--- /dev/null
+
+/* copyright (c) 1998, 1999 William R. Pearson and the U. of Virginia */
+
+/* $Name: fa_34_26_5 $ - $Id: dropnfa.c,v 1.81 2007/04/26 18:37:19 wrp Exp $ */
+
+/* 18-Sep-2006 - removed global variables for alignment from nw_align
+ and bg_align */
+
+/* 18-Oct-2005 - converted to use a_res and aln for alignment coordinates */
+
+/* 14-May-2003 - modified to return alignment start at 0, rather than
+ 1, for begin:end alignments
+*/
+
+/*
+ implements the fasta algorithm, see:
+
+ W. R. Pearson, D. J. Lipman (1988) "Improved tools for biological
+ sequence comparison" Proc. Natl. Acad. Sci. USA 85:2444-2448
+
+ This version uses Smith-Waterman for final protein alignments
+
+ W. R. Pearson (1996) "Effective protein sequence comparison"
+ Methods Enzymol. 266:227-258
+
+
+ 26-April-2001 - -DGAP_OPEN redefines -f, as gap open penalty
+
+ 4-Nov-2001 - modify spam() while(1).
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <math.h>
+
+#include "defs.h"
+#include "param.h"
+
+/* this must be consistent with upam.h */
+#define MAXHASH 32
+#define NMAP MAXHASH+1
+
+/* globals for fasta */
+#define MAXWINDOW 64
+
+#ifndef MAXSAV
+#define MAXSAV 10
+#endif
+
+#ifndef ALLOCN0
+static char *verstr="3.5 Sept 2006";
+#else
+static char *verstr="3.5an0 Sept 2006";
+#endif
+
+extern void w_abort(char *, char *);
+int shscore(const unsigned char *aa0, int n0, int **pam2);
+extern void init_karlin(const unsigned char *aa0, int n0, struct pstruct *ppst,
+ double *aa0_f, double **kp);
+extern void init_karlin_a(struct pstruct *, double *, double **);
+extern int do_karlin(const unsigned char *, int n1, int **,
+ struct pstruct *, double *, double *,
+ double *, double *);
+extern void aancpy(char *to, char *from, int count, struct pstruct pst);
+char *ckalloc(size_t);
+
+#ifdef TFASTA
+extern int aatran(const unsigned char *ntseq, unsigned char *aaseq, int maxs, int frame);
+#endif
+
+#include "dropnfa.h"
+
+#define DROP_INTERN
+#include "drop_func.h"
+
+struct swstr { int H, E;};
+
+static int
+dmatch (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ int hoff, int window,
+ int **pam2, int gdelval, int ggapval,
+ struct f_struct *f_str);
+
+/* initialize for fasta */
+
+void
+init_work (unsigned char *aa0, int n0,
+ struct pstruct *ppst,
+ struct f_struct **f_arg)
+{
+ int mhv, phv;
+ int hmax;
+ int i0, hv;
+ int pamfact;
+ int btemp;
+ struct f_struct *f_str;
+ /* these used to be globals, but do not need to be */
+ int ktup; /* word size examined */
+ int fact; /* factor used to scale ktup match value */
+ int kt1; /* ktup-1 */
+ int lkt; /* last ktup - initiall kt1, but can be increased
+ for hsq >= NMAP */
+
+ int maxn0; /* used in band alignment */
+ int *pwaa; /* pam[aa0[]] profile */
+ int i, j;
+ struct swstr *ss;
+ int *waa;
+ int nsq, ip, *hsq;
+
+ if (ppst->ext_sq_set) {
+ nsq = ppst->nsqx; ip = 1;
+ hsq = ppst->hsqx;
+ }
+ else {
+ nsq = ppst->nsq; ip = 0;
+ hsq = ppst->hsq;
+ }
+
+ f_str = (struct f_struct *)calloc(1,sizeof(struct f_struct));
+
+#ifndef TFASTA
+ if((ppst->zsflag%10) == 6) {
+ f_str->kar_p = NULL;
+ init_karlin(aa0, n0, ppst, &f_str->aa0_f[0], &f_str->kar_p);
+ }
+#endif
+
+ btemp = 2 * ppst->param_u.fa.bestoff / 3 +
+ n0 / ppst->param_u.fa.bestscale +
+ ppst->param_u.fa.bkfact *
+ (ppst->param_u.fa.bktup - ppst->param_u.fa.ktup);
+
+ if (ppst->nt_align)
+ btemp = (btemp*ppst->pam_h)/5; /* normalize to standard +5/-4 */
+
+ btemp = min (btemp, ppst->param_u.fa.bestmax);
+ if (btemp > 3 * n0) btemp = 3 * shscore(aa0,n0,ppst->pam2[0]) / 5;
+
+ ppst->param_u.fa.cgap = btemp + ppst->param_u.fa.bestoff / 3;
+
+ if (ppst->param_u.fa.optcut_set != 1)
+#ifndef TFASTA
+ ppst->param_u.fa.optcut = btemp;
+#else
+ ppst->param_u.fa.optcut = (btemp*3)/2;
+#endif
+
+#ifndef OLD_FASTA_GAP
+ ppst->param_u.fa.pgap = ppst->gdelval + 2*ppst->ggapval;
+#else
+ ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval;
+#endif
+ pamfact = ppst->param_u.fa.pamfact;
+ ktup = ppst->param_u.fa.ktup;
+ fact = ppst->param_u.fa.scfact * ktup;
+
+ if (pamfact == -1) pamfact = 0;
+ else if (pamfact == -2) pamfact = 1;
+
+ for (i0 = 1, mhv = -1; i0 <= ppst->nsq; i0++)
+ if (hsq[i0] < NMAP && hsq[i0] > mhv) mhv = hsq[i0];
+
+ if (mhv <= 0) {
+ fprintf (stderr, " maximum hsq <=0 %d\n", mhv);
+ exit (1);
+ }
+
+ for (f_str->kshft = 0; mhv > 0; mhv /= 2) f_str->kshft++;
+
+/* kshft = 2; */
+ kt1 = ktup - 1;
+ hv = 1;
+ for (i0 = 0; i0 < ktup; i0++) hv = hv << f_str->kshft;
+ hmax = hv;
+ f_str->hmask = (hmax >> f_str->kshft) - 1;
+
+ if ((f_str->harr = (int *) calloc (hmax, sizeof (int))) == NULL) {
+ fprintf (stderr, " cannot allocate hash array: hmax: %d hmask: %d\n",
+ hmax, f_str->hmask);
+ exit (1);
+ }
+
+ if ((f_str->pamh1 = (int *) calloc (nsq+1, sizeof (int))) == NULL) {
+ fprintf (stderr, " cannot allocate pamh1 array nsq=%d\n",nsq);
+ exit (1);
+ }
+
+ if ((f_str->pamh2 = (int *) calloc (hmax, sizeof (int))) == NULL) {
+ fprintf (stderr, " cannot allocate pamh2 array hmax=%d\n",hmax);
+ exit (1);
+ }
+
+ if ((f_str->link = (int *) calloc (n0, sizeof (int))) == NULL) {
+ fprintf (stderr, " cannot allocate hash link array n0=%d",n0);
+ exit (1);
+ }
+
+ for (i0 = 0; i0 < hmax; i0++) f_str->harr[i0] = -1;
+ for (i0 = 0; i0 < n0; i0++) f_str->link[i0] = -1;
+
+ /* encode the aa0 array */
+ phv = hv = 0;
+ lkt = kt1;
+ /* restart hv, phv calculation */
+ for (i0 = 0; i0 < min(lkt,n0); i0++) {
+ if (hsq[aa0[i0]] >= NMAP) {hv=phv=0; lkt = i0+ ktup; continue;}
+ hv = (hv << f_str->kshft) + hsq[aa0[i0]];
+ phv += ppst->pam2[ip][aa0[i0]][aa0[i0]]*ktup;
+ }
+
+ for (; i0 < n0; i0++) {
+ if (hsq[aa0[i0]] >= NMAP) {
+ hv=phv=0;
+ /* restart hv, phv calculation */
+ for (lkt = i0+kt1; (i0 < lkt || hsq[aa0[i0]]>=NMAP) && i0<n0; i0++) {
+ if (hsq[aa0[i0]] >= NMAP) {
+ hv=phv=0;
+ lkt = i0+ktup;
+ continue;
+ }
+ hv = (hv << f_str->kshft) + hsq[aa0[i0]];
+ phv += ppst->pam2[ip][aa0[i0]][aa0[i0]]*ktup;
+ }
+ }
+ if (i0 >= n0) break;
+ hv = ((hv & f_str->hmask) << f_str->kshft) + hsq[aa0[i0]];
+ f_str->link[i0] = f_str->harr[hv];
+ f_str->harr[hv] = i0;
+ if (pamfact) {
+ f_str->pamh2[hv] = (phv += ppst->pam2[ip][aa0[i0]][aa0[i0]] * ktup);
+ /* this check should always be true, but just in case */
+ if (hsq[aa0[i0-kt1]]<NMAP)
+ phv -= ppst->pam2[ip][aa0[i0 - kt1]][aa0[i0 - kt1]] * ktup;
+ }
+ else f_str->pamh2[hv] = fact * ktup;
+ }
+
+/* this has been modified from 0..<ppst->nsq to 1..<=ppst->nsq because the
+ pam2[0][0] is now undefined for consistency with blast
+*/
+
+ if (pamfact)
+ for (i0 = 1; i0 <= nsq; i0++)
+ f_str->pamh1[i0] = ppst->pam2[ip][i0][i0] * ktup;
+ else
+ for (i0 = 1; i0 <= nsq; i0++)
+ f_str->pamh1[i0] = fact;
+
+ f_str->ndo = 0;
+ f_str->noff = n0-1;
+#ifndef ALLOCN0
+ if ((f_str->diag = (struct dstruct *) calloc ((size_t)MAXDIAG,
+ sizeof (struct dstruct)))==NULL) {
+ fprintf (stderr," cannot allocate diagonal arrays: %lu\n",
+ MAXDIAG *sizeof (struct dstruct));
+ exit (1);
+ };
+#else
+ if ((f_str->diag = (struct dstruct *) calloc ((size_t)n0,
+ sizeof (struct dstruct)))==NULL) {
+ fprintf (stderr," cannot allocate diagonal arrays: %ld\n",
+ (long)n0*sizeof (struct dstruct));
+ exit (1);
+ };
+#endif
+
+
+#ifdef TFASTA
+ if ((f_str->aa1x =(unsigned char *)calloc((size_t)ppst->maxlen+2,
+ sizeof(unsigned char)))
+ == NULL) {
+ fprintf (stderr, "cannot allocate aa1x array %d\n", ppst->maxlen+2);
+ exit (1);
+ }
+ f_str->aa1x++;
+#endif
+
+ f_str->bss = (struct bdstr *) calloc((size_t)ppst->param_u.fa.optwid*2+4,
+ sizeof(struct bdstr));
+ f_str->bss++;
+
+ /* allocate space for the scoring arrays */
+ maxn0 = n0 + 4;
+ if ((ss = (struct swstr *) calloc (maxn0, sizeof (struct swstr)))
+ == NULL) {
+ fprintf (stderr, "cannot allocate ss array %3d\n", n0);
+ exit (1);
+ }
+ ss++;
+ f_str->ss = ss;
+
+ /* initialize the "variable" pam array */
+
+ if ((waa= (int *)calloc ((size_t)(nsq+1)*n0,sizeof(int))) == NULL) {
+ fprintf(stderr,"cannot allocate waa struct %3d\n",nsq*n0);
+ exit(1);
+ }
+
+ pwaa = waa;
+ for (i=0; i<=nsq; i++) {
+ for (j=0;j<n0; j++) {
+ *pwaa = ppst->pam2[ip][aa0[j]][i];
+ pwaa++;
+ }
+ }
+ f_str->waa0 = waa;
+
+ /* initialize the "conventional" pam array used for alignments */
+
+ if ((waa= (int *)calloc ((size_t)(nsq+1)*n0,sizeof(int))) == NULL) {
+ fprintf(stderr,"cannot allocate waa struct %3d\n",nsq*n0);
+ exit(1);
+ }
+
+ pwaa = waa;
+ for (i=0; i<=nsq; i++) {
