+++ /dev/null
-/* copyright (c) 1994, 1995, 1996 William R. Pearson */
-
-/* $Name: fa_34_26_5 $ - $Id: dropnsw.c,v 1.35 2006/10/19 14:49:14 wrp Exp $ */
-
-/*
- this is a slower version of dropgsw.c that implements the Smith-Waterman
- algorithm. It lacks the shortcuts in dropgsw.c that prevent scores less
- than the penalty for the first residue in a gap from being generated.
-
- Thus, dropnsw.c should be used for tests with very large gap penalties,
- and is more appropriate for programs like prss3, which are interested
- in accurate low scores.
-*/
-
-/* the do_walign() code in this file is not thread_safe */
-/* init_work(), do_work(), are thread safe */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include <math.h>
-
-#include "defs.h"
-#include "param.h"
-
-static char *verstr="3.5 Sept 2006";
-
-struct swstr { int H, E;};
-
-struct f_struct {
- struct swstr *ss;
- struct swstr *f_ss;
- struct swstr *r_ss;
- int *waa_s, *waa_a;
- int **pam2p[2];
- int *res;
- double aa0_f[MAXSQ];
- double *kar_p;
-};
-
-#define DROP_INTERN
-#include "drop_func.h"
-
-extern int do_karlin(const unsigned char *aa1, int n1,
- int **pam2, struct pstruct *ppst,
- double *aa0_f, double *kar_p, double *lambda, double *H);
-extern void aancpy(char *to, char *from, int count, struct pstruct pst);
-int ALIGN(const unsigned char *A, const unsigned char *B, int M, int N,
- int **W, int IW, int G, int H, int *S, int *NC,
- struct f_struct *f_str);
-
-/* initialize for Smith-Waterman optimal score */
-
-void init_work (unsigned char *aa0, int n0,
- struct pstruct *ppst,
- struct f_struct **f_arg)
-{
- int maxn0;
- int *pwaa_s, *pwaa_a;
- int e, f, i, j, q;
- int *res;
- struct f_struct *f_str;
- int **pam2p;
- struct swstr *ss, *f_ss, *r_ss;
- int nsq, ip;
-
- if (ppst->ext_sq_set) {
- nsq = ppst->nsqx; ip = 1;
- }
- else {
- nsq = ppst->nsq; ip = 0;
- }
-
- f_str = (struct f_struct *)calloc(1,sizeof(struct f_struct));
-
- /* allocate space for the scoring arrays */
- maxn0 = n0 + 2;
- 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;
-
- if ((f_ss = (struct swstr *) calloc (maxn0, sizeof (struct swstr)))
- == NULL) {
- fprintf (stderr, "cannot allocate f_ss array %3d\n", n0);
- exit (1);
- }
- f_ss++;
- f_str->f_ss = f_ss;
-
- if ((r_ss = (struct swstr *) calloc (n0+2, sizeof (struct swstr)))
- == NULL) {
- fprintf (stderr, "cannot allocate r_ss array %3d\n", n0);
- exit (1);
- }
- r_ss++;
- f_str->r_ss = r_ss;
-
- /* initialize variable (-S) pam matrix */
- if ((f_str->waa_s= (int *)calloc((nsq+1)*(n0+1),sizeof(int))) == NULL) {
- fprintf(stderr,"cannot allocate waa_s array %3d\n",nsq*n0);
- exit(1);
- }
-
- if ((f_str->pam2p[1]= (int **)calloc((n0+1),sizeof(int *))) == NULL) {
- fprintf(stderr,"cannot allocate pam2p[1] array %3d\n",n0);
- exit(1);
- }
-
- pam2p = f_str->pam2p[1];
- if ((pam2p[0]=(int *)calloc((nsq+1)*(n0+1),sizeof(int))) == NULL) {
- fprintf(stderr,"cannot allocate pam2p[1][] array %3d\n",nsq*n0);
- exit(1);
- }
-
- for (i=1; i<n0; i++) {
- pam2p[i]= pam2p[0] + (i*(nsq+1));
- }
-
- /* initialize universal (alignment) matrix */
- if ((f_str->waa_a= (int *)calloc((nsq+1)*(n0+1),sizeof(int))) == NULL) {
- fprintf(stderr,"cannot allocate waa_a struct %3d\n",nsq*n0);
- exit(1);
- }
-
- if ((f_str->pam2p[0]= (int **)calloc((n0+1),sizeof(int *))) == NULL) {
- fprintf(stderr,"cannot allocate pam2p[1] array %3d\n",n0);
- exit(1);
- }
-
- pam2p = f_str->pam2p[0];
- if ((pam2p[0]=(int *)calloc((nsq+1)*(n0+1),sizeof(int))) == NULL) {
- fprintf(stderr,"cannot allocate pam2p[1][] array %3d\n",nsq*n0);
- exit(1);
- }
-
- for (i=1; i<n0; i++) {
- pam2p[i]= pam2p[0] + (i*(nsq+1));
- }
-
- /*
- pwaa effectively has a sequence profile --
- pwaa[0..n0-1] has pam score for residue 0 (-BIGNUM)
- pwaa[n0..2n0-1] has pam scores for residue 1 (A)
- pwaa[2n0..3n-1] has pam scores for residue 2 (R), ...
