--- /dev/null
+/* pssm_asn_subs.c */
+
+
+/* $Name: fa_34_26_5 $ - $Id: pssm_asn_subs.c,v 1.15 2007/04/02 18:08:11 wrp Exp $ */
+
+/* copyright (C) 2005 by William R. Pearson and the U. of Virginia */
+
+/* this code is designed to parse the ASN.1 binary encoded scoremat
+ object produced by blastpgp -C file.ckpt_asn -u 2 */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "defs.h"
+
+int parse_pssm_asn();
+int parse_pssm2_asn();
+
+int
+parse_pssm_asn_fa(FILE *afd, int *n_rows, int *n_cols,
+ unsigned char **query, double ***freqs,
+ char *matrix, int *gap_open, int *gap_extend,
+ double *lambda);
+
+
+
+#define COMPO_NUM_TRUE_AA 20
+
+/**positions of true characters in protein alphabet*/
+/*
+static int trueCharPositions[COMPO_NUM_TRUE_AA] = {
+ 1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22
+};
+*/
+
+#define COMPO_LARGEST_ALPHABET 28
+
+/*
+static char ncbieaatoa[COMPO_LARGEST_ALPHABET] = {"-ABCDEFGHIJKLMNOPQRSTUVWXYZ"};
+
+static int alphaConvert[COMPO_LARGEST_ALPHABET] = {
+ (-1), 0, (-1), 4, 3, 6, 13, 7, 8, 9, 11, 10, 12, 2, 14, 5, 1, 15,
+ 16, 19, 17, (-1), 18, (-1), (-1), (-1), (-1), (-1)
+};
+*/
+
+int pssm_aa_order[20] = { 1, /*A*/
+ 16, /*R*/
+ 13, /*N*/
+ 4, /*D*/
+ 3, /*C*/
+ 15, /*Q*/
+ 5, /*E*/
+ 7, /*G*/
+ 8, /*H*/
+ 9, /*I*/
+ 11, /*L*/
+ 10, /*K*/
+ 12, /*M*/
+ 6, /*F*/
+ 14, /*P*/
+ 17, /*S*/
+ 18, /*T*/
+ 20, /*W*/
+ 22, /*Y*/
+ 19}; /*V*/
+
+
+#define ASN_SEQ 48
+#define ASN_SEQOF 49
+
+#define ASN_PSSM_QUERY 166
+#define ASN_PSSM2_QUERY 162
+
+#define ASN_PSSM_IS_PROT 160
+#define ASN_PSSM2_MATRIX 161
+#define ASN_PSSM_NROWS 162
+#define ASN_PSSM_NCOLS 163
+
+#define ASN_PSSM2_NCOLS 163
+#define ASN_PSSM2_NROWS 164
+#define ASN_PSSM_BYCOL 165
+#define ASN_PSSM_INTERMED_DATA 167
+#define ASN_PSSM_FREQS 162
+#define ASN_PSSM2_FREQS 165
+#define ASN_PSSM2_LAMBDA 166
+
+#define ASN_IS_STR 26
+#define ASN_IS_INT 2
+#define ASN_IS_BOOL 1
+#define ASN_IS_ENUM 10
+
+struct asn_bstruct {
+ FILE *fd;
+ unsigned char *buf;
+ unsigned char *abp;
+ unsigned char *buf_max;
+ int len;
+};
+
+#define ASN_BUF 1024
+
+unsigned char *
+chk_asn_buf(struct asn_bstruct *asnp, int v) {
+ int new_buf;
+
+ if (v > ASN_BUF) {
+ fprintf(stderr," attempt to read %d bytes ASN.1 data > buffer size (%d)\n",
+ v, ASN_BUF);
+ exit(1);
+ }
+
+ if (asnp->abp + v > asnp->buf_max) {
+
+ /* move down the left over stuff */
+ asnp->len = asnp->buf_max - asnp->abp;
+
+ memmove(asnp->buf, asnp->abp, asnp->len);
+
+ asnp->abp = asnp->buf;
+ new_buf = ASN_BUF - asnp->len;
+
+ if (!feof(asnp->fd) &&
+ (new_buf=fread(asnp->buf + asnp->len, sizeof(char), new_buf, asnp->fd)) != 0) {
+ asnp->len += new_buf;
+ }
+
+ asnp->buf_max = asnp->buf + asnp->len;
+
+ if (asnp->len < v) {
+ fprintf(stderr, " Unable to read %d bytes\n",v);
+ exit(1);
+ }
+ }
+ /* otherwise, v bytes are currently in the buffer */
+
+ return asnp->abp;
+}
+
+/* read_asn_dest reads v bytes into oct_str if v <= o_len */