+ for (j=0;j<n0; j++) {
+ *pwaa = ppst->pam2[0][aa0[j]][i];
+ pwaa++;
+ }
+ }
+ f_str->waa1 = waa;
+
+ f_str->max_res = max(3*n0/2,MIN_RES);
+
+ /* now we need alignment storage - get it */
+ if ((f_str->res = (int *)calloc((size_t)f_str->max_res,sizeof(int)))==NULL) {
+ fprintf(stderr,"cannot allocate alignment results array %d\n",f_str->max_res);
+ exit(1);
+ }
+
+ *f_arg = f_str;
+}
+
+
+/* pstring1 is a message to the manager, currently 512 */
+/* pstring2 is the same information, but in a markx==10 format */
+void
+get_param (struct pstruct *pstr, char *pstring1, char *pstring2)
+{
+#ifndef TFASTA
+ char *pg_str="FASTA";
+#else
+ char *pg_str="TFASTA";
+#endif
+
+ if (!pstr->param_u.fa.optflag)
+#ifdef OLD_FASTA_GAP
+ sprintf (pstring1, "%s (%s) function [%s matrix, (%d:%d)%s] ktup: %d\n join: %d, gap-pen: %d/%d, width: %3d",
+#else
+ sprintf (pstring1, "%s (%s) function [%s matrix, (%d:%d)%s] ktup: %d\n join: %d, open/ext: %d/%d, width: %3d",
+#endif
+ pg_str,verstr,pstr->pamfile, pstr->pam_h,pstr->pam_l,
+ (pstr->ext_sq_set) ? "xS":"\0",
+ pstr->param_u.fa.ktup, pstr->param_u.fa.cgap,
+ pstr->gdelval, pstr->ggapval, pstr->param_u.fa.optwid);
+ else
+#ifdef OLD_FASTA_GAP
+ sprintf (pstring1, "%s (%s) function [optimized, %s matrix (%d:%d)%s] ktup: %d\n join: %d, opt: %d, gap-pen: %d/%d, width: %3d",
+#else
+ sprintf (pstring1, "%s (%s) function [optimized, %s matrix (%d:%d)%s] ktup: %d\n join: %d, opt: %d, open/ext: %d/%d, width: %3d",
+#endif
+ pg_str,verstr,pstr->pamfile, pstr->pam_h,pstr->pam_l,
+ (pstr->ext_sq_set) ? "xS":"\0",
+ pstr->param_u.fa.ktup, pstr->param_u.fa.cgap,
+ pstr->param_u.fa.optcut, pstr->gdelval, pstr->ggapval,
+ pstr->param_u.fa.optwid);
+ if (pstr->param_u.fa.iniflag) strcat(pstring1," init1");
+ /*
+ if (pstr->zsflag==0) strcat(pstring1," not-scaled");
+ else if (pstr->zsflag==1) strcat(pstring1," reg.-scaled");
+ */
+
+ if (pstring2 != NULL) {
+#ifdef OLD_FASTA_GAP
+ sprintf (pstring2, "; pg_name: %s\n; pg_ver: %s\n; pg_matrix: %s (%d:%d)\n\
+; pg_gap-pen: %d %d\n; pg_ktup: %d\n; pg_optcut: %d\n; pg_cgap: %d\n",
+#else
+ sprintf (pstring2, "; pg_name: %s\n; pg_ver: %s\n; pg_matrix: %s (%d:%d)\n\
+; pg_open-ext: %d %d\n; pg_ktup: %d\n; pg_optcut: %d\n; pg_cgap: %d\n",
+#endif
+ pg_str,verstr,pstr->pamfile, pstr->pam_h,pstr->pam_l, pstr->gdelval,
+ pstr->ggapval,pstr->param_u.fa.ktup,pstr->param_u.fa.optcut,
+ pstr->param_u.fa.cgap);
+ }
+}
+
+void
+close_work (const unsigned char *aa0, int n0,
+ struct pstruct *ppst,
+ struct f_struct **f_arg)
+{
+ struct f_struct *f_str;
+
+
+ f_str = *f_arg;
+
+
+ if (f_str != NULL) {
+ if (f_str->kar_p!=NULL) free(f_str->kar_p);
+ f_str->ss--;
+ f_str->bss--;
+
+ free(f_str->res);
+ free(f_str->waa1);
+ free(f_str->waa0);
+ free(f_str->ss);
+ free(f_str->bss);
+ free(f_str->diag);
+ free(f_str->link);
+ free(f_str->pamh2);
+ free(f_str->pamh1);
+ free(f_str->harr);
+
+ free(f_str);
+ *f_arg = NULL;
+ }
+}
+
+#ifdef ALLOCN0
+void savemax (struct dstruct *, int, struct f_struct *);
+#else
+void savemax (struct dstruct *, struct f_struct *);
+#endif
+
+int spam (const unsigned char *, const unsigned char *, struct savestr *,
+ int **, int, int, int);
+int sconn(struct savestr **, int nsave, int cgap, int pgap, int noff);
+void kpsort(struct savestr **, int);
+
+static int
+ALIGN(const unsigned char *, const unsigned char *, int, int,
+ int **, int, int, int *, int *, struct f_struct *);
+
+static int
+LOCAL_ALIGN(const unsigned char *, const unsigned char *,
+ int, int, int, int,
+ int **, int, int, int *, int *, int *, int *, int,
+ struct f_struct *);
+
+static int
+B_ALIGN(const unsigned char *A, const unsigned char *B, int M,
+ int N, int low, int up, int **W, int G, int H, int *S,
+ int *nS, int MW, int MX, struct bdstr *bss);
+
+static void
+do_fasta (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ struct pstruct *ppst, struct f_struct *f_str,
+ struct rstruct *rst, int *hoff)
+{
+ int nd; /* diagonal array size */
+ int lhval;
+ int kfact;
+ register struct dstruct *dptr;
+ register int tscor;
+
+#ifndef ALLOCN0
+ register struct dstruct *diagp;
+#else
+ register int dpos;
+ int lposn0;
+#endif
+ int noff;
+ struct dstruct *dpmax;
+ register int lpos;
+ int tpos;
+ struct savestr *vmptr;
+ int scor, ib, nsave;
+ int xdrop, do_extend;
+ int ktup, kt1, lkt, *hsq, ip;
+
+ if (ppst->ext_sq_set) {
+ ip = 1;
+ hsq = ppst->hsqx;
+ }
+ else {
+ ip = 0;
+ hsq = ppst->hsq;
+ }
+
+ xdrop = -ppst->pam_l;
+ /* do extended alignment in spam iff protein or short sequences */
+ do_extend = !ppst->nt_align || (n0 < 50) || (n1 < 50);
+
+ ktup = ppst->param_u.fa.ktup;
+ kt1 = ktup-1;
+
+ if (n1 < ktup) {
+ rst->score[0] = rst->score[1] = rst->score[2] = 0;
+ return;
+ }
+
+ if (n0+n1+1 >= MAXDIAG) {
+ fprintf(stderr,"n0,n1 too large: %d, %d\n",n0,n1);
+ rst->score[0] = rst->score[1] = rst->score[2] = -1;
+ return;
+ }
+
+#ifdef ALLOCN0
+ nd = n0;
+#else
+ nd = n0 + n1;
+#endif
+
+ dpmax = &f_str->diag[nd];
+ for (dptr = &f_str->diag[f_str->ndo]; dptr < dpmax;)
+ {
+ dptr->stop = -1;
+ dptr->dmax = NULL;
+ dptr++->score = 0;
+ }
+
+ for (vmptr = f_str->vmax; vmptr < &f_str->vmax[MAXSAV]; vmptr++)
+ vmptr->score = 0;
+ f_str->lowmax = f_str->vmax;
+ f_str->lowscor = 0;
+
+ /* start hashing */
+ lhval = 0;
+ lkt = kt1;
+ for (lpos = 0; (lpos < lkt || hsq[aa1[lpos]]>=NMAP) && lpos <n1; lpos++) {
+ /* restart lhval calculation */
+ if (hsq[aa1[lpos]]>=NMAP) {
+ lhval = 0; lkt = lpos + ktup;
+ continue;
+ }
+ lhval = ((lhval & f_str->hmask) << f_str->kshft) + hsq[aa1[lpos]];
+ }
+
+ noff = f_str->noff;
+#ifndef ALLOCN0
+ diagp = &f_str->diag[noff + lkt];
+ for (; lpos < n1; lpos++, diagp++) {
+ if (hsq[aa1[lpos]]>=NMAP) {
+ lpos++ ; diagp++;
+ while (lpos < n1 && hsq[aa1[lpos]]>=NMAP) {lpos++; diagp++;}
+ if (lpos >= n1) break;
+ lhval = 0;
+ }
+ lhval = ((lhval & f_str->hmask) << f_str->kshft) + hsq[aa1[lpos]];
+ for (tpos = f_str->harr[lhval]; tpos >= 0; tpos = f_str->link[tpos]) {
+ if ((tscor = (dptr = &diagp[-tpos])->stop) >= 0) {
+#else
+ lposn0 = noff + lpos;
+ for (; lpos < n1; lpos++, lposn0++) {
+ if (hsq[aa1[lpos]]>=NMAP) {lhval = 0; goto loopl;}
+ /*
+ if (hsq[aa1[lpos]]>=NMAP) {
+ lpos++; lposn0++;
+ while (lpos < n1 && hsq[aa1[lpos]]>=NMAP) {lpos++; lposn0++;}
+ }
+ */
+ lhval = ((lhval & f_str->hmask) << f_str->kshft) + hsq[aa1[lpos]];
+ for (tpos = f_str->harr[lhval]; tpos >= 0; tpos = f_str->link[tpos]) {
+ dpos = lposn0 - tpos;
+ if ((tscor = (dptr = &f_str->diag[dpos % nd])->stop) >= 0) {
+#endif
+ tscor += ktup;
+ if ((tscor -= lpos) <= 0) {
+ scor = dptr->score;
+ if ((tscor += (kfact = f_str->pamh2[lhval])) < 0 && f_str->lowscor < scor)
+#ifdef ALLOCN0
+ savemax (dptr, dpos, f_str);
+#else
+ savemax (dptr, f_str);
+#endif
+ if ((tscor += scor) >= kfact) {
+ dptr->score = tscor;
+ dptr->stop = lpos;
+ }
+ else {
+ dptr->score = kfact;
+ dptr->start = (dptr->stop = lpos) - kt1;
+ }
+ }
+ else {
+ dptr->score += f_str->pamh1[aa0[tpos]];
+ dptr->stop = lpos;
+ }
+ }
+ else {
+ dptr->score = f_str->pamh2[lhval];
+ dptr->start = (dptr->stop = lpos) - kt1;
+ }
+ } /* end tpos */
+
+#ifdef ALLOCN0
+ /* reinitialize diag structure */
+ loopl:
+ if ((dptr = &f_str->diag[lpos % nd])->score > f_str->lowscor)
+ savemax (dptr, lpos, f_str);
+ dptr->stop = -1;
+ dptr->dmax = NULL;
+ dptr->score = 0;
+#endif
+ } /* end lpos */
+
+#ifdef ALLOCN0
+ for (tpos = 0, dpos = noff + n1 - 1; tpos < n0; tpos++, dpos--) {
+ if ((dptr = &f_str->diag[dpos % nd])->score > f_str->lowscor)
+ savemax (dptr, dpos, f_str);
+ }
+#else
+ for (dptr = f_str->diag; dptr < dpmax;) {
+ if (dptr->score > f_str->lowscor) savemax (dptr, f_str);
+ dptr->stop = -1;
+ dptr->dmax = NULL;
+ dptr++->score = 0;
+ }
+ f_str->ndo = nd;
+#endif
+
+/*
+ at this point all of the elements of aa1[lpos]
+ have been searched for elements of aa0[tpos]
+ with the results in diag[dpos]
+*/
+ for (nsave = 0, vmptr = f_str->vmax; vmptr < &f_str->vmax[MAXSAV]; vmptr++) {
+ /*
+ fprintf(stderr,"0: %4d-%4d 1: %4d-%4d dp: %d score: %d\n",
+ noff+vmptr->start-vmptr->dp,
+ noff+vmptr->stop-vmptr->dp,
+ vmptr->start,vmptr->stop,
+ vmptr->dp,vmptr->score);
+
+ */
+ if (vmptr->score > 0) {
+ vmptr->score = spam (aa0, aa1, vmptr, ppst->pam2[ip], xdrop,
+ noff,do_extend);
+ f_str->vptr[nsave++] = vmptr;
+ }
+ }
+
+ if (nsave <= 0) {
+ rst->score[0] = rst->score[1] = rst->score[2] = 0;
+ return;
+ }