-
- thus: pwaa = f_str->waa_s + (*aa1p++)*n0; sets up pwaa so that
- *pwaa++ rapidly moves though the scores of the aa1p[] position
- without further indexing
-
- For a real sequence profile, pwaa[0..n0-1] vs ['A'] could have
- a different score in each position.
- */
-
- if (ppst->pam_pssm) {
- pwaa_s = f_str->waa_s;
- pwaa_a = f_str->waa_a;
- for (e = 0; e <=nsq; e++) { /* for each residue in the alphabet */
- for (f = 0; f < n0; f++) { /* for each position in aa0 */
- *pwaa_s++ = f_str->pam2p[ip][f][e] = ppst->pam2p[ip][f][e];
- *pwaa_a++ = f_str->pam2p[0][f][e] = ppst->pam2p[0][f][e];
- }
- }
- }
- else { /* initialize scanning matrix */
- pwaa_s = f_str->waa_s;
- pwaa_a = f_str->waa_a;
- for (e = 0; e <=nsq; e++) /* for each residue in the alphabet */
- for (f = 0; f < n0; f++) { /* for each position in aa0 */
- *pwaa_s++ = f_str->pam2p[ip][f][e]= ppst->pam2[ip][e][aa0[f]];
- *pwaa_a++ = f_str->pam2p[0][f][e] = ppst->pam2[0][e][aa0[f]];
- }
- }
-
- maxn0 = max(3*n0/2,MIN_RES);
- if ((res = (int *)calloc((size_t)maxn0,sizeof(int)))==NULL) {
- fprintf(stderr,"cannot allocate alignment results array %d\n",maxn0);
- exit(1);
- }
- f_str->res = res;
-
- *f_arg = f_str;
-}
-
-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--;
- free(f_str->ss);
- free(f_str->res);
- free(f_str->waa_a);
- free(f_str->pam2p[0][0]);
- free(f_str->pam2p[0]);
- free(f_str->waa_s);
- free(f_str->pam2p[1][0]);
- free(f_str->pam2p[1]);
-
- free(f_str);
- *f_arg = NULL;
- }
-}
-
-
-/* pstring1 is a message to the manager, currently 512 */
-/*void get_param(struct pstruct *pstr,char *pstring1)*/
-void get_param (struct pstruct *pstr, char *pstring1, char *pstring2)
-{
- char psi_str[120];
-
- char *pg_str="Smith-Waterman";
-
- if (pstr->pam_pssm) { strncpy(psi_str,"-PSI",sizeof(psi_str));}
- else { psi_str[0]='\0';}
-
-#ifdef OLD_FASTA_GAP
- sprintf (pstring1, " %s (%s) function [%s matrix%s (%d:%d)%s], gap-penalty: %d/%d",
-#else
- sprintf (pstring1, " %s (%s) function [%s matrix%s (%d:%d)%s], open/ext: %d/%d",
-#endif
- pg_str, verstr, pstr->pamfile, psi_str, pstr->pam_h,pstr->pam_l,
- (pstr->ext_sq_set)?"xS":"\0", pstr->gdelval, pstr->ggapval);
-
- if (pstring2 != NULL) {
-#ifdef OLD_FASTA_GAP
- sprintf(pstring2,"; pg_name: %s\n; pg_ver: %s\n; pg_matrix: %s (%d:%d)%s\n; pg_gap-pen: %d %d\n",
-#else
- sprintf(pstring2,"; pg_name: %s\n; pg_ver: %s\n; pg_matrix: %s (%d:%d)%s\n; pg_open-ext: %d %d\n",
-#endif
- pg_str,verstr,psi_str,pstr->pam_h,pstr->pam_l,
- (pstr->ext_sq_set)?"xS":"\0",pstr->gdelval,pstr->ggapval);
- }
-}
-
-
-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)
