+++ /dev/null
-/* copyright (c) 1996 William R. Pearson */
-
-/* $Name: fa_34_26_5 $ - $Id: dropgsw.c,v 1.80 2006/10/19 15:12:11 wrp Exp $ */
-
-/* 17-Aug-2006 - removed globals *sapp/last - alignment should be thread safe */
-
-/* 12-Oct-2005 - converted to use a_res and aln for alignment coordinates */
-
-/* 4-Nov-2004 - Diagonal Altivec Smith-Waterman included */
-
-/* 14-May-2003 - modified to return alignment start at 0, rather than
- 1, for begin:end alignments
-
- 25-Feb-2003 - modified to support Altivec parallel Smith-Waterman
-
- 22-Sep-2003 - removed Altivec support at request of Sencel lawyers
-*/
-
-/* the do_walign() code in this file is not thread_safe */
-/* init_work(), do_work(), are thread safe */
-
-/* this code uses an implementation of the Smith-Waterman algorithm
- designed by Phil Green, U. of Washington, that is 1.5 - 2X faster
- than my Miller and Myers implementation. */
-
-/* the shortcuts used in this program prevent it from calculating scores
- that are less than the gap penalty for the first residue in a gap. As
- a result this code cannot be used with very large gap penalties, or
- with very short sequences, and probably should not be used with prss3.
-*/
-
-/* version 3.2 fixes a subtle bug that was encountered while running
- do_walign() interspersed with do_work(). This happens only with -m
- 9 and pvcomplib. The fix was to more explicitly zero-out ss[] at
- the beginning of do_work.
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include <math.h>
-
-#include "defs.h"
-#include "param.h"
-
-static char *verstr="5.5 Sept 2006";
-
-#include "dropgsw.h"
-
-#define DROP_INTERN
-#include "drop_func.h"
-
-#ifdef SW_ALTIVEC
-#include "smith_waterman_altivec.h"
-#endif
-#ifdef SW_SSE2
-#include "smith_waterman_sse2.h"
-#endif
-
-struct swstr {int H, E;};
-
-extern void init_karlin(const unsigned char *aa0, int n0, struct pstruct *ppst,
- double *aa0_f, double **kp);
-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);
-
-static int
-ALIGN(const unsigned char *A, const unsigned char *B,
- int M, int N,
- int **W, int IW, int G, int H, int *res, int *nres,
- struct f_struct *f_str);
-
-static int
-FLOCAL_ALIGN(const unsigned char *aa0, const unsigned char *aa1,
- int n0, int n1, int low, int up,
- int **W, int GG,int HH, int MW,
- struct f_struct *f_str);
-
-static
-void DISPLAY(const unsigned char *A, const unsigned char *B,
- int M, int N,
- int *S, int AP, int BP, char *sq);
-
-extern void aancpy(char *to, char *from, int count, struct pstruct pst);
-
-/* initialize for Smith-Waterman optimal score */
-
-void
-init_work (unsigned char *aa0, int n0,
- struct pstruct *ppst,
- struct f_struct **f_arg)
-{
- int maxn0, ip;
- int *pwaa_s, *pwaa_a;
- int e, f, i, j, l;
- int *res;
- struct f_struct *f_str;
- int **pam2p;
- struct swstr *ss;
- int nsq;
-
-#if defined(SW_ALTIVEC) || defined(SW_SSE2)
- int data,bias;
- unsigned char * pc;
- unsigned short * ps;
- int overflow;
-
- int n_count;
- int col_len;
-#endif
-
- if (ppst->ext_sq_set) {
- nsq = ppst->nsqx; ip = 1;
- }
- else {
- nsq = ppst->nsq; ip = 0;
- }
-
- /* allocate space for function globals */
-
- f_str = (struct f_struct *)calloc(1,sizeof(struct f_struct));
-
- if(ppst->zsflag == 6 || ppst->zsflag == 16) {
- f_str->kar_p = NULL;
- init_karlin(aa0, n0, ppst, &f_str->aa0_f[0], &f_str->kar_p);
- }
-
- /* allocate space for the scoring arrays */
- if ((ss = (struct swstr *) calloc (n0+2, sizeof (struct swstr)))
- == NULL) {
- fprintf (stderr, "cannot allocate ss array %3d\n", n0);
- exit (1);
- }
- ss++;
-
- ss[n0].H = -1; /* this is used as a sentinel - normally H >= 0 */
- ss[n0].E = 1;
- f_str->ss = 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);
- }
-
- /* initialize pam2p[1] pointers */
- 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);
- }
-
- /* initialize pam2p[0] pointers */
- 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][aa0[f]][e];
- *pwaa_a++ = f_str->pam2p[0][f][e] = ppst->pam2[0][aa0[f]][e];
- }
- }
-
-#if defined(SW_ALTIVEC)
-
- /* First we allocate memory for the workspace - i.e. the single row
- * of storage for H/F. Since this might be run on Linux or AIX too,
- * we don't assume anything about the memory allocation but align
- * it ourselves. We need two vectors (16 bytes each) per element,
- * and some padding space to make it cache-line aligned.