+
+ /*
+ fprintf(stderr,"n0: %d; n1: %d; noff: %d\n",n0,n1,noff);
+ for (ib=0; ib<nsave; ib++) {
+ fprintf(stderr,"0: %4d-%4d 1: %4d-%4d dp: %d score: %d\n",
+ noff+f_str->vptr[ib]->start-f_str->vptr[ib]->dp,
+ noff+f_str->vptr[ib]->stop-f_str->vptr[ib]->dp,
+ f_str->vptr[ib]->start,f_str->vptr[ib]->stop,
+ f_str->vptr[ib]->dp,f_str->vptr[ib]->score);
+ }
+ fprintf(stderr,"---\n");
+ */
+
+ scor = sconn (f_str->vptr, nsave, ppst->param_u.fa.cgap,
+ ppst->param_u.fa.pgap, noff);
+
+ for (vmptr=f_str->vptr[0],ib=1; ib<nsave; ib++)
+ if (f_str->vptr[ib]->score > vmptr->score) vmptr=f_str->vptr[ib];
+
+/* kssort (f_str->vptr, nsave); */
+
+ rst->score[1] = vmptr->score;
+ rst->score[0] = max (scor, vmptr->score);
+ rst->score[2] = rst->score[0]; /* initn */
+
+ if (ppst->param_u.fa.optflag) {
+ if (rst->score[0] > ppst->param_u.fa.optcut)
+ rst->score[2] = dmatch (aa0, n0, aa1, n1, *hoff=noff - vmptr->dp,
+ ppst->param_u.fa.optwid, ppst->pam2[ip],
+ ppst->gdelval,ppst->ggapval,f_str);
+ }
+}
+
+void do_work (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ int frame,
+ struct pstruct *ppst, struct f_struct *f_str,
+ int qr_flg, struct rstruct *rst)
+{
+ int hoff, n10;
+
+ double lambda, H;
+
+ rst->score[0] = rst->score[1] = rst->score[2] = 0;
+ rst->escore = 1.0;
+ rst->segnum = rst->seglen = 1;
+
+ if (n1 < ppst->param_u.fa.ktup) return;
+
+#ifdef TFASTA
+ n10=aatran(aa1,f_str->aa1x,n1,frame);
+ do_fasta (aa0, n0, f_str->aa1x, n10, ppst, f_str, rst, &hoff);
+#else /* FASTA */
+ do_fasta (aa0, n0, aa1, n1, ppst, f_str, rst, &hoff);
+#endif
+
+#ifndef TFASTA
+ if((ppst->zsflag%10) == 6 &&
+ (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f,
+ f_str->kar_p, &lambda, &H)>0)) {
+ rst->comp = 1.0/lambda;
+ rst->H = H;
+ }
+ else {rst->comp = rst->H = -1.0;}
+#else
+ rst->comp = rst->H = -1.0;
+#endif
+}
+
+void do_opt (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ int frame,
+ struct pstruct *ppst,
+ struct f_struct *f_str,
+ struct rstruct *rst)
+{
+ int optflag, tscore, hoff, n10;
+
+ optflag = ppst->param_u.fa.optflag;
+ ppst->param_u.fa.optflag = 1;
+
+#ifdef TFASTA
+ n10=aatran(aa1,f_str->aa1x,n1,frame);
+ do_fasta (aa0, n0, f_str->aa1x, n10, ppst, f_str, rst, &hoff);
+#else /* FASTA */
+ do_fasta(aa0,n0,aa1,n1,ppst,f_str,rst, &hoff);
+#endif
+ ppst->param_u.fa.optflag = optflag;
+}
+
+#ifdef ALLOCN0
+void
+savemax (dptr, dpos, f_str)
+ register struct dstruct *dptr;
+ int dpos;
+ struct f_struct *f_str;
+{
+ register struct savestr *vmptr;
+ register int i;
+
+#else
+void
+savemax (dptr, f_str)
+ register struct dstruct *dptr;
+ struct f_struct *f_str;
+{
+ register int dpos;
+ register struct savestr *vmptr;
+ register int i;
+
+ dpos = (int) (dptr - f_str->diag);
+
+#endif
+
+/* check to see if this is the continuation of a run that is already saved */
+
+ if ((vmptr = dptr->dmax) != NULL && vmptr->dp == dpos &&
+ vmptr->start == dptr->start)
+ {
+ vmptr->stop = dptr->stop;
+ if ((i = dptr->score) <= vmptr->score)
+ return;
+ vmptr->score = i;
+ if (vmptr != f_str->lowmax)
+ return;
+ }
+ else
+ {
+ i = f_str->lowmax->score = dptr->score;
+ f_str->lowmax->dp = dpos;
+ f_str->lowmax->start = dptr->start;
+ f_str->lowmax->stop = dptr->stop;
+ dptr->dmax = f_str->lowmax;
+ }
+
+ for (vmptr = f_str->vmax; vmptr < &f_str->vmax[MAXSAV]; vmptr++)
+ if (vmptr->score < i)
+ {
+ i = vmptr->score;
+ f_str->lowmax = vmptr;
+ }
+ f_str->lowscor = i;
+}
+
+int spam (const unsigned char *aa0, const unsigned char *aa1,
+ struct savestr *dmax, int **pam2, int xdrop,
+ int noff, int do_extend)
+{
+ register int lpos, tot;
+ register const unsigned char *aa0p, *aa1p;
+
+ int drop_thresh;
+
+ struct {
+ int start, stop, score;
+ } curv, maxv;
+
+ aa1p = &aa1[lpos= dmax->start]; /* get the start of lib seq */
+ aa0p = &aa0[lpos - dmax->dp + noff]; /* start of query */
+#ifdef DEBUG
+ /* also add check in calling routine */
+ if (aa0p < aa0) { return -99; }
+#endif
+ curv.start = lpos; /* start index in lib seq */
+
+ tot = curv.score = maxv.score = 0;
+
+ for (; lpos <= dmax->stop; lpos++) {
+ tot += pam2[*aa0p++][*aa1p++];
+ if (tot > curv.score) { /* update current score */
+ curv.stop = lpos;
+ curv.score = tot;
+ }
+ else if (tot < 0) {
+ if (curv.score > maxv.score) { /* save score, start, stop */
+ maxv.start = curv.start;
+ maxv.stop = curv.stop;
+ maxv.score = curv.score;
+ }
+ tot = curv.score = 0; /* reset running score */
+ curv.start = lpos+1; /* reset start */
+ if(lpos >= dmax->stop) break; /* if the zero is beyond stop, quit */
+ }
+ }
+
+ if (curv.score > maxv.score) {
+ maxv.start = curv.start;
+ maxv.stop = curv.stop;
+ maxv.score = curv.score;
+ }
+
+#ifndef NOSPAM_EXT
+
+ /* now check to see if the score gets better by extending */
+ if (do_extend && maxv.score > xdrop) {
+
+ if (maxv.stop == dmax->stop) {
+ tot = maxv.score;
+ drop_thresh = maxv.score - xdrop;
+ aa1p = &aa1[lpos= dmax->stop];
+ aa0p = &aa0[lpos - dmax->dp + noff];
+ while (tot > drop_thresh ) {
+ ++lpos;
+ tot += pam2[*(++aa0p)][*(++aa1p)];
+ if (tot > maxv.score) {
+ maxv.start = lpos;
+ maxv.score = tot;
+ drop_thresh = tot - xdrop;
+ }
+ }
+ }
+
+ /* scan backwards now */
+
+ if (maxv.start == dmax->start) {
+ tot = maxv.score;
+ drop_thresh = maxv.score - xdrop;
+ aa1p = &aa1[lpos= dmax->start];
+ aa0p = &aa0[lpos - dmax->dp + noff];
+ while (tot > drop_thresh) {
+ --lpos;
+ tot += pam2[*(--aa0p)][*(--aa1p)];
+ if (tot > maxv.score) {
+ maxv.start = lpos;
+ maxv.score = tot;
+ drop_thresh = tot - xdrop;
+ }
+ }
+ }
+ }
+#endif
+
+/* if (maxv.start != dmax->start || maxv.stop != dmax->stop)
+ printf(" new region: %3d %3d %3d %3d\n",maxv.start,
+ dmax->start,maxv.stop,dmax->stop);
+*/
+ dmax->start = maxv.start;
+ dmax->stop = maxv.stop;
+
+ return maxv.score;
+}
+
+int sconn (struct savestr **v, int n, int cgap, int pgap, int noff)
+{
+ int i, si;
+ struct slink
+ {
+ int score;
+ struct savestr *vp;
+ struct slink *next;
+ } *start, *sl, *sj, *so, sarr[MAXSAV];
+ int lstart, tstart, plstop, ptstop;
+
+/* sort the score left to right in lib pos */
+
+ kpsort (v, n);
+
+ start = NULL;
+
+/* for the remaining runs, see if they fit */
+
+ for (i = 0, si = 0; i < n; i++)
+ {
+
+/* if the score is less than the gap penalty, it never helps */
+ if (v[i]->score < cgap)
+ continue;
+ lstart = v[i]->start;
+ tstart = lstart - v[i]->dp + noff;
+
+/* put the run in the group */
+ sarr[si].vp = v[i];
+ sarr[si].score = v[i]->score;
+ sarr[si].next = NULL;
+
+/* if it fits, then increase the score */
+ for (sl = start; sl != NULL; sl = sl->next)
+ {
+ plstop = sl->vp->stop;
+ ptstop = plstop - sl->vp->dp + noff;
+ if (plstop < lstart && ptstop < tstart)
+ {
+ sarr[si].score = sl->score + v[i]->score + pgap;
+ break;
+ }
+ }
+
+/* now recalculate where the score fits */
+ if (start == NULL)
+ start = &sarr[si];
+ else
+ for (sj = start, so = NULL; sj != NULL; sj = sj->next) {
+ if (sarr[si].score > sj->score) {
+ sarr[si].next = sj;
+ if (so != NULL) so->next = &sarr[si];
+ else start = &sarr[si];
+ break;
+ }
+ so = sj;
+ }
+ si++;
+ }
+
+ if (start != NULL)
+ return (start->score);
+ else
+ return (0);
+}
+
+void
+kssort (v, n)
+struct savestr *v[];
+int n;
+{
+ int gap, i, j;
+ struct savestr *tmp;
+
+ for (gap = n / 2; gap > 0; gap /= 2)
+ for (i = gap; i < n; i++)
+ for (j = i - gap; j >= 0; j -= gap)
+ {
+ if (v[j]->score >= v[j + gap]->score)
+ break;
+ tmp = v[j];
+ v[j] = v[j + gap];
+ v[j + gap] = tmp;
+ }
+}
+
+void
+kpsort (v, n)
+struct savestr *v[];
+int n;
+{
+ int gap, i, j;
+ struct savestr *tmp;
+
+ for (gap = n / 2; gap > 0; gap /= 2)
+ for (i = gap; i < n; i++)
+ for (j = i - gap; j >= 0; j -= gap)
+ {
+ if (v[j]->start <= v[j + gap]->start)
+ break;
+ tmp = v[j];
+ v[j] = v[j + gap];
+ v[j + gap] = tmp;
+ }
+}
+
+static int dmatch (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ int hoff, int window,
+ int **pam2, int gdelval, int ggapval,
+ struct f_struct *f_str)
+{
+ int low, up;
+
+ window = min (n1, window);
+ /* hoff is the offset found from aa1 to seq 2 by hmatch */
+
+ low = -window/2-hoff;
+ up = low+window;
+
+ return FLOCAL_ALIGN(aa0-1,aa1-1,n0,n1, low, up,
+ pam2,
+#ifdef OLD_FASTA_GAP
+ -(gdelval-ggapval),
+#else
+ -gdelval,
+#endif
+ -ggapval,window,f_str);
+ }
+
+
+/* A PACKAGE FOR LOCALLY ALIGNING TWO SEQUENCES WITHIN A BAND:
+
+ To invoke, call LOCAL_ALIGN(A,B,M,N,L,U,W,G,H,MW).