+/* read_asn_dest is required for ASN data entities that are longer than ASN_BUF (1024) */
+unsigned char *
+read_asn_dest(struct asn_bstruct *asnp, int v, unsigned char *oct_str, int o_len) {
+ int new_buf;
+ unsigned char *oct_ptr;
+
+
+ if (v > o_len) {
+ fprintf(stderr, " read_asn_dest - cannot read %d bytes into %d buffer\n",
+ v, o_len);
+ exit(1);
+ }
+
+ if (asnp->abp + v <= asnp->buf_max) {
+ memmove(oct_str, asnp->abp, v);
+ return asnp->abp+v;
+ }
+ else {
+ /* move down the left over stuff */
+
+ asnp->len = asnp->buf_max - asnp->abp;
+
+ memmove(oct_str, asnp->abp, asnp->len);
+ oct_ptr = oct_str+asnp->len;
+ v -= asnp->len;
+
+ asnp->abp = asnp->buf;
+ new_buf = ASN_BUF;
+
+ while ((new_buf=fread(asnp->buf, sizeof(char), new_buf, asnp->fd)) != 0) {
+ asnp->len = new_buf;
+ asnp->buf_max = asnp->buf + asnp->len;
+ if (v <= new_buf) { /* we have it all this time */
+ memmove(oct_ptr, asnp->buf, v);
+ asnp->len -= v;
+ asnp->abp = asnp->buf + v;
+ break;
+ }
+ else { /* we need to read some more */
+ memmove(oct_ptr, asnp->buf, new_buf);
+ v -= new_buf;
+ new_buf = ASN_BUF;
+ }
+ }
+ }
+ return asnp->buf + v;
+}
+
+unsigned char *
+get_astr_bool(struct asn_bstruct *asnp, int *val) {
+
+ int v_len, v;
+
+ asnp->abp = chk_asn_buf(asnp,5);
+
+ v = 0;
+ if (*asnp->abp++ != 1) { /* check for int */
+ fprintf(stderr," bool missing\n");
+ }
+ else {
+ v_len = *asnp->abp++;
+ if (v_len != 1) {
+ fprintf(stderr, "boolean length != 1 : %d\n", v_len);
+ v = *asnp->abp++;
+ }
+ else { v = *asnp->abp++;}
+ }
+ asnp->abp += 2; /* skip over null's */
+ *val = v;
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_int(struct asn_bstruct *asnp,
+ int *val) {
+
+ int v_len, v;
+
+ v = 0;
+
+ asnp->abp = chk_asn_buf(asnp,8);
+
+ if (*asnp->abp++ != 2) { /* check for int */
+ fprintf(stderr," int missing\n");
+ }
+ else {
+ v_len = *asnp->abp++;
+ while (v_len-- > 0) {
+ v *= 256;
+ v += *asnp->abp++;
+ }
+ asnp->abp += 2; /* skip over null's */
+ }
+ *val = v;
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_enum(struct asn_bstruct *asnp, int *val) {
+
+ int v_len, v;
+
+ asnp->abp = chk_asn_buf(asnp,5);
+
+ v = 0;
+ if (*asnp->abp++ != ASN_IS_ENUM) { /* check for int */
+ fprintf(stderr," enum missing\n");
+ }
+ else {
+ v_len = *asnp->abp++;
+ while (v_len-- > 0) { v *= 256; v += *asnp->abp++; }
+ asnp->abp += 2; /* skip over null's */
+ }
+ *val = v;
+
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_packedfloat(struct asn_bstruct *asnp, double *val) {
+
+ int v_len, v;
+ char tmp_str[64];
+
+ asnp->abp = chk_asn_buf(asnp,2);
+
+ v = 0;
+ if (*asnp->abp++ != 9) { /* check for packed float */
+ fprintf(stderr," float missing\n");
+ *val = 0;
+ return asnp->abp;
+ }
+ else {
+ v_len = *asnp->abp++;
+
+ if (v_len > 63) {
+ fprintf(stderr," real string too long: %d\n",v_len);
+ }
+
+ asnp->abp = chk_asn_buf(asnp,v_len);
+
+ if (v_len == 2 && *asnp->abp == '\0' && *(asnp->abp+1)=='0') {
+ asnp->abp += 2;
+ *val = 0.0;
+ }