-
- * MAXTST+MAXLIB is longest allowed database sequence length...
- * this should be m_msg.max_tot, but m_msg is not available, but
- * ppst->maxlen has maxn, which is appropriate.
- */
-
- f_str->workspace_memory = (void *)malloc(2*16*(ppst->maxlen+SEQ_PAD)+256);
- f_str->workspace = (void *) ((((size_t) f_str->workspace_memory) + 255) & (~0xff));
-
-
-
- /* We always use a scoring profile in altivec, but the layout is a bit strange
- * in order to optimize memory access order and thus cache efficiency.
- * Normally we first try 8-bit scoring in altivec, and if this leads to overflow
- * we recompute the score with 16-bit accuracy. Because of this we need to construct
- * two score profiles.
- * Since altivec always loads 16 bytes from aligned memory, corresponding to 8 or 16
- * elements (for 16 and 8 bit scoring, respectively), we organize the scoring
- * profile like this for 8-bit accuracy:
- *
- * 1. The profile starts on 256-byte aligned memory (cache line on G5 is 128 bytes).
- * 2. First we have the score for the full alphabet for the first 16 residues of
- * the query, i.e. positions 0-15 are the scores for the first 16 query letters
- * vs. the first in the alphabet, positions 16-31 the scores for the same 16
- * query positions against alphabet letter two, etc.
- * 3. After alphabet_size*16bytes we start with the scores for residues 16-31 in
- * the query, organized in the same way.
- * 4. At the end of the query sequence, we pad the scoring to the next 16-tuple
- * with neutral scores.
- * 5. The total size of the profile is thus alphabet_size*N, where N is the
- * size of the query rounded up to the next 16-tuple.
- *
- * The word (16-bit) profile is identical, but scores are stored as 8-tuples.
- */
-
- f_str->word_score_memory = (void *)malloc(10*2*(nsq+2)*(n0+1+16)+256);
- f_str->byte_score_memory = (void *)malloc(10*(nsq+2)*(n0+1+16)+256);
-
- f_str->word_score = (unsigned short *) ((((size_t) f_str->word_score_memory) + 255) & (~0xff));
- f_str->byte_score = (unsigned char *) ((((size_t) f_str->byte_score_memory) + 255) & (~0xff));
-
- overflow = 0;
-
- if (ppst->pam_pssm) {
- /* Use a position-specific scoring profile.
- * This is essentially what we are going to construct anyway, but we'll
- * reorder it to suit altivec.
