- fprintf( fp, "%-*.*s ", namelen, namelen, extractfirstword( name[order[j]]+1 ) );
- fprintf( fp, "%.60s\n", seq[order[j]]+pos ); // Ťµ¤¬°ã¤¦¤È¤À¤á¡£
- }
- if( mark )
- {
- fprintf( fp, "%-*.*s ", namelen, namelen, "" );
- fprintf( fp, "%.60s\n", mark + pos ); // Ťµ¤¬°ã¤¦¤È¤À¤á¡£
- }
- pos += 60;
- }
-}
-
-
-void writeData_reorder_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq, int *order )
-{
- int i, j, k;
- int nalen;
-
- for( i=0; i<locnjob; i++ )
- {
- k = order[i];
-#if DEBUG
- fprintf( stderr, "i = %d in writeData\n", i );
-#endif
- nalen = strlen( aseq[k] );
- fprintf( fp, ">%s\n", name[k]+1 );
- for( j=0; j<nalen; j=j+C )
- {
-#if 0
- strncpy( b, aseq[k]+j, C ); b[C] = 0;
- fprintf( fp, "%s\n",b );
-#else
- fprintf( fp, "%.*s\n", C, aseq[k]+j );
-#endif
- }
- }
-}
-void writeData_reorder( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq, int *order )
-{
- int i, j, k;
- int nalen;
-
- for( i=0; i<locnjob; i++ )
- {
- k = order[i];
-#if DEBUG
- fprintf( stderr, "i = %d in writeData\n", i );
-#endif
- nalen = strlen( aseq[k] );
- fprintf( fp, ">%s\n", name[k]+1 );
- for( j=0; j<nalen; j=j+C )
- {
-#if 0
- strncpy( b, aseq[k]+j, C ); b[C] = 0;
- fprintf( fp, "%s\n",b );
-#else
- fprintf( fp, "%.*s\n", C, aseq[k]+j );
-#endif
- }
- }
-}
-static void showaamtxexample()
-{
- fprintf( stderr, "Format error in aa matrix\n" );
- fprintf( stderr, "# Example:\n" );
- fprintf( stderr, "# comment\n" );
- fprintf( stderr, " A R N D C Q E G H I L K M F P S T W Y V\n" );
- fprintf( stderr, "A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0\n" );
- fprintf( stderr, "R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3\n" );
- fprintf( stderr, "...\n" );
- fprintf( stderr, "V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4\n" );
- fprintf( stderr, "frequency 0.07 0.05 0.04 0.05 0.02 .. \n" );
- fprintf( stderr, "# Example end\n" );
- fprintf( stderr, "Only the lower half is loaded\n" );
- fprintf( stderr, "The last line (frequency) is optional.\n" );
- exit( 1 );
-}
-
-double *loadaamtx( void )
-{
- int i, j, k, ii, jj;
- double *val;
- double **raw;
- int *map;
- char *aaorder = "ARNDCQEGHILKMFPSTWYV";
- char *inorder;
- char *line;
- char *ptr1;
- char *ptr2;
- char *mtxfname = "_aamtx";
- FILE *mf;
-
- raw = AllocateDoubleMtx( 21, 20 );
- val = AllocateDoubleVec( 420 );
- map = AllocateIntVec( 20 );
-
- if( dorp != 'p' )
- {
- fprintf( stderr, "User-defined matrix is not supported for DNA\n" );
- exit( 1 );
- }
-
- mf = fopen( mtxfname, "r" );
- if( mf == NULL )
- {
- fprintf( stderr, "Cannot open the _aamtx file\n" );
- exit( 1 );
- }
-
- inorder = calloc( 1000, sizeof( char ) );
- line = calloc( 1000, sizeof( char ) );
-
-
- while( !feof( mf ) )
- {
- fgets( inorder, 999, mf );
- if( inorder[0] != '#' ) break;
- }
- ptr1 = ptr2 = inorder;
- while( *ptr2 )
- {
- if( isalpha( *ptr2 ) )
- {
- *ptr1 = toupper( *ptr2 );
- ptr1++;
- }
- ptr2++;
- }
- inorder[20] = 0;
-
- for( i=0; i<20; i++ )
- {
- ptr2 = strchr( inorder, aaorder[i] );
- if( ptr2 == NULL )
- {
- fprintf( stderr, "%c: not found in the first 20 letters.\n", aaorder[i] );
- showaamtxexample();
- }
- else
- {
- map[i] = ptr2 - inorder;
- }
- }
-
- i = 0;
- while( !feof( mf ) )
- {
- fgets( line, 999, mf );
-// fprintf( stderr, "line = %s\n", line );
- if( line[0] == '#' ) continue;
- ptr1 = line;
-// fprintf( stderr, "line = %s\n", line );