+ The parameters are explained as follows:
+ A, B : two sequences to be aligned
+ M : the length of sequence A
+ N : the length of sequence B
+ L : lower bound of the band
+ U : upper bound of the band
+ W : scoring table for matches and mismatches
+ G : gap-opening penalty
+ H : gap-extension penalty
+ MW : maximum window size
+*/
+
+#include <stdio.h>
+
+#define MININT -9999999
+
+static int
+FLOCAL_ALIGN(const unsigned char *A, const unsigned char *B,
+ int M, int N, int low, int up,
+ int **W, int G,int H, int MW,
+ struct f_struct *f_str)
+{
+ int band;
+ register struct bdstr *bssp;
+ int i, j, si, ei;
+ int c, d, e, m;
+ int leftd, rightd;
+ int best_score;
+ int *wa, curd;
+ int ib;
+
+ bssp = f_str->bss;
+
+ m = G+H;
+ low = max(-M, low);
+ up = min(N, up);
+
+ if (N <= 0) return 0;
+
+ if (M <= 0) return 0;
+
+ band = up-low+1;
+ if (band < 1) {
+ fprintf(stderr,"low > up is unacceptable!: M: %d N: %d l/u: %d/%d\n",
+ M, N, low, up);
+ return 0;
+ }
+
+ if (low > 0) leftd = 1;
+ else if (up < 0) leftd = band;
+ else leftd = 1-low;
+ rightd = band;
+ si = max(0,-up); /* start index -1 */
+ ei = min(M,N-low); /* end index */
+ bssp[leftd].CC = 0;
+ for (j = leftd+1; j <= rightd; j++) {
+ bssp[j].CC = 0;
+ bssp[j].DD = -G;
+ }
+
+ bssp[rightd+1].CC = MININT;
+ bssp[rightd+1].DD = MININT;
+
+ best_score = 0;
+ bssp[leftd-1].CC = MININT;
+ bssp[leftd].DD = -G;
+
+ for (i = si+1; i <= ei; i++) {
+ if (i > N-up) rightd--;
+ if (leftd > 1) leftd--;
+ wa = W[A[i]];
+ if ((c = bssp[leftd+1].CC-m) > (d = bssp[leftd+1].DD-H)) d = c;
+ if ((ib = leftd+low-1+i ) > 0) c = bssp[leftd].CC+wa[B[ib]];
+
+ if (d > c) c = d;
+ if (c < 0) c = 0;
+ e = c-G;
+ bssp[leftd].DD = d;
+ bssp[leftd].CC = c;
+ if (c > best_score) best_score = c;
+
+ for (curd=leftd+1; curd <= rightd; curd++) {
+ if ((c = c-m) > (e = e-H)) e = c;
+ if ((c = bssp[curd+1].CC-m) > (d = bssp[curd+1].DD-H)) d = c;
+ c = bssp[curd].CC + wa[B[curd+low-1+i]];
+ if (e > c) c = e;
+ if (d > c) c = d;
+ if (c < 0) c = 0;
+ bssp[curd].CC = c;
+ bssp[curd].DD = d;
+ if (c > best_score) best_score = c;
+ }
+ }
+
+ return best_score;
+}
+
+/* ckalloc - allocate space; check for success */
+char *ckalloc(size_t amount)
+{
+ char *p;
+
+ if ((p = malloc( (unsigned) amount)) == NULL)
+ w_abort("Ran out of memory.","");
+ return(p);
+}
+
+/* calculate the 100% identical score */
+int
+shscore(const unsigned char *aa0, int n0, int **pam2)
+{
+ int i, sum;
+ for (i=0,sum=0; i<n0; i++)
+ sum += pam2[aa0[i]][aa0[i]];
+ return sum;
+}
+
+int sw_walign (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ struct pstruct *ppst,
+ struct f_struct *f_str,
+ struct a_res_str *a_res
+ )
+{
+ register const unsigned char *aa0p, *aa1p;
+ register int *pwaa;
+ register int i, j;
+ register struct swstr *ssj;
+ struct swstr *ss;
+ int *waa;
+ int e, f, h, p;
+ int q, r, m;
+ int score;
+ int cost, I, J, K, L;
+
+ ss = f_str->ss;
+ waa = f_str->waa1;
+
+#ifdef OLD_FASTA_GAP
+ q = -(ppst->gdelval - ppst->ggapval);
+#else
+ q = -ppst->gdelval;
+#endif
+ r = -ppst->ggapval;
+ m = q + r;
+
+ /* initialize 0th row */
+ for (ssj=ss; ssj<ss+n0; ssj++) {
+ ssj->H = 0;
+ ssj->E = -q;
+ }
+
+ score = I = J = 0;
+ aa1p = aa1;
+ i = 0;
+ while (*aa1p) {
+ h = p = 0;
+ f = -q;
+ pwaa = waa + (*aa1p++ * n0);
+ for (ssj = ss, aa0p = aa0; ssj < ss+n0; ssj++) {
+ if ((h = h - m) > (f = f - r)) f = h;
+ if ((h = ssj->H - m) > (e = ssj->E - r)) e = h;
+ h = p + *pwaa++;
+ if (h < 0 ) h = 0;
+ if (h < f ) h = f;
+ if (h < e ) h = e;
+ p = ssj->H;
+ ssj->H = h;
+ ssj->E = e;
+ if (h > score) {
+ score = h;
+ I = i;
+ J = (int)(ssj-ss);
+ }
+ }
+ i++;
+ } /* done with forward pass */
+ if (score <= 0) return 0;
+
+ /* to get the start point, go backwards */
+
+ cost = K = L = 0;
+ for (ssj=ss+J; ssj>=ss; ssj--) ssj->H= ssj->E= -1;
+
+ for (i=I; i>=0; i--) {
+ h = f = -1;
+ p = (i == I) ? 0 : -1;
+ ssj = ss+J; /* bug in compiler */
+ for (aa0p = &aa0[J]; ssj>=ss; ssj--,aa0p--) {
+ f = max (f,h-q)-r;
+ ssj->E=max(ssj->E,ssj->H-q)-r;
+ h = max(max(ssj->E,f),p+ppst->pam2[0][*aa0p][aa1[i]]);
+ p = ssj->H;
+ ssj->H=h;
+ if (h > cost) {
+ cost = h;
+ K = i;
+ L = (int)(ssj-ss);
+ if (cost >= score) goto found;
+ }
+ }
+ }
+
+found:
+
+ /* printf(" %d: L: %3d-%3d/%3d; K: %3d-%3d/%3d\n",score,L,J,n0,K,I,n1); */
+
+/* in the f_str version, the *res array is already allocated at 4*n0/3 */
+
+ a_res->max0 = J+1; a_res->min0 = L; a_res->max1 = I+1; a_res->min1 = K;
+
+ /* the seq array arguments in this call have been reversed to allow
+ assymetric scoring matrices - this affects the score decoding,
+ and allocation of the score row matrix */
+ ALIGN(&aa0[L-1],&aa1[K-1],J-L+1,I-K+1,ppst->pam2[0],q,r,a_res->res,&a_res->nres,f_str);
+
+ /* DISPLAY(&aa1[K-1],&aa0[L-1],I-K+1,J-L+1,res,L,K,ppst->sq); */
+
+ return score;
+}
+
+static int CHECK_SCORE(const unsigned char *A, const unsigned char *B,
+ int M, int N,
+ int *S, int **W, int G, int H, int *nres);
+
+#define gap(k) ((k) <= 0 ? 0 : g+h*(k)) /* k-symbol indel cost */
+
+/* static int *sapp; */ /* Current script append ptr */
+/* static int last; */ /* Last script op appended */
+
+ /* Append "Delete k" op */
+#define DEL(k) \
+{ if (*last < 0) \
+ *last = (*sapp)[-1] -= (k); \
+ else { \
+ *last = (*sapp)[0] = -(k); \
+ (*sapp)++; \
+ } \
+}
+ /* Append "Insert k" op */
+#define INS(k) \
+{ if (*last > 0) \
+ *last = (*sapp)[-1] += (k); \
+ else { \
+ *last = (*sapp)[0] = (k); \
+ (*sapp)++; \
+ } \
+}
+
+#define REP { *last = (*sapp)[0] = 0; (*sapp)++;} /* Append "Replace" op */
+
+/* align(A,B,M,N,tb,te) returns the cost of an optimum conversion between
+ A[1..M] and B[1..N] that begins(ends) with a delete if tb(te) is zero
+ and appends such a conversion to the current script. */
+
+static int
+nw_align(const unsigned char *A, const unsigned char *B,
+ int M, int N,
+ int tb, int te, int **w, int g, int h,
+ struct f_struct *f_str,
+ int **sapp, int *last)
+{
+ int midi, midj, type; /* Midpoint, type, and cost */
+ int midc;
+
+ register int i, j;
+ register int c, e, d, s;
+ int m, t, *wa;
+ struct swstr *f_ss, *r_ss;
+
+ m = g + h;
+
+ f_ss = f_str->f_ss;
+ r_ss = f_str->r_ss;
+
+/* Boundary cases: M <= 1 or N == 0 */
+
+ if (N <= 0) {
+ if (M > 0) {DEL(M)}
+ return -gap(M);
+ }
+
+ if (M <= 1) {
+ if (M <= 0) {
+ INS(N);
+ return -gap(N);
+ }
+ if (tb < te) tb = te;
+ midc = (tb-h) - gap(N);
+ midj = 0;
+ wa = w[A[1]]; /* in the original version of this code, A[]
+ is the second sequence */
+ for (j = 1; j <= N; j++) {
+ c = -gap(j-1) + wa[B[j]] - gap(N-j);
+ if (c > midc) {
+ midc = c;
+ midj = j;
+ }
+ }
+ if (midj == 0) { DEL(1) INS(N) }
+ else {
+ if (midj > 1) { INS(midj-1) }
+ REP
+ if (midj < N) { INS(N-midj) }
+ }
+ return midc;
+ }
+
+/* Divide: Find optimum midpoint (midi,midj) of cost midc */
+
+ midi = M/2; /* Forward phase: */
+ f_ss[0].H = 0; /* Compute H(M/2,k) & E(M/2,k) for all k */
+ t = -g;
+ for (j = 1; j <= N; j++) {
+ f_ss[j].H = t = t-h;
+ f_ss[j].E = t-g;
+ }
+ t = tb;
+ for (i = 1; i <= midi; i++) {
+ s = f_ss[0].H;
+ f_ss[0].H = c = t = t-h;
+ e = t-g;
+ wa = w[A[i]];
+ for (j = 1; j <= N; j++) {
+ if ((c = c - m) > (e = e - h)) e = c;
+ if ((c = f_ss[j].H - m) > (d = f_ss[j].E - h)) d = c;
+ c = s + wa[B[j]];
+ if (e > c) c = e;
+ if (d > c) c = d;
+ s = f_ss[j].H;
+ f_ss[j].H = c;
+ f_ss[j].E = d;
+ }
+ }
+ f_ss[0].E = f_ss[0].H;
+
+ r_ss[N].H = 0; /* Reverse phase: */
+ t = -g; /* Compute R(M/2,k) & S(M/2,k) for all k */
+ for (j = N-1; j >= 0; j--)
+ { r_ss[j].H = t = t-h;
+ r_ss[j].E = t-g;
+ }
+ t = te;
+ for (i = M-1; i >= midi; i--)
+ { s = r_ss[N].H;
+ r_ss[N].H = c = t = t-h;
+ e = t-g;
+ wa = w[A[i+1]];
+ for (j = N-1; j >= 0; j--)
+ { if ((c = c - m) > (e = e - h)) e = c;
+ if ((c = r_ss[j].H - m) > (d = r_ss[j].E - h)) d = c;
+ c = s + wa[B[j+1]];
+ if (e > c) c = e;
+ if (d > c) c = d;
+ s = r_ss[j].H;
+ r_ss[j].H = c;
+ r_ss[j].E = d;
+ }
+ }
+ r_ss[N].E = r_ss[N].H;
+
+ midc = f_ss[0].H+r_ss[0].H; /* Find optimal midpoint */
+ midj = 0;
+ type = 1;
+ for (j = 0; j <= N; j++)
+ if ((c = f_ss[j].H + r_ss[j].H) >= midc)
+ if (c > midc || (f_ss[j].H != f_ss[j].E && r_ss[j].H == r_ss[j].E))
+ { midc = c;
+ midj = j;
+ }
+ for (j = N; j >= 0; j--)
+ if ((c = f_ss[j].E + r_ss[j].E + g) > midc)
+ { midc = c;
+ midj = j;
+ type = 2;
+ }
+
+
+/* Conquer: recursively around midpoint */
+
+ if (type == 1) {
+ nw_align(A,B,midi,midj,tb,-g,w,g,h,f_str, sapp, last);
+ nw_align(A+midi,B+midj,M-midi,N-midj,-g,te,w,g,h,f_str,sapp, last);
+ }
+ else {
+ nw_align(A,B,midi-1,midj,tb,0,w,g,h,f_str, sapp, last);
+ DEL(2);
+ nw_align(A+midi+1,B+midj,M-midi-1,N-midj,0,te,w,g,h,f_str, sapp, last);
+ }
+ return midc;
+}
+
+/* Interface and top level of comparator */
+
+static int
+ALIGN(const unsigned char *A, const unsigned char *B,
+ int M, int N,
+ int **W, int G, int H, int *S, int *nS,
+ struct f_struct *f_str)
+{
+ int c, ck;
+ struct swstr *f_ss, *r_ss;
+ int *sapp, last;
+
+ sapp = S;
+ last = 0;
+
+ if ((f_ss = (struct swstr *) calloc (N+2, sizeof (struct swstr)))
+ == NULL) {