- */
- bias = 127;
- for(i = 1; i <= nsq ; i++) {
- for(j = 0; j < n0 ; j++) {
- data = ppst->pam2p[ip][j][i];
- if(data<bias) bias = data;
- }
- }
-
- /* Fill our specially organized byte- and word-size scoring arrays. */
- ps = f_str->word_score;
- for(f = 0; f<n0 ; f+=8) {
- /* e=0 */
- for(i=0 ; i<8 ; i++) {
- *ps++ = (unsigned short) 0;
- }
- /* for each chunk of 8 residues in our query */
- for(e = 1; e<=nsq; e++) {
- for(i=0 ; i<8 ; i++) {
- l = f + i;
- if(l<n0) {
- data = ppst->pam2p[ip][l][e] - bias;
- }
- else {
- data = 0;
- }
- *ps++ = (unsigned short)data;
- }
- }
- }
- pc = f_str->byte_score;
- for(f = 0; f<n0 ; f+=16) {
- /* e=0 */
- for(i=0 ; i<16 ; i++) {
- *pc++ = (unsigned char)0;
- }
-
- for(e = 1; e<=nsq; e++) {
- for(i=0 ; i<16 ; i++) {
- l = f + i;
- if(l<n0) {
- data = ppst->pam2p[ip][l][e] - bias;
- }
- else {
- data = 0;
- }
- if(data>255) {
- /*
- printf("Fatal error. data: %d bias: %d, position: %d/%d, Score out of range for 8-bit Altivec/VMX datatype.\n",data,bias,l,e);
- exit(1);
- */
- overflow = 1;
- }
- *pc++ = (unsigned char)data;
- }
- }
- }
- }
- else {
- /* Classical simple substitution matrix */
- /* Find the bias to use in the substitution matrix */
- bias = 127;
- for(i = 1; i <= nsq ; i++) {
- for(j = 1; j <= nsq ; j++) {
- data = ppst->pam2[ip][i][j];
- if(data<bias) bias = data;
- }
- }
- /* Fill our specially organized byte- and word-size scoring arrays. */
- ps = f_str->word_score;
- for(f = 0; f<n0 ; f+=8) {
- /* e=0 */
- for(i=0 ; i<8 ; i++) {
- *ps++ = (unsigned short) 0;
- }
- /* for each chunk of 8 residues in our query */
- for(e = 1; e<=nsq; e++) {
- for(i=0 ; i<8 ; i++) {
- l = f + i;
- if(l<n0) {
- data = ppst->pam2[ip][aa0[l]][e] - bias;
- }
- else {
- data = 0;
- }
- *ps++ = (unsigned short)data;
- }
- }
- }
- pc = f_str->byte_score;
- for(f = 0; f<n0 ; f+=16) {
- /* e=0 */
- for(i=0 ; i<16 ; i++) {
- *pc++ = (unsigned char)0;
- }
-
- for(e = 1; e<=nsq; e++) {
- for(i=0 ; i<16 ; i++) {
- l = f + i;
- if (l<n0) {
- data = ppst->pam2[ip][aa0[l]][e] - bias;
- }
- else {
- data = 0;
- }
- if(data>255) {
- /*
- printf("Fatal error. Score out of range for 8-bit Altivec/VMX datatype.\n");
- exit(1);
- */
- overflow = 1;
- }
- *pc++ = (unsigned char)data;
- }
- }
- }
- }
-
- f_str->bias = (unsigned char) (-bias);
- f_str->alphabet_size = nsq+1;
-
- /* Some variable to keep track of how many 8-bit runs we need to rerun
- * in 16-bit accuracy. If there are too many reruns it can be faster
- * to use 16-bit alignments directly.
- */
-
- /* We can only do 8-bit alignments if the scores were small enough. */
- if(overflow==0) f_str->try_8bit = 1;
- else f_str->try_8bit = 0;
-
- f_str->done_8bit = 0;
- f_str->done_16bit = 0;
-
-#endif /* SW_ALTIVEC */
-
-#if defined(SW_SSE2)
- /* First we allocate memory for the workspace - i.e. two rows for H and
- * one row for F. We also need enough space to hold a temporary
- * scoring profile which will be query_length * 16 (sse2 word length).
- * Since this might be run on Linux or AIX too, we don't assume
- * anything about the memory allocation but align it ourselves.
- */
- f_str->workspace_memory = (void *)malloc(3*16*(MAXTST+MAXLIB+32)+256);
- f_str->workspace = (void *) ((((size_t) f_str->workspace_memory) + 255) & (~0xff));
-
- /* We always use a scoring profile for the SSE2 implementation, but the layout
- * is a bit strange. The scoring profile is parallel to the query, but is
- * accessed in a stripped pattern. The query is divided into equal length
- * segments. The number of segments is equal to the number of elements
- * processed in the SSE2 register. For 8-bit calculations, the query will
- * be divided into 16 equal length parts. If the query is not long enough
- * to fill the last segment, it will be filled with neutral weights. The
- * first element in the SSE register will hold a value from the first segment,
- * the second element of the SSE register will hold a value from the
- * second segment and so on. So if the query length is 288, then each
- * segment will have a length of 18. So the first 16 bytes will have
- * the following weights: Q1, Q19, Q37, ... Q271; the next 16 bytes will
- * have the following weights: Q2, Q20, Q38, ... Q272; and so on until
- * all parts of all segments have been written. The last seqment will
- * have the following weights: Q18, Q36, Q54, ... Q288. This will be
- * done for the entire alphabet.
