--- /dev/null
+
+/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
+ U. of Virginia */
+
+/* $Name: fa_34_26_5 $ - $Id: workacc.c,v 1.19 2006/02/07 17:58:19 wrp Exp $ */
+
+/* Concurrent read version */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "param.h"
+
+#define XTERNAL
+#include "uascii.h"
+#include "upam.h"
+#undef XTERNAL
+
+char err_str[128];
+
+/* Initialization - set up defaults - assume protein sequence */
+void w_init ()
+{
+ pascii=aascii;
+}
+
+#ifndef MPI_SRC
+/* allocate memory for pam matrix - identical to version in initfa/sw.c */
+alloc_pam (int d1, int d2, struct pstruct *ppst)
+{
+ int i, *d2p;
+ char err_str[128];
+
+ if ((ppst->pam2[0] = (int **) malloc (d1 * sizeof (int *))) == NULL) {
+ sprintf(err_str,"Cannot allocate 2D pam matrix: %d",d1);
+ return -1;
+ }
+
+ if ((ppst->pam2[1] = (int **) malloc (d1 * sizeof (int *))) == NULL) {
+ sprintf(err_str,"Cannot allocate 2D pam matrix: %d",d1);
+ return -1;
+ }
+
+ if ((d2p = pam12 = (int *) malloc (d1 * d2 * sizeof (int))) == NULL) {
+ sprintf(err_str,"Cannot allocate 2D pam matrix: %d",d1);
+ return -1;
+ }
+ for (i = 0; i < d1; i++, d2p += d2) ppst->pam2[0][i] = d2p;
+
+ if ((d2p=pam12x= (int *) malloc (d1 * d2 * sizeof (int))) == NULL) {
+ sprintf(err_str,"Cannot allocate 2d pam matrix: %d",d2);
+ return -1;
+ }
+ for (i = 0; i < d1; i++, d2p += d2) ppst->pam2[1][i] = d2p;
+
+ return 1;
+}
+
+int **
+alloc_pam2p(int len, int nsq) {
+ int i;
+ int **pam2p;
+
+ if ((pam2p = (int **)calloc(len,sizeof(int *)))==NULL) {
+ fprintf(stderr," Cannot allocate pam2p: %d\n",len);
+ return NULL;
+ }
+
+ if((pam2p[0] = (int *)calloc((nsq+1)*len,sizeof(int)))==NULL) {
+ fprintf(stderr, "Cannot allocate pam2p[0]: %d\n", (nsq+1)*len);
+ free(pam2p);
+ return NULL;
+ }
+
+ for (i=1; i<len; i++) {
+ pam2p[i] = pam2p[0] + (i*(nsq+1));
+ }
+
+ return pam2p;
+}
+
+void free_pam2p(int **pam2p) {
+ if (pam2p) {
+ free(pam2p[0]);
+ free(pam2p);
+ }
+}
+
+void
+aancpy(char *to, char *from, int count, struct pstruct pst)
+{
+ char *tp, *sq;
+ int nsq;
+
+ tp=to;
+
+ if (pst.ext_sq_set) {
+ nsq = pst.nsqx;
+ sq = pst.sqx;
+ }
+ else {
+ nsq = pst.nsq;
+ sq = pst.sq;
+ }
+
+ while (count-- && *from) {
+ if (*from <= nsq) *tp++ = sq[*(from++)];
+ else *tp++ = *from++;
+ }
+ *tp='\0';
+}
+#endif
+
+/* copies from from to to shuffling */
+
+void
+shuffle(unsigned char *from, unsigned char *to, int n)
+{
+ int i,j; unsigned char tmp;
+
+ if (from != to) memcpy((void *)to,(void *)from,(size_t)n);
+
+ for (i=n; i>0; i--) {
+ j = nrand(i);
+ tmp = to[j];
+ to[j] = to[i-1];
+ to[i-1] = tmp;