+ fprintf (stderr, "cannot allocate f_ss array %3d\n", N+2);
+ exit (1);
+ }
+ f_ss++;
+ f_str->f_ss = f_ss;
+
+ if ((r_ss = (struct swstr *) calloc (N+2, sizeof (struct swstr)))
+ == NULL) {
+ fprintf (stderr, "cannot allocate r_ss array %3d\n", N+2);
+ exit (1);
+ }
+ r_ss++;
+ f_str->r_ss = r_ss;
+
+ c = nw_align(A,B,M,N,-G,-G,W,G,H,f_str,&sapp, &last); /* OK, do it */
+
+ ck = CHECK_SCORE(A,B,M,N,S,W,G,H,nS);
+ if (c != ck) fprintf(stderr,"Check_score error %d != %d\n",c,ck);
+
+ f_ss--; r_ss--;
+ free(r_ss); free(f_ss);
+
+ return c;
+}
+
+/* Alignment display routine */
+
+static char ALINE[51], BLINE[51], CLINE[51];
+
+void DISPLAY(unsigned char *A, unsigned char *B, int M, int N,
+ int *S, int AP, int BP, char *sq)
+{ register char *a, *b, *c;
+ register int i, j, op;
+ int lines, ap, bp;
+
+ i = j = op = lines = 0;
+ ap = AP;
+ bp = BP;
+ a = ALINE;
+ b = BLINE;
+ c = CLINE;
+ while (i < M || j < N)
+ { if (op == 0 && *S == 0)
+ { op = *S++;
+ *a = sq[A[++i]];
+ *b = sq[B[++j]];
+ *c++ = (*a++ == *b++) ? '|' : ' ';
+ }
+ else
+ { if (op == 0)
+ op = *S++;
+ if (op > 0)
+ { *a++ = ' ';
+ *b++ = sq[B[++j]];
+ op--;
+ }
+ else
+ { *a++ = sq[A[++i]];
+ *b++ = ' ';
+ op++;
+ }
+ *c++ = '-';
+ }
+ if (a >= ALINE+50 || (i >= M && j >= N))
+ { *a = *b = *c = '\0';
+ printf("\n%5d ",50*lines++);
+ for (b = ALINE+10; b <= a; b += 10)
+ printf(" . :");
+ if (b <= a+5)
+ printf(" .");
+ printf("\n%5d %s\n %s\n%5d %s\n",ap,ALINE,CLINE,bp,BLINE);
+ ap = AP + i;
+ bp = BP + j;
+ a = ALINE;
+ b = BLINE;
+ c = CLINE;
+ }
+ }
+}
+
+/* CHECK_SCORE - return the score of the alignment stored in S */
+
+static int CHECK_SCORE(const unsigned char *A, const unsigned char *B,
+ int M, int N, int *S, int **w, int g, int h,
+ int *nres)
+{
+ register int i, j, op, nc;
+ int score;
+
+ score = i = j = op = nc = 0;
+ while (i < M || j < N) {
+ op = *S++;
+ if (op == 0) {
+ score = w[A[++i]][B[++j]] + score;
+ nc++;
+ /* fprintf(stderr,"=%4d %4d %4d %4d\n",i,j,w[A[i]][B[i]],score); */
+ }
+ else if (op > 0) {
+ score = score - (g+op*h);
+ /* fprintf(stderr,">%4d %4d %4d %4d\n",i,j,-(g+op*h),score); */
+ j += op;
+ nc += op;
+ } else {
+ score = score - (g-op*h);
+ /* fprintf(stderr,"<%4d %4d %4d %4d\n",i,j,-(g-op*h),score); */
+ i -= op;
+ nc -= op;
+ }
+ }
+ *nres = nc;
+ return score;
+}
+
+
+static int
+BCHECK_SCORE(const unsigned char *A, const unsigned char *B,
+ int M, int N, int *S, int **w, int g, int h,
+ int *nres)
+{
+ register int i, j, op, nc;
+ int *Ssave;
+ int score;
+
+ score = i = j = op = nc = 0;
+ Ssave = S;
+ while (i < M || j < N) {
+ op = *S++;
+ if (op == 0) {
+ score = w[A[++i]][B[++j]] + score;
+ nc++;
+/* fprintf(stderr,"op0 %4d %4d %4d %4d\n",i,j,w[A[i]][B[i]],score); */
+ }
+ else if (op > 0) {
+ score = score - (g+op*h);
+/* fprintf(stderr,"op> %4d %4d %4d %4d %4d\n",i,j,op,-(g+op*h),score); */
+ j += op;
+ nc += op;
+ } else {
+ score = score - (g-op*h);
+/* fprintf(stderr,"op< %4d %4d %4d %4d %4d\n",i,j,op,-(g-op*h),score); */
+ i -= op;
+ nc -= op;
+ }
+ }
+ *nres = nc;
+ return score;
+}
+
+
+/* A PACKAGE FOR LOCALLY ALIGNING TWO SEQUENCES WITHIN A BAND:
+
+ To invoke, call LOCAL_ALIGN(A,B,M,N,L,U,W,G,H,S,dflag,&SI,&SJ,&EI,&EJ,MW).
+ The parameters are explained as follows:
+ A, B : two sequences to be aligned
+ M : the length of sequence A
+ N : the length of sequence B
+ L : lower bound of the band
+ U : upper bound of the band
+ W : scoring table for matches and mismatches
+ G : gap-opening penalty
+ H : gap-extension penalty
+ dflag : 0 - no display or backward pass
+ *SI : starting position of sequence A in the optimal local alignment
+ *SJ : starting position of sequence B in the optimal local alignment
+ *EI : ending position of sequence A in the optimal local alignment
+ *EJ : ending position of sequence B in the optimal local alignment
+ MW : maximum window size
+*/
+
+int bd_walign (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ struct pstruct *ppst,
+ struct f_struct *f_str, int hoff,
+ struct a_res_str *a_res)
+{
+ int low, up, score;
+ int min0, min1, max0, max1;
+ int window;
+
+ window = min (n1, ppst->param_u.fa.optwid);
+ /* hoff is the offset found from aa1 to seq 2 by hmatch */
+
+ low = -window/2-hoff;
+ up = low+window;
+
+ score=LOCAL_ALIGN(aa0-1,aa1-1,n0,n1, low, up,
+ ppst->pam2[0],
+#ifdef OLD_FASTA_GAP
+ -(ppst->gdelval-ppst->ggapval),
+#else
+ -ppst->gdelval,
+#endif
+ -ppst->ggapval,
+ &min0,&min1,&max0,&max1,ppst->param_u.fa.optwid,f_str);
+
+ if (score <=0) {
+ fprintf(stderr,"n0/n1: %d/%d hoff: %d window: %d\n",
+ n0, n1, hoff, window);
+ return 0;
+ }
+
+/*
+ fprintf(stderr," ALIGN: start0: %d start1: %d stop0: %d stop1: %d, bot: %d top: %d, win: %d MX %d\n",
+ min0-1,min1-1,max0-min0+1,max1-min1+1,low-(min1-min0),up-(min1-min0),
+ ppst->param_u.fa.optwid,n0);
+*/
+
+ a_res->min0 = min0-1; a_res->min1 = min1-1;
+ a_res->max0 = max0; a_res->max1 = max1;
+
+ B_ALIGN(aa0-1+min0-1,aa1-1+min1-1,max0-min0+1,max1-min1+1,
+ low-(min1-min0),up-(min1-min0),
+ ppst->pam2[0],
+#ifdef OLD_FASTA_GAP
+ -(ppst->gdelval-ppst->ggapval),
+#else
+ -ppst->gdelval,
+#endif
+ -ppst->ggapval,
+ a_res->res,&a_res->nres,ppst->param_u.fa.optwid,n0,f_str->bss);
+
+ return score;
+}
+
+static int
+LOCAL_ALIGN(const unsigned char *A, const unsigned char *B,
+ int M, int N,
+ int low, int up, int **W, int G,int H,
+ int *psi, int *psj, int *pei, int *pej, int MW,
+ struct f_struct *f_str)
+{
+ int band;
+ register struct bdstr *bssp;
+ int i, j, si, ei;
+ int c, d, e, t, m;
+ int leftd, rightd;
+ int best_score, starti, startj, endi, endj;
+ int *wa, curd;
+ int ib;
+ char flag;
+
+ bssp = f_str->bss;
+
+ m = G+H;
+ low = max(-M, low);
+ up = min(N, up);
+
+ if (N <= 0) {
+ *psi = *psj = *pei = *pej;
+ return 0;
+ }
+ if (M <= 0) {
+ *psi = *psj = *pei = *pej;
+ return 0;
+ }
+ band = up-low+1;
+ if (band < 1) {
+ fprintf(stderr,"low > up is unacceptable!: M: %d N: %d l/u: %d/%d\n",
+ M, N, low, up);
+ return -1;
+ }
+
+ j = (MW + 2 + 2) * sizeof(struct bdstr);
+
+ /* already done by init_work();
+ if (f_str->bss==NULL) f_str->bss = (struct bdstr *) ckalloc(j);
+ */
+
+ if (low > 0) leftd = 1;
+ else if (up < 0) leftd = band;
+ else leftd = 1-low;
+ rightd = band;
+ si = max(0,-up);
+ ei = min(M,N-low);
+ bssp[leftd].CC = 0;
+ for (j = leftd+1; j <= rightd; j++) {
+ bssp[j].CC = 0;
+ bssp[j].DD = -G;
+ }
+ bssp[rightd+1].CC = MININT;
+ bssp[rightd+1].DD = MININT;
+ best_score = 0;
+ endi = si;
+ endj = si+low;
+ bssp[leftd-1].CC = MININT;
+ bssp[leftd].DD = -G;
+ for (i = si+1; i <= ei; i++) {
+ if (i > N-up) rightd--;
+ if (leftd > 1) leftd--;
+ wa = W[A[i]];
+ if ((c = bssp[leftd+1].CC-m) > (d = bssp[leftd+1].DD-H)) d = c;
+ if ((ib = leftd+low-1+i ) > 0) c = bssp[leftd].CC+wa[B[ib]];
+/*
+ if (ib > N) fprintf(stderr,"B[%d] out of range %d\n",ib,N);
+*/
+ if (d > c) c = d;
+ if (c < 0) c = 0;
+ e = c-G;
+ bssp[leftd].DD = d;
+ bssp[leftd].CC = c;
+ if (c > best_score) {
+ best_score = c;
+ endi = i;
+ endj = ib;
+ }
+ for (curd=leftd+1; curd <= rightd; curd++) {
+ if ((c = c-m) > (e = e-H)) e = c;
+ if ((c = bssp[curd+1].CC-m) > (d = bssp[curd+1].DD-H)) d = c;
+/*
+ if ((ib=curd+low-1+i) <= 0 || ib > N)
+ fprintf(stderr,"B[%d]:%d\n",ib,B[ib]);
+*/
+ c = bssp[curd].CC + wa[B[curd+low-1+i]];
+ if (e > c) c = e;
+ if (d > c) c = d;
+ if (c < 0) c = 0;
+ bssp[curd].CC = c;
+ bssp[curd].DD = d;
+ if (c > best_score) {
+ best_score = c;
+ endi = i;
+ endj = curd+low-1+i;
+ }
+ }
+ }
+
+ leftd = max(1,-endi-low+1);
+ rightd = band-(up-(endj-endi));
+ bssp[rightd].CC = 0;
+ t = -G;
+ for (j = rightd-1; j >= leftd; j--) {
+ bssp[j].CC = t = t-H;
+ bssp[j].DD = t-G;
+ }
+ for (j = rightd+1; j <= band; ++j) bssp[j].CC = MININT;
+ bssp[leftd-1].CC = bssp[leftd-1].DD = MININT;
+ bssp[rightd].DD = -G;
+ flag = 0;
+ for (i = endi; i >= 1; i--) {
+ if (i+low <= 0) leftd++;
+ if (rightd < band) rightd++;
+ wa = W[A[i]];
+ if ((c = bssp[rightd-1].CC-m) > (d = bssp[rightd-1].DD-H)) d = c;
+ if ((ib = rightd+low-1+i) <= N) c = bssp[rightd].CC+wa[B[ib]];
+
+/*
+ if (ib <= 0) fprintf(stderr,"rB[%d] <1\n",ib);
+*/
+ if (d > c) c = d;
+ e = c-G;
+ bssp[rightd].DD = d;
+ bssp[rightd].CC = c;
+ if (c == best_score) {
+ starti = i;
+ startj = ib;
+ flag = 1;
+ break;
+ }
+ for (curd=rightd-1; curd >= leftd; curd--) {
+ if ((c = c-m) > (e = e-H)) e = c;
+ if ((c = bssp[curd-1].CC-m) > (d = bssp[curd-1].DD-H)) d = c;
+
+/*
+ if ((ib=curd+low-1+i) <= 0 || ib > N)
+ fprintf(stderr,"i: %d, B[%d]:%d\n",i,ib,B[ib]);
+*/
+ c = bssp[curd].CC + wa[B[curd+low-1+i]];
+ if (e > c) c = e;
+ if (d > c) c = d;
+ bssp[curd].CC = c;
+ bssp[curd].DD = d;
+ if (c == best_score) {
+ starti = i;
+ startj = curd+low-1+i;
+ flag = 1;
+ break;
+ }
+ }
+ if (flag == 1) break;
+ }
+
+ if (starti < 0 || starti > M || startj < 0 || startj > N) {
+ printf("starti=%d, startj=%d\n",starti,startj);
+ *psi = *psj = *pei = *pej;
+ exit(1);
+ }
+ *psi = starti;
+ *psj = startj;
+ *pei = endi;
+ *pej = endj;
+ return best_score;
+}
+
+/* A PACKAGE FOR GLOBALLY ALIGNING TWO SEQUENCES WITHIN A BAND:
+
+ To invoke, call B_ALIGN(A,B,M,N,L,U,W,G,H,S,MW,MX).