- */
-
- f_str->word_score_memory = (void *)malloc((n0 + 32) * sizeof (short) * (nsq + 1) + 256);
- f_str->byte_score_memory = (void *)malloc((n0 + 32) * sizeof (char) * (nsq + 1) + 256);
-
- f_str->word_score = (unsigned short *) ((((size_t) f_str->word_score_memory) + 255) & (~0xff));
- f_str->byte_score = (unsigned char *) ((((size_t) f_str->byte_score_memory) + 255) & (~0xff));
-
- overflow = 0;
-
- if (ppst->pam_pssm) {
- /* Use a position-specific scoring profile.
- * This is essentially what we are going to construct anyway, but we'll
- * reorder it to suit sse2.
- */
- bias = 127;
- for (i = 1; i <= nsq ; i++) {
- for (j = 0; j < n0 ; j++) {
- data = ppst->pam2p[ip][j][i];
- if (data < bias) {
- bias = data;
- }
- }
- }
-
- /* Fill our specially organized byte- and word-size scoring arrays. */
- ps = f_str->word_score;
- col_len = (n0 + 7) / 8;
- n_count = (n0 + 7) & 0xfffffff8;
- for (f = 0; f < n_count; ++f) {
- *ps++ = 0;
- }
- for (f = 1; f <= nsq ; f++) {
- for (e = 0; e < col_len; e++) {
- for (i = e; i < n_count; i += col_len) {
- if ( i < n0) { data = ppst->pam2p[ip][i][f];}
- else {data = 0;}
- *ps++ = (unsigned short)data;
- }
- }
- }
- pc = f_str->byte_score;
- col_len = (n0 + 15) / 16;
- n_count = (n0 + 15) & 0xfffffff0;
- for (f = 0; f < n_count; ++f) {
- *pc++ = 0;
- }
- for (f = 1; f <= nsq ; f++) {
- for (e = 0; e < col_len; e++) {
- for (i = e; i < n_count; i += col_len) {
- if ( i < n0 ) { data = ppst->pam2p[ip][i][f] - bias;}
- else {data = 0 - bias;}
- if (data > 255) {
- printf("Fatal error. data: %d bias: %d, position: %d/%d, "
- "Score out of range for 8-bit SSE2 datatype.\n",
- data, bias, f, e);
- exit(1);
- }
- *pc++ = (unsigned char)data;
- }
- }
- }
- }
- else
- {
- /* Classical simple substitution matrix */
- /* Find the bias to use in the substitution matrix */
- bias = 127;
- for (i = 1; i <= nsq ; i++) {
- for (j = 1; j <= nsq ; j++) {
- data = ppst->pam2[ip][i][j];
- if (data < bias) {
- bias = data;
- }
- }
- }
-
- /* Fill our specially organized byte- and word-size scoring arrays. */
- ps = f_str->word_score;
- col_len = (n0 + 7) / 8;
- n_count = (n0 + 7) & 0xfffffff8;
- for (f = 0; f < n_count; ++f) {
- *ps++ = 0;
- }
- for (f = 1; f <= nsq ; f++) {
- for (e = 0; e < col_len; e++) {
- for (i = e; i < n_count; i += col_len) {
- if (i >= n0) {
- data = 0;
- } else {
- data = ppst->pam2[ip][aa0[i]][f];
- }
- *ps++ = (unsigned short)data;
- }
- }
- }
-
- pc = f_str->byte_score;
- col_len = (n0 + 15) / 16;
- n_count = (n0 + 15) & 0xfffffff0;
- for (f = 0; f < n_count; ++f) {
- *pc++ = 0;
- }
- for (f = 1; f <= nsq ; f++) {
- for (e = 0; e < col_len; e++) {
- for (i = e; i < n_count; i += col_len) {
- if (i >= n0) {
- data = -bias;
- } else {
- data = ppst->pam2[ip][aa0[i]][f] - bias;
- }
- if (data > 255) {
- printf("Fatal error. data: %d bias: %d, position: %d/%d, "
- "Score out of range for 8-bit SSE2 datatype.\n",
- data, bias, f, e);
- exit(1);
- }
- *pc++ = (unsigned char)data;
- }
- }
- }
- }
-
- f_str->bias = (unsigned char) (-bias);
- f_str->alphabet_size = nsq+1;
-
- /* Some variable to keep track of how many 8-bit runs we need to rerun
- * in 16-bit accuracy. If there are too many reruns it can be faster
- * to use 16-bit alignments directly.