-{
- const unsigned char *aa0p, *aa1p;
- register struct swstr *ssj;
- struct swstr *ss, *f_ss, *r_ss;
- register int *pwaa;
- int *waa;
- register int i, j;
- int e, f, h, p;
- int q, r, m;
- int score;
-
- double lambda, H, K;
-
- rst->escore = 1.0;
- rst->segnum = rst->seglen = 1;
-
- waa = f_str->waa_s;
- ss = f_str->ss;
- f_ss = f_str->f_ss;
- r_ss = f_str->r_ss;
-
-#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 = 0;
- aa1p = aa1;
- 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;
- }
- } /* done with forward pass */
-
- rst->score[0] = score;
-
- if(ppst->zsflag == 6 || ppst->zsflag == 16 &&
- (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;}
-} /* here we should be all done */
-
-void do_opt (const unsigned char *aa0, int n0,
- const unsigned char *aa1, int n1,
- int frame,
- struct pstruct *pst, struct f_struct *f_str,
- struct rstruct *rstr)
-{
-}
-
-int do_walign (const unsigned char *aa0, const int n0,
- const unsigned char *aa1, const int n1,
- int frame,
- struct pstruct *ppst,
- struct f_struct *f_str,
- struct a_res_str *a_res,
- int *have_ares )
-{
- const unsigned char *aa0p, *aa1p;
- register int *pwaa;
- register int i, j;
- register struct swstr *ssj;
- struct swstr *f_ss, *r_ss, *ss;
- int *res, *waa;
- int e, f, h, p;
- int q, r, m;
- int score;
- int cost, I, J, K, L;
-
- ss = f_str->ss;
-
- res = f_str->res;
- waa = f_str->waa_a; /* this time use universal pam2[0] */
-
-#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 = 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) > /* gap open from left best */
- /* gap extend from left gapped */
- (f = f - r)) f = h; /* if better, use new gap opened */
- if ((h = ssj->H - m) > /* gap open from up best */
- /* gap extend from up gap */
- (e = ssj->E - r)) e = h; /* if better, use new gap opened */
- h = p + *pwaa++; /* diagonal match */
- if (h < 0 ) h = 0; /* ? < 0, reset to 0 */
- if (h < f ) h = f; /* left gap better, reset */
- if (h < e ) h = e; /* up gap better, reset */
- p = ssj->H; /* save previous best score */
- ssj->H = h; /* save (new) up diag-matched */
- ssj->E = e; /* save upper gap opened */
- if (h > score) { /* ? new best score */
- score = h; /* save best */
- I = i; /* row */
- J = (int)(ssj-ss); /* column */
- }
- }
- i++;
- } /* done with forward pass */
- if (score <= 0) return 0;
-
- /* to get the start point, go backwards */
-
- /* 18-June-2003 fix bug in backtracking code to identify start of
- alignment. Code used pam2[0][aa0[j]][aa1[i]] instead of
- pam2p[0][j][aa1[i]]. Ideally, it would use waa_a.