+ The parameters are explained as follows:
+ A, B : two sequences to be aligned
+ M : the length of sequence A
+ N : the length of sequence B
+ L : lower bound of the band
+ U : upper bound of the band
+ W : scoring table for matches and mismatches
+ G : gap-opening penalty
+ H : gap-extension penalty
+ S : script for DISPLAY routine
+ MW : maximum window size
+ MX : maximum length sequence M to be aligned
+*/
+
+static int IP;
+static int *MP[3]; /* save crossing points */
+static int *FP; /* forward dividing points */
+static char *MT[3]; /* 0: rep, 1: del, 2: ins */
+static char *FT;
+
+/* bg_align(A,B,M,N,up,low,tb,te) returns the cost of an optimum conversion between
+ A[1..M] and B[1..N] and appends such a conversion to the current script.
+ tb(te)= 1 no gap-open penalty if the conversion begins(ends) with a delete.
+ tb(te)= 2 no gap-open penalty if the conversion begins(ends) with an insert.
+*/
+static int
+bg_align(const unsigned char *A, const unsigned char *B,
+ int M, int N,
+ int low, int up, int tb, int te,
+ int **w, int g, int h,
+ struct bdstr *bss, int **sapp, int *last)
+{
+ int rmid, k, l, r, v, kt;
+ int t1, t2, t3;
+
+ {
+ int band, midd;
+ int leftd, rightd; /* for CC, DD, CP and DP */
+ register int curd; /* current index for CC, DD CP and DP */
+ register int i, j;
+ register int c, d, e;
+ int t, fr, *wa, ib, m;
+
+ /* Boundary cases: M <= 0 , N <= 0, or up-low <= 0 */
+ if (N <= 0) {
+ if (M > 0) { DEL(M) }
+ return 0;
+ }
+ if (M <= 0) {
+ INS(N)
+ return 0;
+ }
+ if ((band = up-low+1) <= 1) {
+ for (i = 1; i <= M; i++) { REP }
+ return 0;
+ }
+
+ /* Divide: Find all crossing points */
+
+ /* Initialization */
+ m = g + h;
+
+ midd = band/2 + 1;
+ rmid = low + midd - 1;
+ leftd = 1-low;
+ rightd = up-low+1;
+ if (leftd < midd) {
+ fr = -1;
+ for (j = 0; j < midd; j++)
+ bss[j].CP = bss[j].DP = -1;
+ for (j = midd; j <= rightd; j++) {
+ bss[j].CP = bss[j].DP = 0;
+ }
+ MP[0][0] = -1;
+ MP[1][0] = -1;
+ MP[2][0] = -1;
+ MT[0][0] = MT[1][0] = MT[2][0] = 0;
+ } else if (leftd > midd) {
+ fr = leftd-midd;
+ for (j = 0; j <= midd; j++) {
+ bss[j].CP = bss[j].DP = fr;
+ }
+ for (j = midd+1; j <= rightd; j++)
+ bss[j].CP = bss[j].DP = -1;
+ MP[0][fr] = -1;
+ MP[1][fr] = -1;
+ MP[2][fr] = -1;
+ MT[0][fr] = MT[1][fr] = MT[2][fr] = 0;
+ } else {
+ fr = 0;
+ for (j = 0; j < midd; j++) {
+ bss[j].CP = bss[j].DP = 0;
+ }
+ for (j = midd; j <= rightd; j++) {
+ bss[j].CP = bss[j].DP = 0;
+ }
+ MP[0][0] = -1;
+ MP[1][0] = -1;
+ MP[2][0] = -1;
+ MT[0][0] = MT[1][0] = MT[2][0] = 0;
+ }
+
+ bss[leftd].CC = 0;
+ if (tb == 2) t = 0;
+ else t = -g;
+ for (j = leftd+1; j <= rightd; j++) {
+ bss[j].CC = t = t-h;
+ bss[j].DD = t-g;
+ }
+ bss[rightd+1].CC = MININT;
+ bss[rightd+1].DD = MININT;
+ if (tb == 1) bss[leftd].DD = 0;
+ else bss[leftd].DD = -g;
+ bss[leftd-1].CC = MININT;
+ for (i = 1; i <= M; i++) {
+ if (i > N-up) rightd--;
+ if (leftd > 1) leftd--;
+ wa = w[A[i]];
+ if ((c = bss[leftd+1].CC-m) > (d = bss[leftd+1].DD-h)) {
+ d = c;
+ bss[leftd].DP = bss[leftd+1].CP;
+ } else bss[leftd].DP = bss[leftd+1].DP;
+ if ((ib = leftd+low-1+i) > 0) c = bss[leftd].CC+wa[B[ib]];
+ if (d > c || ib <= 0) {
+ c = d;
+ bss[leftd].CP = bss[leftd].DP;
+ }
+ e = c-g;
+ bss[leftd].DD = d;
+ bss[leftd].CC = c;
+ IP = bss[leftd].CP;
+ if (leftd == midd) bss[leftd].CP = bss[leftd].DP = IP = i;
+ for (curd=leftd+1; curd <= rightd; curd++) {
+ if (curd != midd) {
+ if ((c = c-m) > (e = e-h)) {
+ e = c;
+ IP = bss[curd-1].CP;
+ } /* otherwise, IP is unchanged */
+ if ((c = bss[curd+1].CC-m) > (d = bss[curd+1].DD-h)) {
+ d = c;
+ bss[curd].DP = bss[curd+1].CP;
+ } else {
+ bss[curd].DP = bss[curd+1].DP;
+ }
+ c = bss[curd].CC + wa[B[curd+low-1+i]];
+ if (c < d || c < e) {
+ if (e > d) {
+ c = e;
+ bss[curd].CP = IP;
+ } else {
+ c = d;
+ bss[curd].CP = bss[curd].DP;
+ }
+ } /* otherwise, CP is unchanged */
+ bss[curd].CC = c;
+ bss[curd].DD = d;
+ } else {
+ if ((c = c-m) > (e = e-h)) {
+ e = c;
+ MP[1][i] = bss[curd-1].CP;
+ MT[1][i] = 2;
+ } else {
+ MP[1][i] = IP;
+ MT[1][i] = 2;
+ }
+ if ((c = bss[curd+1].CC-m) > (d = bss[curd+1].DD-h)) {
+ d = c;
+ MP[2][i] = bss[curd+1].CP;
+ MT[2][i] = 1;
+ } else {
+ MP[2][i] = bss[curd+1].DP;
+ MT[2][i] = 1;
+ }
+ c = bss[curd].CC + wa[B[curd+low-1+i]];
+ if (c < d || c < e) {
+ if (e > d) {
+ c = e;
+ MP[0][i] = MP[1][i];
+ MT[0][i] = 2;
+ } else {
+ c = d;
+ MP[0][i] = MP[2][i];
+ MT[0][i] = 1;
+ }
+ } else {
+ MP[0][i] = i-1;
+ MT[0][i] = 0;
+ }
+ if (c-g > e) {
+ MP[1][i] = MP[0][i];
+ MT[1][i] = MT[0][i];
+ }
+ if (c-g > d) {
+ MP[2][i] = MP[0][i];
+ MT[2][i] = MT[0][i];
+ }
+ bss[curd].CP = bss[curd].DP = IP = i;
+ bss[curd].CC = c;
+ bss[curd].DD = d;
+ }
+ }
+ }
+
+ /* decide which path to be traced back */
+ if (te == 1 && d+g > c) {
+ k = bss[rightd].DP;
+ l = 2;
+ } else if (te == 2 && e+g > c) {
+ k = IP;
+ l = 1;
+ } else {
+ k = bss[rightd].CP;
+ l = 0;
+ }
+ if (rmid > N-M) l = 2;
+ else if (rmid < N-M) l = 1;
+ v = c;
+ }
+ /* Conquer: Solve subproblems recursively */
+
+ /* trace back */
+ r = -1;
+ for (; k > -1; r=k, k=MP[l][r], l=MT[l][r]){
+ FP[k] = r;
+ FT[k] = l; /* l=0,1,2 */
+ }
+ /* forward dividing */
+ if (r == -1) { /* optimal alignment did not cross the middle diagonal */
+ if (rmid < 0) {
+ bg_align(A,B,M,N,rmid+1,up,tb,te,w,g,h,bss, sapp, last);
+ }
+ else {
+ bg_align(A,B,M,N,low,rmid-1,tb,te,w,g,h,bss, sapp, last);
+ }
+ } else {
+ k = r;
+ l = FP[k];
+ kt = FT[k];
+
+ /* first block */
+ if (rmid < 0) {
+ bg_align(A,B,r-1,r+rmid,rmid+1,min(up,r+rmid),tb,1,w,g,h,bss,sapp,last);
+ DEL(1)
+ } else if (rmid > 0) {
+ bg_align(A,B,r,r+rmid-1,max(-r,low),rmid-1,tb,2,w,g,h,bss,sapp,last);
+ INS(1)
+ }
+
+ /* intermediate blocks */
+ t2 = up-rmid-1;
+ t3 = low-rmid+1;
+ for (; l > -1; k = l, l = FP[k], kt = FT[k]) {
+ if (kt == 0) { REP }
+ else if (kt == 1) { /* right-hand side triangle */
+ INS(1)
+ t1 = l-k-1;
+ bg_align(A+k,B+k+rmid+1,t1,t1,0,min(t1,t2),2,1,w,g,h,bss,sapp,last);
+ DEL(1)
+ }
+ else { /* kt == 2, left-hand side triangle */
+ DEL(1)
+ t1 = l-k-1;
+ bg_align(A+k+1,B+k+rmid,t1,t1,max(-t1,t3),0,1,2,w,g,h,bss,sapp,last);
+ INS(1)
+ }
+ }
+
+ /* last block */
+ if (N-M > rmid) {
+ INS(1)
+ t1 = k+rmid+1;
+ bg_align(A+k,B+t1,M-k,N-t1,0,min(N-t1,t2),2,te,w,g,h,bss,sapp,last);
+ } else if (N-M < rmid) {
+ DEL(1)
+ t1 = M-(k+1);
+ bg_align(A+k+1,B+k+rmid,t1,N-(k+rmid),max(-t1,t3),0,1,te,w,g,h,
+ bss,sapp,last);
+ }
+ }
+ return(v);
+}
+
+int B_ALIGN(const unsigned char *A, const unsigned char *B,
+ int M, int N,
+ int low, int up, int **W, int G, int H, int *S, int *nS,
+ int MW, int MX, struct bdstr *bss)
+{
+ int c, i, j;
+ int g, h;
+ size_t mj;
+ int check_score;
+ int **sapp, *sapp_v, *last, last_v;
+
+ g = G;
+ h = H;
+ sapp_v = S;
+ sapp = &sapp_v;
+
+ last_v = 0;
+ last = &last_v;
+
+ low = min(max(-M, low),min(N-M,0));
+ up = max(min(N, up),max(N-M,0));
+
+ if (N <= 0) {
+ if (M > 0) { DEL(M); }
+ return -gap(M);
+ }
+ if (M <= 0) {
+ INS(N);
+ return -gap(N);
+ }
+ if (up-low+1 <= 1) {
+ c = 0;
+ for (i = 1; i <= M; i++) {
+ REP;
+ c += W[A[i]][B[i]];
+ }
+ return c;
+ }
+
+ if (MT[0]==NULL) {
+ mj = MX+1;
+ MT[0] = (char *) ckalloc(mj);
+ MT[1] = (char *) ckalloc(mj);
+ MT[2] = (char *) ckalloc(mj);
+ FT = (char *) ckalloc(mj);
+
+ mj *= sizeof(int);
+ MP[0] = (int *) ckalloc(mj);
+ MP[1] = (int *) ckalloc(mj);
+ MP[2] = (int *) ckalloc(mj);
+ FP = (int *) ckalloc(mj);
+ }
+
+ c = bg_align(A,B,M,N,low,up,0,0,W,G,H,bss, sapp, last);
+
+ check_score = BCHECK_SCORE(A,B,M,N,S,W,G,H,nS);
+
+ free(FP); free(MP[2]); free(MP[1]); free(MP[0]);
+ free(FT); free(MT[2]); free(MT[1]); free(MT[0]);
+ MT[0]=NULL;
+
+ if (check_score != c)
+ printf("\nBCheck_score=%d != %d\n", check_score,c);
+ return c;
+}
+
+int do_walign (const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ int frame,
+ struct pstruct *ppst,