- */
-
- /* We can only do 8-bit alignments if the scores were small enough. */
- f_str->try_8bit = (overflow == 0) ? 1 : 0;
-
- f_str->done_8bit = 0;
- f_str->done_16bit = 0;
-#endif /* SW_SSE2 */
-
- /* these structures are used for producing alignments */
-
- maxn0 = max(3*n0/2,MIN_RES); /* minimum allocation for alignment */
- 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]);
-
-#if defined(SW_ALTIVEC) || defined(SW_SSE2)
- free(f_str->workspace_memory);
- free(f_str->word_score_memory);
- free(f_str->byte_score_memory);
-#endif
- 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 pg_str[120];
- char psi_str[120];
-
-#if defined(SW_ALTIVEC)
- strncpy(pg_str,"Smith-Waterman (Altivec/VMX, Erik Lindahl 2004)",sizeof(pg_str));
-#endif
-#if defined(SW_SSE2)
- strncpy(pg_str,"Smith-Waterman (SSE2, Michael Farrar 2006)",sizeof(pg_str));
-#endif
-#if !defined(SW_ALTIVEC) && !defined(SW_SSE2)
- strncpy(pg_str,"Smith-Waterman (PGopt)",sizeof(pg_str));
-#endif
-
- 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 (pstr->zsflag==0) strcat(pstring1," not-scaled\n");
- 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)%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)
-{
- int score;
- double lambda, H;
- int i;
-
-#ifdef SW_ALTIVEC
- if(f_str->try_8bit)
- {
- score = smith_waterman_altivec_byte(aa0,
- f_str->byte_score,
- n0,
- aa1,
- n1,
- f_str->bias,
-#ifndef OLD_FASTA_GAP
- -(ppst->gdelval + ppst->ggapval),
-#else
- -ppst->gdelval,
-#endif
- -ppst->ggapval,
- f_str);
-
- f_str->done_8bit++;
-
- if(score>=255)
- {
- /* Overflow, so we have to redo it in 16 bits. */
- score = smith_waterman_altivec_word(aa0,
- f_str->word_score,
- n0,
- aa1,
- n1,
- f_str->bias,
-#ifndef OLD_FASTA_GAP
- -(ppst->gdelval + ppst->ggapval),
-#else
- -ppst->gdelval,
-#endif
- -ppst->ggapval,
- f_str);
-
- /* The 8 bit version is roughly 50% faster than the 16 bit version,
- * so we are fine if less than about 1/3 of the runs have to
- * be rerun with 16 bits. If it is more, and we have tried at least
- * 500 sequences, we switch off the 8-bit mode.