- */
-
- 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;
- for (ssj=ss+J, j= J; ssj>=ss; ssj--,j--) {
- f = max (f,h-q)-r;
- ssj->E=max(ssj->E,ssj->H-q)-r;
- h = max(max(ssj->E,f),p+f_str->pam2p[0][j][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->res = f_str->res;
- *have_ares = 1;
- a_res->max0 = J+1; a_res->min0 = L; a_res->max1 = I+1; a_res->min1 = K;
-
-/* ALIGN(&aa1[K-1],&aa0[L-1],I-K+1,J-L+1,ppst->pam2[0],q,r,res,nres,f_str); */
-
-/* this code no longer refers to aa0[], it used pam2p[0][L] instead */
- ALIGN(&aa0[L-1],&aa1[K-1],J-L+1,I-K+1,f_str->pam2p[0],L,q,r,
- a_res->res,&a_res->nres,f_str);
-
-/* DISPLAY(&aa0[L-1],&aa1[K-1],J-L+1,I-K+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 IW, int G, int H, int *nres);
-
-#define gap(k) ((k) <= 0 ? 0 : g+h*(k)) /* k-symbol indel cost */
-
-/* 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 */
-
-/*
-#define XTERNAL
-#include "upam.h"
-
-void
-print_seq_prof(unsigned char *A, int M,
- unsigned char *B, int N,
- int **w, int iw, int dir) {
- char c_max;
- int i_max, j_max, i,j;
-
- char *c_dir="LRlr";
-
- for (i=1; i<=min(60,M); i++) {
- fprintf(stderr,"%c",aa[A[i]]);
- }
- fprintf(stderr, - %d\n,M);
-
- for (i=0; i<min(60,M); i++) {
- i_max = -1;
- for (j=1; j<21; j++) {
- if (w[iw+i][j]> i_max) {
- i_max = w[iw+i][j];
- j_max = j;
- }
- }
- fprintf(stderr,"%c",aa[j_max]);
- }
- fputc(':',stderr);
- for (i=1; i<=min(60,N); i++) {
- fprintf(stderr,"%c",aa[B[i]]);
- }
- fprintf(stderr," -%c: %d,%d\n",c_dir[dir],M,N);
-}
-*/
-
-/* 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
-align(const unsigned char *A, const unsigned char *B, int M, int N,
- int tb, int te, int **w, int iw, int g, int h,
- struct f_struct *f_str, int dir,
- int **sapp, int *last)
-{
- int midi, midj, type; /* Midpoint, type, and cost */
- int midc;
- int c1, c2;
-
-{ register int i, j;
- register int c, e, d, s;
- int m, t, *wa;
- struct swstr *f_ss, *r_ss;
-
-/* print_seq_prof(A,M,B,N,w,iw,dir); */
-
- 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]]; */
- wa = w[iw];
- 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]]; */
- wa = w[iw+i-1];
- 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]]; */
- wa = w[iw+i];
- 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)
- { c1 = align(A,B,midi,midj,tb,-g,w,iw,g,h,f_str,0, sapp, last);
- c2 = align(A+midi,B+midj,M-midi,N-midj,-g,te,w,iw+midi,g,h,f_str,1,sapp,last);
- }
- else
- { align(A,B,midi-1,midj,tb,0,w,iw,g,h,f_str,2,sapp, last);
- DEL(2);
- align(A+midi+1,B+midj,M-midi-1,N-midj,0,te,w,iw+midi+1,g,h,f_str,3,sapp,last);
- }
- return midc;
-}
-
-/* Interface and top level of comparator */
-
-int ALIGN(const unsigned char *A, const unsigned char *B, int M, int N,
- int **W, int IW, int G, int H, int *S, int *NC,
- struct f_struct *f_str)
-{
- struct swstr *f_ss, *r_ss;
- int *sapp, last;
- int c, ck;
-
- 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;
-
- /* print_seq_prof(A,M,W,IW); */
- c = align(A,B,M,N,-G,-G,W,IW,G,H,f_str,0,&sapp, &last); /* OK, do it */
-
- ck = CHECK_SCORE(A,B,M,N,S,W,IW,G,H,NC);
- if (c != ck) printf("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 iw,
- int g, int h, int *NC)
-{
- register int i, j, op, nc;
- int score;
-
- /* print_seq_prof(A,M,w,iw); */
-
- score = i = j = op = nc = 0;
- while (i < M || j < N) {
- op = *S++;