+ struct f_struct *f_str,
+ struct a_res_str *a_res,
+ int *have_ares)
+{
+ int hoff, optflag_s, optcut_s, optwid_s, n10, score;
+ const unsigned char *aa1p;
+ struct rstruct rst;
+
+#ifdef TFASTA
+ f_str->n10 = n10=aatran(aa1,f_str->aa1x,n1,frame);
+ do_fasta (aa0, n0, f_str->aa1x, n10, ppst, f_str, &rst, &hoff);
+ aa1p = f_str->aa1x;
+
+#else
+ n10 = n1;
+ aa1p = aa1;
+#endif
+
+ a_res->res = f_str->res;
+ *have_ares = 1;
+
+ if (ppst->sw_flag)
+ return sw_walign(aa0, n0, aa1p, n10, ppst, f_str, a_res);
+ else {
+ optflag_s = ppst->param_u.fa.optflag;
+ optcut_s = ppst->param_u.fa.optcut;
+ optwid_s = ppst->param_u.fa.optwid;
+ ppst->param_u.fa.optflag = 1;
+ ppst->param_u.fa.optcut = 0;
+ ppst->param_u.fa.optwid *= 2;
+
+ do_fasta(aa0, n0, aa1p, n10, ppst, f_str, &rst, &hoff);
+
+ if (rst.score[0]>0) {
+ score=bd_walign(aa0, n0, aa1p, n10, ppst, f_str, hoff, a_res);
+ }
+ else {
+ a_res->nres = 0;
+ score=0;
+ }
+
+ ppst->param_u.fa.optflag = optflag_s;
+ ppst->param_u.fa.optcut = optcut_s;
+ ppst->param_u.fa.optwid = optwid_s;
+ return score;
+ }
+}
+
+void
+pre_cons(const unsigned char *aa1, int n1, int frame, struct f_struct *f_str) {
+
+#ifdef TFASTA
+ f_str->n10 = aatran(aa1,f_str->aa1x,n1,frame);
+#endif
+}
+
+/* aln_func_vals - set up aln.qlfact, qlrev, llfact, llmult, frame, llrev */
+/* call from calcons, calc_id, calc_code */
+void
+aln_func_vals(int frame, struct a_struct *aln) {
+
+#ifdef TFASTA
+ aln->qlfact = 1;
+ aln->llfact = 3;
+ aln->llmult = 3;
+ aln->qlrev = 0;
+ aln->frame = frame;
+ if (frame > 2) {
+ aln->llrev = 1;
+ aln->frame = 3 - frame;
+ }
+ else aln->llrev = 0;
+#else /* FASTA */
+ aln->llfact = aln->qlfact = aln->llmult = 1;
+ aln->llrev = 0;
+ if (frame > 0) aln->qlrev = 1;
+ else aln->qlrev = 0;
+ aln->frame = 0;
+#endif
+}
+
+#include "a_mark.h"
+
+int calcons(const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ int *nc,
+ struct a_struct *aln, struct a_res_str a_res,
+ struct pstruct pst,
+ char *seqc0, char *seqc1, char *seqca,
+ struct f_struct *f_str)
+{
+ int i0, i1, nn1;
+ int op, lenc, nd, ns, itmp;
+ const unsigned char *aa1p;
+ char *sp0, *sp1, *spa, *sq;
+ int *rp;
+ int smins, mins;
+
+ if (pst.ext_sq_set) { sq = pst.sqx; }
+ else { sq = pst.sq; }
+
+#ifndef TFASTA
+ aa1p = aa1;
+ nn1 = n1;
+#else
+ aa1p = f_str->aa1x;
+ nn1 = f_str->n10;
+#endif
+
+ aln->amin0 = a_res.min0;
+ aln->amax0 = a_res.max0;
+ aln->amin1 = a_res.min1;
+ aln->amax1 = a_res.max1;
+ /* will we show all the start ?*/
+ if (min(a_res.min0,a_res.min1) < aln->llen || aln->showall==1)
+ if (a_res.min0 >= a_res.min1) { /* aa0 extends more to left */
+ smins=0;
+ if (aln->showall==1) mins = a_res.min0;
+ else mins = min(a_res.min0,aln->llcntx);
+ aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
+ aln->smin0 = a_res.min0-mins;
+ if ((mins-a_res.min1)>0) {
+ memset(seqc1,' ',mins-a_res.min1);
+ aancpy(seqc1+mins-a_res.min1,(char *)aa1p,a_res.min1,pst);
+ aln->smin1 = 0;
+ }
+ else {
+ aancpy(seqc1,(char *)aa1p+a_res.min1-mins,mins,pst);
+ aln->smin1 = a_res.min1-mins;
+ }
+ }
+ else {
+ smins=0;
+ if (aln->showall == 1) mins=a_res.min1;
+ else mins = min(a_res.min1,aln->llcntx);
+ aancpy(seqc1,(char *)(aa1p+a_res.min1-mins),mins,pst);
+ aln->smin1 = a_res.min1-mins;
+ if ((mins-a_res.min0)>0) {
+ memset(seqc0,' ',mins-a_res.min0);
+ aancpy(seqc0+mins-a_res.min0,(char *)aa0,a_res.min0,pst);
+ aln->smin0 = 0;
+ }
+ else {
+ aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
+ aln->smin0 = a_res.min0-mins;
+ }
+ }
+ else {
+ mins= min(aln->llcntx,min(a_res.min0,a_res.min1));
+ smins=mins;
+ aln->smin0=a_res.min0 - mins;
+ aln->smin1=a_res.min1 - mins;
+ aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
+ aancpy(seqc1,(char *)aa1p+a_res.min1-mins,mins,pst);
+ }
+ /* set the alignment code to zero for context */
+ memset(seqca,0,mins);
+
+ /* TFASTA
+ smins = mins = 0;
+ aln->smin0=a_res.min0;
+ aln->smin1=a_res.min1;
+ */
+
+/* now get the middle */
+
+ spa = seqca+mins;
+ sp0 = seqc0+mins;
+ sp1 = seqc1+mins;
+ rp = a_res.res;
+ lenc = aln->nident = aln->nsim = aln->ngap_q = aln->ngap_l = aln->nfs = op = 0;
+ i0 = a_res.min0;
+ i1 = a_res.min1;
+
+ while (i0 < a_res.max0 || i1 < a_res.max1) {
+ if (op == 0 && *rp == 0) {
+ op = *rp++;
+ lenc++;
+ if ((itmp=pst.pam2[0][aa0[i0]][aa1p[i1]])<0) { *spa = M_NEG; }
+ else if (itmp == 0) { *spa = M_ZERO;}
+ else {*spa = M_POS;}
+ if (*spa == M_POS || *spa==M_ZERO) aln->nsim++;
+
+
+ *sp0 = sq[aa0[i0++]];
+ *sp1 = sq[aa1p[i1++]];
+ if (toupper(*sp0) == toupper(*sp1)) {
+ aln->nident++;
+ *spa = M_IDENT;
+ }
+ else if (pst.nt_align) {
+ if ((toupper(*sp0) == 'T' && toupper(*sp1) == 'U') ||
+ (toupper(*sp0)=='U' && toupper(*sp1)=='T')) {
+ aln->nident++;
+ *spa = M_IDENT;
+ }
+ else if (toupper(*sp0) == 'N') aln->ngap_q++;
+ else if (toupper(*sp1) == 'N') aln->ngap_l++;
+ }
+ sp0++; sp1++; spa++;
+ }
+ else {
+ if (op==0) op = *rp++;
+ if (op > 0) {
+ *sp0++ = '-';
+ *sp1++ = sq[aa1p[i1++]];
+ *spa++ = M_DEL;
+ op--;
+ lenc++;
+ aln->ngap_q++;
+ }
+ else {
+ *sp0++ = sq[aa0[i0++]];
+ *sp1++ = '-';
+ *spa++ = M_DEL;
+ op++;
+ lenc++;
+ aln->ngap_l++;
+ }
+ }
+ }
+
+ *nc = lenc;
+ *spa = '\0';
+
+/* now we have the middle, get the right end */
+ if (!aln->llcntx_flg) {
+ ns = mins + lenc + aln->llen; /* show an extra line? */
+ ns -= (itmp = ns %aln->llen); /* itmp = left over on last line */
+ if (itmp>aln->llen/2) ns += aln->llen; /* more than 1/2 , use another*/
+ nd = ns - (mins+lenc); /* this much extra */
+ }
+ else nd = aln->llcntx;
+
+ if (nd > max(n0-a_res.max0,nn1-a_res.max1))
+ nd = max(n0-a_res.max0,nn1-a_res.max1);
+
+ if (aln->showall==1) {
+ nd = max(n0-a_res.max0,nn1-a_res.max1); /* reset for showall=1 */
+ /* get right end */
+ aancpy(seqc0+mins+lenc,(char *)aa0+a_res.max0,n0-a_res.max0,pst);
+ aancpy(seqc1+mins+lenc,(char *)aa1p+a_res.max1,nn1-a_res.max1,pst);
+ /* fill with blanks - this is required to use one 'nc' */
+ memset(seqc0+mins+lenc+n0-a_res.max0,' ',nd-(n0-a_res.max0));
+ memset(seqc1+mins+lenc+nn1-a_res.max1,' ',nd-(nn1-a_res.max1));
+ }
+ else {
+ if ((nd-(n0-a_res.max0))>0) {
+ aancpy(seqc0+mins+lenc,(char *)aa0+a_res.max0,(n0-a_res.max0),pst);
+ memset(seqc0+mins+lenc+n0-a_res.max0,' ',nd-(n0-a_res.max0));
+ }
+ else aancpy(seqc0+mins+lenc,(char *)aa0+a_res.max0,nd,pst);
+
+ if ((nd-(nn1-a_res.max1))>0) {
+ aancpy(seqc1+mins+lenc,(char *)aa1p+a_res.max1,nn1-a_res.max1,pst);
+ memset(seqc1+mins+lenc+nn1-a_res.max1,' ',nd-(nn1-a_res.max1));
+ }
+ else aancpy(seqc1+mins+lenc,(char *)aa1p+a_res.max1,nd,pst);
+ }
+
+ /* fprintf(stderr,"%d\n",mins+lenc+nd); */
+
+ return mins+lenc+nd;
+}
+
+int calcons_a(const unsigned char *aa0, unsigned char *aa0a, int n0,
+ const unsigned char *aa1, int n1,
+ int *nc,
+ struct a_struct *aln,
+ struct a_res_str a_res,
+ struct pstruct pst,
+ char *seqc0, char *seqc0a, char *seqc1, char *seqca,
+ char *ann_arr, struct f_struct *f_str)
+{
+ int i0, i1, nn1;
+ int op, lenc, nd, ns, itmp;
+ const unsigned char *aa1p;
+ char *sp0, *sp0a, *sp1, *spa, *sq;
+ int *rp;
+ int smins, mins;
+
+ if (pst.ext_sq_set) {
+ sq = pst.sqx;
+ }
+ else {
+ sq = pst.sq;
+ }
+
+#ifndef TFASTA
+ aa1p = aa1;
+ nn1 = n1;
+#else
+ aa1p = f_str->aa1x;
+ nn1 = f_str->n10;
+#endif
+
+ aln->amin0 = a_res.min0;
+ aln->amax0 = a_res.max0;
+ aln->amin1 = a_res.min1;
+ aln->amax1 = a_res.max1;
+ /* will we show all the start ?*/
+ /* will we show all the start ?*/
+ if (min(a_res.min0,a_res.min1)<aln->llen || aln->showall==1)
+ if (a_res.min0>=a_res.min1) { /* aa0 extends more to left */
+ smins=0;
+ if (aln->showall==1) mins = a_res.min0;
+ else mins = min(a_res.min0,aln->llcntx);
+ aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
+ aln->smin0 = a_res.min0-mins;
+ if ((mins-a_res.min1)>0) {
+ memset(seqc1,' ',mins-a_res.min1);
+ aancpy(seqc1+mins-a_res.min1,(char *)aa1p,a_res.min1,pst);