- */
- f_str->done_16bit++;
- if(f_str->done_8bit>500 && (3*f_str->done_16bit)>(f_str->done_8bit))
- f_str->try_8bit = 0;
- }
- }
- else
- {
- /* Just use the 16-bit altivec version directly */
- score = smith_waterman_altivec_word(aa0,
- f_str->word_score,
- n0,
- aa1,
- n1,
- f_str->bias,
-#ifndef OLD_FASTA_GAP
- -(ppst->gdelval + ppst->ggapval),
-#else
- -ppst->gdelval,
-#endif
- -ppst->ggapval,
- f_str);
- }
-
-#endif /* not Altivec */
-
-#if defined(SW_SSE2)
-
- if(f_str->try_8bit)
- {
- score = smith_waterman_sse2_byte(aa0,
- f_str->byte_score,
- n0,
- aa1,
- n1,
- f_str->bias,
-#ifndef OLD_FASTA_GAP
- -(ppst->gdelval + ppst->ggapval),
-#else
- -ppst->gdelval,
-#endif
- -ppst->ggapval,
- f_str);
-
- f_str->done_8bit++;
-
- if(score>=255)
- {
- /* Overflow, so we have to redo it in 16 bits. */
- score = smith_waterman_sse2_word(aa0,
- f_str->word_score,
- n0,
- aa1,
- n1,
-#ifndef OLD_FASTA_GAP
- -(ppst->gdelval + ppst->ggapval),
-#else
- -ppst->gdelval,
-#endif
- -ppst->ggapval,
- f_str);
-
- /* The 8 bit version is roughly 50% faster than the 16 bit version,
- * so we are fine if less than about 1/3 of the runs have to
- * be rerun with 16 bits. If it is more, and we have tried at least
- * 500 sequences, we switch off the 8-bit mode.
- */
- f_str->done_16bit++;
- if(f_str->done_8bit>500 && (3*f_str->done_16bit)>(f_str->done_8bit))
- f_str->try_8bit = 0;
- }
- }
- else
- {
- /* Just use the 16-bit altivec version directly */
- score = smith_waterman_sse2_word(aa0,
- f_str->word_score,
- n0,
- aa1,
- n1,
-#ifndef OLD_FASTA_GAP
- -(ppst->gdelval + ppst->ggapval),
-#else
- -ppst->gdelval,
-#endif
- -ppst->ggapval,
- f_str);
- }
-#endif
-
-#if !defined(SW_ALTIVEC) && !defined(SW_SSE2)
-
- score = FLOCAL_ALIGN(aa0,aa1,n0,n1,0,0,
- NULL,
-#ifndef OLD_FASTA_GAP
- -(ppst->gdelval + ppst->ggapval),
-#else
- -ppst->gdelval,
-#endif
- ppst->ggapval,0,f_str);
-#endif
-
- 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;}
-
-}
-
-static int
-FLOCAL_ALIGN(const unsigned char *aa0, const unsigned char *aa1,
- int n0, int n1, int low, int up,
- int **W, int GG,int HH, int MW,
- struct f_struct *f_str) {
-
- register int *pwaa;
- register struct swstr *ssj;
- struct swstr *ss;
- register int h, e, f, p;
- int temp, score;
- int gap_ext, n_gap_init;
-
- const unsigned char *aa1p;
- ss = f_str->ss;
- ss[n0].H = -1;
- ss[n0].E = 1;
-
- n_gap_init = GG;
- gap_ext = HH;
-
- score = 0;
- for (h=0; h<n0; h++) { /* initialize 0th row */
- ss[h].H = ss[h].E = 0;
- }
-
- aa1p=aa1;
- while (*aa1p) { /* relies on aa1[n1]==0 for EOS flag */
- /* waa_s has the offsets for each residue in aa0 into pam2 */
- /* waa_s has complexity (-S) dependent scores */
- pwaa = f_str->waa_s + (*aa1p++)*n0;
- ssj = ss;
-
- e = f = h = p = 0;
- zero_f: /* in this section left-gap f==0, and is never examined */
-
- while (1) { /* build until h > n_gap_init (f < 0 until h > n_gap_init) */
- /* bump through the pam[][]'s for each of the aa1[] matches to
- aa0[], because of the way *pwaa is set up */
-
- h = p + *pwaa++; /* increment diag value */
- p = ssj->H; /* get next diag value */
- if ((e = ssj->E) > 0 ) { /* >0 from up-gap */
- if (p == -1) goto next_row; /* done, -1=ss[n0].H sentinel */
- if (h < e) h = e; /* up-gap better than diag */
- else
- if (h > n_gap_init) { /* we won't starting a new up-gap */
- e += gap_ext; /* but we might be extending one */
- goto transition; /* good h > n_gap_diag; scan f */
- }
- e += gap_ext; /* up-gap decreased */
- ssj->E = (e > 0) ? e : 0; /* set to 0 if < 0 */
- ssj++->H = h; /* diag match updated */
- }
- else { /* up-gap (->E) is 0 */
- if ( h > 0) { /* diag > 0 */
- if (h > n_gap_init) { /* we won't be starting a new up-gap */
- e = 0; /* and we won't be extending one */
- goto transition; /* good h > n_gap_diag; scan f */
- }
- ssj++->H = h; /* update diag */
- }
- else ssj++->H = 0; /* update diag to 0 */
- }
- }
-
- /* here h > n_gap_init and h > e, => the next f will be > 0 */
- transition:
-#ifdef DEBUG
- if ( h > 10000)
- fprintf(stderr,"h: %d ssj: %d\n",h, (int)(ssj-ss));
-#endif
- if ( score < h ) score = h; /* save best score, only when h > n_gap_init */
-