+ }
+ to[n] = 0;
+}
+
+/* this shuffle is for FASTS */
+/* convert ',' -> '\0', shuffle each of the substrings */
+qshuffle(unsigned char *aa0, int n0, int nm0)
+{
+ unsigned char **aa0start, *aap, tmp;
+ int i,j,k, ns;
+
+ if ((aa0start=(unsigned char **)calloc(nm0+1,
+ sizeof(unsigned char *)))==NULL) {
+ fprintf(stderr,"cannot calloc for qshuffle %d\n",nm0);
+ exit(1);
+ }
+ aa0start[0]=aa0;
+ for (k=1,i=0; i<n0; i++) {
+ if (aa0[i]==EOSEQ || aa0[i]==ESS) {
+ aa0[i]='\0';
+ aa0start[k++] = &aa0[i+1];
+ }
+ }
+
+ /* aa0start has the beginning of each substring */
+ for (k=0; k<nm0; k++) {
+ aap=aa0start[k];
+ ns = strlen((char *)aap);
+ for (i=ns; i>1; i--) {
+ j = nrand(i);
+ tmp = aap[j];
+ aap[j] = aap[i-1];
+ aap[i-1] = tmp;
+ }
+ aap[ns] = 0;
+ }
+
+ for (k=1; k<nm0; k++) {
+/* aap = aa0start[k];
+ while (*aap) fputc(pst.sq[*aap++],stderr);
+ fputc('\n',stderr);
+*/
+ aa0start[k][-1]=ESS;
+ }
+
+ free(aa0start);
+}
+
+/* copies from from to from shuffling */
+void
+wshuffle(unsigned char *from, unsigned char *to, int n, int wsiz, int *ieven)
+{
+ int i,j, k, mm;
+ unsigned char tmp, *top;
+
+ memcpy((void *)to,(void *)from,n);
+
+ mm = n%wsiz;
+
+ if (*ieven) {
+ for (k=0; k<(n-wsiz); k += wsiz) {
+ top = &to[k];
+ for (i=wsiz; i>0; i--) {
+ j = nrand(i);
+ tmp = top[j];
+ top[j] = top[i-1];
+ top[i-1] = tmp;
+ }
+ }
+ top = &to[n-mm];
+ for (i=mm; i>0; i--) {
+ j = nrand(i);
+ tmp = top[j];
+ top[j] = top[i-1];
+ top[i-1] = tmp;
+ }
+ *ieven = 0;
+ }
+ else {
+ for (k=n; k>=wsiz; k -= wsiz) {
+ top = &to[k-wsiz];
+ for (i=wsiz; i>0; i--) {
+ j = nrand(i);
+ tmp = top[j];
+ top[j] = top[i-1];
+ top[i-1] = tmp;
+ }
+ }
+ top = &to[0];
+ for (i=mm; i>0; i--) {
+ j = nrand(i);
+ tmp = top[j];
+ top[j] = top[i-1];
+ top[i-1] = tmp;
+ }
+ *ieven = 1;
+ }
+ to[n] = 0;
+}
+
+void initseq(char **seqc0, char **seqc0a, char **seqc1, char **seqca, int seqsiz) /* initialize arrays */
+{
+ *seqc0=(char *)calloc((size_t)(seqsiz+1)*4,sizeof(char));
+ *seqc0a= *seqc0+seqsiz+1;
+ *seqc1= *seqc0a+seqsiz+1;
+ *seqca= *seqc1+seqsiz+1;
+ if (*seqc0==NULL)
+ {fprintf(stderr,"cannot allocate consensus arrays %d\n",seqsiz);
+ exit(1);}
+}
+
+void freeseq(char **seqc0, char **seqc1, char **seqca)
+{
+ free(*seqc0);
+}
+
+#define ESS 49
+
+void
+revcomp(unsigned char *seq, int n, int *c_nt)
+{
+ unsigned char tmp;
+ int i, ni;
+
+ for (i=0, ni = n-1; i< n/2; i++,ni--) {
+ tmp = c_nt[seq[i]];
+ seq[i] = c_nt[seq[ni]];
+ seq[ni] = tmp;
+ }
+ if ((n%2)==1) {
+ i = n/2;
+ seq[i] = c_nt[seq[i]];
+ }
+ seq[n]=0;
+}
git://source.jalview.org / jabaws.git / blobdiff