- if (op == 0) {
- score = w[iw+i][B[++j]] + score;
- i++;
- nc++;
- }
- else if (op > 0) {
- score = score - (g+op*h);
- j += op;
- nc += op;
- } else {
- score = score - (g-op*h);
- i -= op;
- nc -= op;
- }
- }
- *NC = nc;
- return score;
-}
-
-void
-pre_cons(const unsigned char *aa1, int n1, int frame, struct f_struct *f_str) {}
-
-/* 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) {
-
- aln->llfact = aln->llmult = aln->qlfact = 1;
- aln->qlrev = aln->llrev = 0;
- aln->frame = 0;
-}
-
-/* 29-June-2003 this version has been modified to use pst.pam2p
- instead of pam2 to indicate similarity */
-
-#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;
- int op, lenc, nd, ns, itmp;
- char *sp0, *sp1, *spa, *sq;
- int *rp;
- int mins, smins;
-
- if (pst.ext_sq_set) { sq = pst.sqx;}
- else {sq = pst.sq;}
-
- aln->amin0 = a_res.min0;
- aln->amax0 = a_res.max0;
- aln->amin1 = a_res.min1;
- aln->amax1 = a_res.max1;
-
- /* #define LFASTA */
-#ifndef LFASTA
- if (min(a_res.min0,a_res.min1)<aln->llen || aln->showall==1) /* will we show all the start ?*/
- 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 *)aa1,a_res.min1,pst);
- aln->smin1 = 0;
- }
- else {
- aancpy(seqc1,(char *)aa1+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 *)(aa1+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;
- aln->smin1=a_res.min1;
- aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
- aancpy(seqc1,(char *)aa1+a_res.min1-mins,mins,pst);
- }
-#else
- aln->smin0 = a_res.min0;
- aln->smin1 = a_res.min1;
- smins = mins = 0;
-#endif
-
-/* now get the middle */
-
- memset(seqca,M_BLANK,mins);
-
- 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=f_str->pam2p[0][i0][aa1[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[aa1[i1++]];
-
- if (toupper(*sp0) == toupper(*sp1)) {aln->nident++; *spa = M_IDENT;}
- else if (pst.dnaseq==1 && ((*sp0 == 'T' && *sp1 == 'U') ||
- (*sp0=='U' && *sp1=='T'))) {
- aln->nident++; *spa=M_IDENT;
- }
-
- sp0++; sp1++; spa++;
- }
- else {
- if (op==0) op = *rp++;
- if (op>0) {
- *sp0++ = '-';
- *sp1++ = sq[aa1[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 */
-
-#ifndef LFASTA
- /* how much extra to show at 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,n1-a_res.max1))
- nd = max(n0-a_res.max0,n1-a_res.max1);
-
- if (aln->showall==1) {
- nd = max(n0-a_res.max0,n1-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 *)aa1+a_res.max1,n1-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+n1-a_res.max1,' ',nd-(n1-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-(n1-a_res.max1))>0) {
- aancpy(seqc1+mins+lenc,(char *)aa1+a_res.max1,n1-a_res.max1,pst);
- memset(seqc1+mins+lenc+n1-a_res.max1,' ',nd-(n1-a_res.max1));
- }
- else aancpy(seqc1+mins+lenc,(char *)aa1+a_res.max1,nd,pst);
- }
-
-#else /* LFASTA */
- nd = 0;
-#endif
- /* #undef LFASTA */
- 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;
- int op, lenc, nd, ns, itmp;
- char *sp0, *sp0a, *sp1, *spa, *sq;
- int *rp;
- int mins, smins;
-
- if (pst.ext_sq_set) {sq = pst.sqx;}
- else {sq = pst.sq;}
-
- aln->amin0 = a_res.min0;
- aln->amax0 = a_res.max0;
- aln->amin1 = a_res.min1;
- aln->amax1 = a_res.max1;
-
- /* first fill in the ends */
-
- /* #define LFASTA */
-#ifndef LFASTA
- if (min(a_res.min0,a_res.min1)<aln->llen || aln->showall==1) /* will we show all the start ?*/