- for( j=0; j<=i; j++ )
- {
- while( !isdigit( *ptr1 ) && *ptr1 != '-' && *ptr1 != '.' )
- ptr1++;
-
- raw[i][j] = atof( ptr1 );
-// fprintf( stderr, "raw[][]=%f, %c-%c %d-%d\n", raw[i][j], inorder[i], inorder[j], i, j );
- ptr1 = strchr( ptr1, ' ' );
- if( ptr1 == NULL && j<i) showaamtxexample();
- }
- i++;
- if( i > 19 ) break;
- }
-
- for( i=0; i<20; i++ ) raw[20][i] = -1.0;
- while( !feof( mf ) )
- {
- fgets( line, 999, mf );
- if( line[0] == 'f' )
- {
-// fprintf( stderr, "line = %s\n", line );
- ptr1 = line;
- for( j=0; j<20; j++ )
- {
- while( !isdigit( *ptr1 ) && *ptr1 != '-' && *ptr1 != '.' )
- ptr1++;
-
- raw[20][j] = atof( ptr1 );
-// fprintf( stderr, "raw[20][]=%f, %c %d\n", raw[20][j], inorder[i], j );
- ptr1 = strchr( ptr1, ' ' );
- if( ptr1 == NULL && j<19) showaamtxexample();
- }
- break;
- }
- }
-
- k = 0;
- for( i=0; i<20; i++ )
- {
- for( j=0; j<=i; j++ )
- {
- if( i != j )
- {
- ii = MAX( map[i], map[j] );
- jj = MIN( map[i], map[j] );
- }
- else ii = jj = map[i];
- val[k++] = raw[ii][jj];
-// fprintf( stderr, "%c-%c, %f\n", aaorder[i], aaorder[j], val[k-1] );
- }
- }
- for( i=0; i<20; i++ ) val[400+i] = raw[20][map[i]];
-
- fprintf( stderr, "inorder = %s\n", inorder );
- fclose( mf );
- free( inorder );
- free( line );
- FreeDoubleMtx( raw );
- free( map );
- return( val );
-}
-
-
-void readmccaskill( FILE *fp, RNApair **pairprob, int length )
-{
- char gett[1000];
- int *pairnum;
- int i;
- int left, right;
- float prob;
- int c;
-
- pairnum = (int *)calloc( length, sizeof( int ) );
- for( i=0; i<length; i++ ) pairnum[i] = 0;
-
- c = getc( fp );
- {
- if( c != '>' )
- {
- fprintf( stderr, "format error in hat4\n" );
- exit( 1 );
- }
- }
- fgets( gett, 999, fp );
- while( 1 )
- {
- if( feof( fp ) ) break;
- c = getc( fp );
- ungetc( c, fp );
- if( c == '>' )
- {
- break;
- }
- fgets( gett, 999, fp );
-// fprintf( stderr, "gett = %s\n", gett );
- sscanf( gett, "%d %d %f", &left, &right, &prob );
-
- if( left >= length || right >= length )
- {
- fprintf( stderr, "format error in hat4\n" );
- exit( 1 );
- }
-
- if( prob < 0.01 ) continue; // 080607, mafft ni dake eikyou
-
- if( left != right && prob > 0.0 )
- {
- pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
- pairprob[left][pairnum[left]].bestscore = prob;
- pairprob[left][pairnum[left]].bestpos = right;
- pairnum[left]++;
- pairprob[left][pairnum[left]].bestscore = -1.0;
- pairprob[left][pairnum[left]].bestpos = -1;
-// fprintf( stderr, "%d-%d, %f\n", left, right, prob );
-
- pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
- pairprob[right][pairnum[right]].bestscore = prob;
- pairprob[right][pairnum[right]].bestpos = left;
- pairnum[right]++;
- pairprob[right][pairnum[right]].bestscore = -1.0;
- pairprob[right][pairnum[right]].bestpos = -1;
-// fprintf( stderr, "%d-%d, %f\n", right, left, prob );
- }
- }
- free( pairnum );
-}
-
-void readpairfoldalign( FILE *fp, char *s1, char *s2, char *aln1, char *aln2, int q1, int q2, int *of1, int *of2, int sumlen )
-{
- char gett[1000];
- int *maptoseq1;
- int *maptoseq2;
- char dumc;
- int dumi;
- char sinseq[100], sinaln[100];
- int posinseq, posinaln;
- int alnlen;
- int i;
- int pos1, pos2;
- char *pa1, *pa2;
- char qstr[1000];
-
- *of1 = -1;
- *of2 = -1;
-
- maptoseq1 = AllocateIntVec( sumlen+1 );
- maptoseq2 = AllocateIntVec( sumlen+1 );
-
- posinaln = 0; // foldalign ga alingment wo kaesanaitok no tame.