- temp = h - n_gap_init; /* best score for starting a new gap */
- if ( f < temp ) f = temp; /* start a left-gap? */
- if ( e < temp ) e = temp; /* start an up-gap? */
- ssj->E = ( e > 0 ) ? e : 0; /* update up-gap */
- ssj++->H = h; /* update diag */
- e = 0;
-
- do { /* stay here until f <= 0 */
- h = p + *pwaa++; /* diag + match/mismatch */
- p = ssj->H; /* save next (right) diag */
-
- if ( h < f ) h = f; /* update diag using left gap */
- f += gap_ext; /* update next left-gap */
-
- if ((e = ssj->E) > 0) { /* good up gap */
- if (p == -1) goto next_row; /* at the end of the row */
- if ( h < e ) h = e; /* update diag using up-gap */
- else
- if ( h > n_gap_init ) {
- e += gap_ext; /* update up gap */
- goto transition; /* good diag > n_gap_init, restart */
- }
- e += gap_ext; /* update up-gap */
- ssj->E = (e > 0) ? e : 0; /* e must be >= 0 */
- ssj++->H = h; /* update diag */
- }
- else { /* up-gap <= 0 */
- if ( h > n_gap_init ) {
- e = 0;
- goto transition; /* good diag > n_gap_init; restart */
- }
- ssj++->H = h; /* update diag */
- }
- } while ( f > 0 ); /* while left gap f > 0 */
- goto zero_f; /* otherwise, go to f==0 section */
- next_row:
- ;
- } /* end while(*aap1) {} */
-
- return score;
-
-} /* 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 *ppst, struct f_struct *f_str,
- struct rstruct *rst)
-{
-}
-
-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)
-{
- const unsigned char *aa0p, *aa1p;
- register int *pwaa;
- register int i, j;
- register struct swstr *ssj;
- struct swstr *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 uses 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 *res and nres */
-
- 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 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,last) 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)}
- *last = (*sapp)[0] = 0;
- (*sapp)++;
- 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 */
-
-static 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) {
- fprintf(stdout,"*** Check_score error. %d != %d ***\n",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 void
-DISPLAY(const unsigned char *A, const 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;
-
- char ALINE[51], BLINE[51], CLINE[51];
-
- 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) {
-
-#ifdef TFAST
- 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) {
-
- 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 mins, smins;
- int *rp;
-
- 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 */
-
- 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 { /* we are not showing the start */
- /* mins has the amount of unaligned context to be shown */
- 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 *)aa1+a_res.min1-mins,mins,pst);
- }
-
-/* 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.nt_align && ((*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 */
-
- 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 - smins;
- aln->smin1=a_res.min1 - smins;
- aancpy(seqc0,(char *)aa0+a_res.min0-mins,mins,pst);
- aancpy(seqc1,(char *)aa1+a_res.min1-mins,mins,pst);
- }
-
-/* 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.nt_align && ((*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;
- *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 */
-
- /* 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);
- }
-
- 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, 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 tmp_cnt[20];
- char sp0, sp1, *sq;
- int *rp;
-
- if (pst.ext_sq_set) {
- sq = pst.sqx;
- }
- else {
- sq = pst.sq;
- }
-
-#ifndef TFAST
- 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.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;
-}
-
-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, 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, n_id;
- 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 TFAST
- 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 = 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.nt_align &&
- ((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
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