- 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 *)aa1,a_res.min1,pst);
- aln->smin1 = 0;
- }
- else {
- aancpy(seqc1,(char *)aa1+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 *)(aa1+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;
- aln->smin1=a_res.min1;
- aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
- aancpy(seqc1,(char *)aa1+a_res.min1-mins,mins,pst);
- }
-#else
- aln->smin0 = a_res.min0;
- aln->smin1 = a_res.min1;
- smins = mins = 0;
-#endif
-
-/* now get the middle */
-
- memset(seqca,M_BLANK,mins);
- memset(seqc0a,' ',mins);
-
- 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=f_str->pam2p[0][i0][aa1[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[aa1[i1++]];
-
- if (toupper(*sp0) == toupper(*sp1)) {aln->nident++; *spa = M_IDENT;}
- else if (pst.dnaseq==1 && ((*sp0 == 'T' && *sp1 == 'U') ||
- (*sp0=='U' && *sp1=='T'))) {
- aln->nident++; *spa=M_IDENT;
- }
-
- sp0++; sp1++; spa++;
- }
- else {
- if (op==0) op = *rp++;
- if (op>0) {
- *sp0++ = '-';
- *sp0a++ = ' ';
- *sp1++ = sq[aa1[i1++]];
- *spa++ = M_DEL;
- 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;
- *spa = '\0';
-/* now we have the middle, get the right end */
-
-#ifndef LFASTA
- /* how much extra to show at 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,n1-a_res.max1))
- nd = max(n0-a_res.max0,n1-a_res.max1);
-
- if (aln->showall==1) {
- nd = max(n0-a_res.max0,n1-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 *)aa1+a_res.max1,n1-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+n1-a_res.max1,' ',nd-(n1-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-(n1-a_res.max1))>0) {
- aancpy(seqc1+mins+lenc,(char *)aa1+a_res.max1,n1-a_res.max1,pst);
- memset(seqc1+mins+lenc+n1-a_res.max1,' ',nd-(n1-a_res.max1));
- }
- else aancpy(seqc1+mins+lenc,(char *)aa1+a_res.max1,nd,pst);
- }
-
-#else /* LFASTA */
- nd = 0;
-#endif
- /* #undef LFASTA */
- return mins+lenc+nd;
-}
-
-static void
-update_code(char *al_str, int al_str_max, int op, int op_cnt);
-
-/* build an array of match/ins/del - length strings */
-int calc_code(const unsigned char *aa0, const int n0,
- const unsigned char *aa1, const 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, nd, ns, itmp;
- int p_op, op_cnt;
- const unsigned char *aa1p;
- char tmp_cnt[20];
- char sp0, sp1, *sq;
- int *rp;
- int mins, smins;
-
- 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;
- tmp_cnt[0]='\0';
-
- 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.dnaseq==1) {
- 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;
-}
-
-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);
-}
-
-int calc_id(const unsigned char *aa0, const int n0,
- const unsigned char *aa1, const int n1,
- struct a_struct *aln,
- struct a_res_str a_res,
- struct pstruct pst,
- struct f_struct *f_str)
-{
- int i0, i1, nn1, n_id;
- int op, lenc, nd, ns, itmp;
- 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
-
- rp = a_res.res;
- lenc = n_id = 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)) n_id++;
- else if (pst.dnaseq==1 &&
- ((sp0=='T' && sp1== 'U')||(sp0=='U' && sp1=='T'))) n_id++;
- }
- else {
- if (op==0) op = *rp++;
- if (op>0) {op--; lenc++; i1++; aln->ngap_q++; }
- else {op++; lenc++; i0++; aln->ngap_l++; }
- }
- }
- aln->nident = n_id;
- return lenc;
-}
-
-#ifdef PCOMPLIB
-#include "p_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