-
- while( !feof( fp ) )
- {
- fgets( gett, 999, fp );
- if( !strncmp( gett, "; ALIGNING", 10 ) ) break;
- }
- sprintf( qstr, "; ALIGNING %d against %d\n", q1+1, q2+1 );
- if( strcmp( gett, qstr ) )
- {
- fprintf( stderr, "Error in FOLDALIGN\n" );
- fprintf( stderr, "qstr = %s, but gett = %s\n", qstr, gett );
- exit( 1 );
- }
-
- while( !feof( fp ) )
- {
- fgets( gett, 999, fp );
- if( !strncmp( gett, "; --------", 10 ) ) break;
- }
-
-
- while( !feof( fp ) )
- {
- fgets( gett, 999, fp );
- if( !strncmp( gett, "; ********", 10 ) ) break;
-// fprintf( stderr, "gett = %s\n", gett );
- sscanf( gett, "%c %c %s %s %d %d", &dumc, &dumc, sinseq, sinaln, &dumi, &dumi );
- posinaln = atoi( sinaln );
- posinseq = atoi( sinseq );
-// fprintf( stderr, "posinseq = %d\n", posinseq );
-// fprintf( stderr, "posinaln = %d\n", posinaln );
- maptoseq1[posinaln-1] = posinseq-1;
- }
- alnlen = posinaln;
-
- while( !feof( fp ) )
- {
- fgets( gett, 999, fp );
- if( !strncmp( gett, "; --------", 10 ) ) break;
- }
-
- while( !feof( fp ) )
- {
- fgets( gett, 999, fp );
- if( !strncmp( gett, "; ********", 10 ) ) break;
-// fprintf( stderr, "gett = %s\n", gett );
- sscanf( gett, "%c %c %s %s %d %d", &dumc, &dumc, sinseq, sinaln, &dumi, &dumi );
- posinaln = atof( sinaln );
- posinseq = atof( sinseq );
-// fprintf( stderr, "posinseq = %d\n", posinseq );
-// fprintf( stderr, "posinaln = %d\n", posinaln );
- maptoseq2[posinaln-1] = posinseq-1;
- }
- if( alnlen != posinaln )
- {
- fprintf( stderr, "Error in foldalign?\n" );
- exit( 1 );
- }
-
- pa1 = aln1;
- pa2 = aln2;
- for( i=0; i<alnlen; i++ )
- {
- pos1 = maptoseq1[i];
- pos2 = maptoseq2[i];
-
- if( pos1 > -1 )
- *pa1++ = s1[pos1];
- else
- *pa1++ = '-';
-
- if( pos2 > -1 )
- *pa2++ = s2[pos2];
- else
- *pa2++ = '-';
- }
- *pa1 = 0;
- *pa2 = 0;
-
- *of1 = 0;
- for( i=0; i<alnlen; i++ )
- {
- *of1 = maptoseq1[i];
- if( *of1 > -1 ) break;
- }
- *of2 = 0;
- for( i=0; i<alnlen; i++ )
- {
- *of2 = maptoseq2[i];
- if( *of2 > -1 ) break;
- }
-
-// fprintf( stderr, "*of1=%d, aln1 = :%s:\n", *of1, aln1 );
-// fprintf( stderr, "*of2=%d, aln2 = :%s:\n", *of2, aln2 );
-
- free( maptoseq1 );
- free( maptoseq2 );
-}
git://source.jalview.org / jabaws.git / blobdiff