+ aln->smin1 = 0;
+ }
+ else {
+ aancpy(seqc1,(char *)aa1p+a_res.min1-mins,mins,pst);
+ aln->smin1 = a_res.min1-mins;
+ }
+ }
+ else {
+ smins=0;
+ if (aln->showall == 1) mins=a_res.min1;
+ else mins = min(a_res.min1,aln->llcntx);
+ aancpy(seqc1,(char *)(aa1p+a_res.min1-mins),mins,pst);
+ aln->smin1 = a_res.min1-mins;
+ if ((mins-a_res.min0)>0) {
+ memset(seqc0,' ',mins-a_res.min0);
+ aancpy(seqc0+mins-a_res.min0,(char *)aa0,a_res.min0,pst);
+ aln->smin0 = 0;
+ }
+ else {
+ aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
+ aln->smin0 = a_res.min0-mins;
+ }
+ }
+ else {
+ mins= min(aln->llcntx,min(a_res.min0,a_res.min1));
+ smins=mins;
+ aln->smin0=a_res.min0 - smins;
+ aln->smin1=a_res.min1 - smins;
+ aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
+ aancpy(seqc1,(char *)aa1p+a_res.min1-mins,mins,pst);
+ }
+ /* set the alignment code to zero for context */
+ memset(seqca,0,mins);
+ memset(seqc0a,' ',mins);
+
+ /* TFASTA
+ smins = mins = 0;
+ aln->smin0=a_res.min0;
+ aln->smin1=a_res.min1;
+ */
+
+/* now get the middle */
+
+ spa = seqca+mins;
+ sp0 = seqc0+mins;
+ sp0a = seqc0a+mins;
+ sp1 = seqc1+mins;
+ rp = a_res.res;
+ lenc = aln->nident = aln->nsim = aln->ngap_q = aln->ngap_l = aln->nfs = op = 0;
+ i0 = a_res.min0;
+ i1 = a_res.min1;
+
+ while (i0 < a_res.max0 || i1 < a_res.max1) {
+ if (op == 0 && *rp == 0) {
+ op = *rp++;
+ lenc++;
+ if ((itmp=pst.pam2[0][aa0[i0]][aa1p[i1]])<0) { *spa = M_NEG; }
+ else if (itmp == 0) { *spa = M_ZERO;}
+ else {*spa = M_POS;}
+ if (*spa == M_POS || *spa==M_ZERO) aln->nsim++;
+
+ *sp0a++ = ann_arr[aa0a[i0]];
+
+ *sp0 = sq[aa0[i0++]];
+ *sp1 = sq[aa1p[i1++]];
+
+ if (toupper(*sp0) == toupper(*sp1)) {
+ aln->nident++;
+ *spa = M_IDENT;
+ }
+ else if (pst.nt_align) {
+ if ((toupper(*sp0) == 'T' && toupper(*sp1) == 'U') ||
+ (toupper(*sp0)=='U' && toupper(*sp1)=='T')) {
+ aln->nident++;
+ *spa = M_IDENT;
+ }
+ else if (toupper(*sp0) == 'N') aln->ngap_q++;
+ else if (toupper(*sp1) == 'N') aln->ngap_l++;
+ }
+ sp0++; sp1++; spa++;
+ }
+ else {
+ if (op==0) op = *rp++;
+ if (op>0) {
+ *sp0++ = '-';
+ *sp1++ = sq[aa1p[i1++]];
+ *spa++ = M_DEL;
+ *sp0a++ = ' ';
+ op--;
+ lenc++;
+ aln->ngap_q++;
+ }
+ else {
+ *sp0a++ = ann_arr[aa0a[i0]];
+ *sp0++ = sq[aa0[i0++]];
+ *sp1++ = '-';
+ *spa++ = M_DEL;
+ op++;
+ lenc++;
+ aln->ngap_l++;
+ }
+ }
+ }
+
+ *nc = lenc;
+ *sp0a = *spa = '\0';
+
+/* now we have the middle, get the right end */
+ if (!aln->llcntx_flg) {
+ ns = mins + lenc + aln->llen; /* show an extra line? */
+ ns -= (itmp = ns %aln->llen); /* itmp = left over on last line */
+ if (itmp>aln->llen/2) ns += aln->llen; /* more than 1/2 , use another*/
+ nd = ns - (mins+lenc); /* this much extra */
+ }
+ else nd = aln->llcntx;
+
+ if (nd > max(n0-a_res.max0,nn1-a_res.max1))
+ nd = max(n0-a_res.max0,nn1-a_res.max1);
+
+ if (aln->showall==1) {
+ nd = max(n0-a_res.max0,nn1-a_res.max1); /* reset for showall=1 */
+ /* get right end */
+ aancpy(seqc0+mins+lenc,(char *)aa0+a_res.max0,n0-a_res.max0,pst);
+ aancpy(seqc1+mins+lenc,(char *)aa1p+a_res.max1,nn1-a_res.max1,pst);
+ /* fill with blanks - this is required to use one 'nc' */
+ memset(seqc0+mins+lenc+n0-a_res.max0,' ',nd-(n0-a_res.max0));
+ memset(seqc1+mins+lenc+nn1-a_res.max1,' ',nd-(nn1-a_res.max1));
+ }
+ else {
+ if ((nd-(n0-a_res.max0))>0) {
+ aancpy(seqc0+mins+lenc,(char *)aa0+a_res.max0,(n0-a_res.max0),pst);
+ memset(seqc0+mins+lenc+n0-a_res.max0,' ',nd-(n0-a_res.max0));
+ }
+ else aancpy(seqc0+mins+lenc,(char *)aa0+a_res.max0,nd,pst);
+
+ if ((nd-(nn1-a_res.max1))>0) {
+ aancpy(seqc1+mins+lenc,(char *)aa1p+a_res.max1,nn1-a_res.max1,pst);
+ memset(seqc1+mins+lenc+nn1-a_res.max1,' ',nd-(nn1-a_res.max1));
+ }
+ else aancpy(seqc1+mins+lenc,(char *)aa1p+a_res.max1,nd,pst);
+ }
+
+ /* fprintf(stderr,"%d\n",mins+lenc+nd); */
+
+ return mins+lenc+nd;
+}
+
+static void
+update_code(char *al_str, int al_str_max, int op, int op_cnt) {
+
+ char op_char[5]={"=-+*"};
+ char tmp_cnt[20];
+
+ sprintf(tmp_cnt,"%c%d",op_char[op],op_cnt);
+ strncat(al_str,tmp_cnt,al_str_max);
+}
+
+
+/* build an array of match/ins/del - length strings */
+int calc_code(const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ struct a_struct *aln, struct a_res_str a_res,
+ struct pstruct pst,
+ char *al_str, int al_str_n, struct f_struct *f_str)
+{
+ int i0, i1, nn1;
+ int op, lenc;
+ int p_op, op_cnt;
+ const unsigned char *aa1p;
+ char sp0, sp1, *sq;
+ int *rp;
+
+ if (pst.ext_sq_set) {
+ sq = pst.sqx;
+ }
+ else {
+ sq = pst.sq;
+ }
+
+#ifndef TFASTA
+ aa1p = aa1;
+ nn1 = n1;
+#else
+ aa1p = f_str->aa1x;
+ nn1 = f_str->n10;
+#endif
+
+ aln->amin0 = a_res.min0;
+ aln->amax0 = a_res.max0;
+ aln->amin1 = a_res.min1;
+ aln->amax1 = a_res.max1;
+
+ rp = a_res.res;
+ lenc = aln->nident = aln->nsim = aln->ngap_q = aln->ngap_l = aln->nfs = op = p_op = 0;
+ op_cnt = 0;
+
+ i0 = a_res.min0;
+ i1 = a_res.min1;
+
+ while (i0 < a_res.max0 || i1 < a_res.max1) {
+ if (op == 0 && *rp == 0) {
+
+ if (pst.pam2[0][aa0[i0]][aa1p[i1]]>=0) { aln->nsim++;}
+
+ sp0 = sq[aa0[i0++]];
+ sp1 = sq[aa1p[i1++]];
+
+ if (p_op == 0 || p_op==3) {
+ if (sp0 != '*' && sp1 != '*') {
+ if (p_op == 3) {
+ update_code(al_str,al_str_n-strlen(al_str),p_op,op_cnt);
+ op_cnt = 1; p_op = 0;
+ }
+ else {op_cnt++;}
+ }
+ else {
+ update_code(al_str,al_str_n-strlen(al_str),p_op,op_cnt);
+ op_cnt = 1; p_op = 3;
+ }
+ }
+ else {
+ update_code(al_str,al_str_n-strlen(al_str),p_op,op_cnt);
+ op_cnt = 1; p_op = 0;
+ }
+
+ op = *rp++;
+ lenc++;
+
+ if (toupper(sp0) == toupper(sp1)) aln->nident++;
+ else if (pst.nt_align) {
+ if ((toupper(sp0) == 'T' && toupper(sp1) == 'U') ||
+ (toupper(sp0)=='U' && toupper(sp1)=='T')) aln->nident++;
+ else if (toupper(sp0) == 'N') aln->ngap_q++;
+ else if (toupper(sp1) == 'N') aln->ngap_l++;
+ }
+ }
+ else {
+ if (op==0) op = *rp++;
+ if (op>0) {
+ if (p_op == 1) { op_cnt++;}
+ else {
+ update_code(al_str,al_str_n - strlen(al_str),p_op,op_cnt);
+ op_cnt = 1; p_op = 1;
+ }
+ op--; lenc++; i1++; aln->ngap_q++;
+ }
+ else {
+ if (p_op == 2) { op_cnt++;}
+ else {
+ update_code(al_str,al_str_n - strlen(al_str),p_op,op_cnt);
+ op_cnt = 1; p_op = 2;
+ }
+ op++; lenc++; i0++; aln->ngap_l++;
+ }
+ }
+ }
+ update_code(al_str,al_str_n - strlen(al_str),p_op,op_cnt);
+
+ return lenc;
+}
+
+int calc_id(const unsigned char *aa0, int n0,
+ const unsigned char *aa1, int n1,
+ struct a_struct *aln,
+ struct a_res_str a_res,
+ struct pstruct pst,
+ struct f_struct *f_str)
+{
+ int i0, i1, nn1;
+ int op, lenc;
+ int sp0, sp1;
+ const unsigned char *aa1p;
+ int *rp;
+ char *sq;
+
+ if (pst.ext_sq_set) { sq = pst.sqx; }
+ else { sq = pst.sq; }
+
+#ifndef TFASTA
+ aa1p = aa1;
+ nn1 = n1;
+#else
+ aa1p = f_str->aa1x;
+ nn1 = f_str->n10;
+#endif
+
+ aln->amin0 = a_res.min0;
+ aln->amax0 = a_res.max0;
+ aln->amin1 = a_res.min1;
+ aln->amax1 = a_res.max1;
+
+ rp = a_res.res;
+ lenc = aln->nident = aln->nsim = aln->ngap_q = aln->ngap_l = aln->nfs = op = 0;
+ i0 = a_res.min0;
+ i1 = a_res.min1;
+
+ while (i0 < a_res.max0 || i1 < a_res.max1) {
+ if (op == 0 && *rp == 0) {
+ op = *rp++;
+ lenc++;
+
+ if (pst.pam2[0][aa0[i0]][aa1p[i1]]>=0) { aln->nsim++;}
+
+ sp0 = sq[aa0[i0++]];
+ sp1 = sq[aa1p[i1++]];
+ if (toupper(sp0) == toupper(sp1)) {aln->nident++;}
+ else if (pst.nt_align) {
+ if ((toupper(sp0)=='T' && toupper(sp1)== 'U')||
+ (toupper(sp0)=='U' && toupper(sp1)=='T')) {aln->nident++;}
+ else if (toupper(sp0) == 'N') aln->ngap_q++;
+ else if (toupper(sp1) == 'N') aln->ngap_l++;
+ }
+ }
+ else {
+ if (op==0) op = *rp++;
+ if (op>0) {op--; lenc++; i1++; aln->ngap_q++;}
+ else {op++; lenc++; i0++; aln->ngap_l++; }
+ }
+ }
+ return lenc;
+}
+
+#ifdef PCOMPLIB
+
+#include "w_mw.h"
+
+void
+update_params(struct qmng_str *qm_msg, struct pstruct *ppst)
+{
+ ppst->n0 = qm_msg->n0;
+}
+#endif
git://source.jalview.org / jabaws.git / blobdiff