+ else { /* copy and scan it */
+ if (*asnp->abp != '\0') {
+ fprintf(stderr, " packedfloat - expected 0, got %d\n", *asnp->abp);
+ *val = -1.0;
+ return asnp->abp;
+ }
+ asnp->abp++;
+ strncpy(tmp_str, (char *)asnp->abp, sizeof(tmp_str)-1);
+ tmp_str[v_len-1] = '\0';
+ tmp_str[63] = '\0';
+ sscanf(tmp_str,"%lg",val);
+ asnp->abp += v_len-1;
+ }
+ }
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_str(struct asn_bstruct *asnp, char *text, int t_len) {
+
+ int v_len;
+
+ asnp->abp = chk_asn_buf(asnp,2);
+
+ text[0] = '\0';
+ if (*asnp->abp++ != ASN_IS_STR) { /* check for str */
+ fprintf(stderr," str missing\n");
+ }
+ else {
+ v_len = *asnp->abp++;
+ if (v_len > 128) { /* need to read the length from the next bytes */
+ t_len = v_len &0x7f;
+
+ asnp->abp = chk_asn_buf(asnp,t_len);
+
+ for (v_len =0; t_len; t_len--) { v_len = (v_len << 8) + *asnp->abp++; }
+ }
+
+ /* read v_len bytes */
+
+ asnp->abp = read_asn_dest(asnp,v_len, (unsigned char *)text, t_len);
+ asnp->abp += 2; /* skip over last nulls */
+ }
+ return asnp->abp;
+}
+
+#define ASN_BIOSEQ_SEQ 160
+#define ASN_BIOSEQ_ID 160
+#define ASN_BIOSEQ_ID_VAL 160
+
+#define ASN_BIOSEQ_ID_LOCAL 161
+#define ASN_BIOSEQ_ID_GIBBSQ 162
+#define ASN_BIOSEQ_ID_GIBBMT 163
+#define ASN_BIOSEQ_ID_GB 164
+#define ASN_BIOSEQ_ID_EMBL 165
+#define ASN_BIOSEQ_ID_PIR 166
+#define ASN_BIOSEQ_ID_SP 167
+#define ASN_BIOSEQ_ID_PATENT 168
+#define ASN_BIOSEQ_ID_OTHER 169
+#define ASN_BIOSEQ_ID_GEN 170
+#define ASN_BIOSEQ_ID_GI 171
+
+#define ASN_BIOSEQ_TEXTID_NAME 160
+#define ASN_BIOSEQ_TEXTID_ACC 161
+#define ASN_BIOSEQ_TEXTID_REL 162
+#define ASN_BIOSEQ_TEXTID_VER 163
+
+#define ASN_BIOSEQ_DESCR 161
+#define ASN_BIOSEQ_INST 162
+#define ASN_BIOSEQ_TITLE 164
+#define ASN_BIOSEQ_INST_REPR 160
+#define ASN_BIOSEQ_INST_MOL 161
+#define ASN_BIOSEQ_INST_LEN 162
+#define ASN_BIOSEQ_INST_TOPOL 166
+#define ASN_BIOSEQ_INST_SEQD 167
+#define ASN_OCTET_STR 65
+#define ASN_NCBIeaa 65
+
+unsigned char *
+get_astr_seqdescr(struct asn_bstruct *asnp,
+ char *descr) {
+
+ int end_seq=0;
+
+ /* get seqof '1' */
+ /* get 164/128 - title */
+ /* get string */
+ /* pop nulls */
+
+ asnp->abp = chk_asn_buf(asnp,6);
+
+ if (*asnp->abp == ASN_SEQOF) {
+ end_seq++;
+ asnp->abp += 2;
+ }
+ else {
+ fprintf(stderr, " missing ASN_SEQOF '1': %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_TITLE) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_str(asnp, descr, MAX_STR);
+ }
+ else {
+ fprintf(stderr, " missing ASN_BIOSEQ_TITLE '1': %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ }
+
+ asnp->abp = chk_asn_buf(asnp,2);
+
+ asnp->abp += 2; /* skip over nulls */
+
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_octstr(struct asn_bstruct *asnp,
+ unsigned char *oct_str,
+ int o_len) {
+
+ int q_len, v_len;
+
+ asnp->abp = chk_asn_buf(asnp,2);
+
+ if (*asnp->abp++ == ASN_NCBIeaa) {
+ /* get length of length */
+ if (*asnp->abp > 128) {
+ v_len = *asnp->abp++ & 0x7f;
+
+ asnp->abp = chk_asn_buf(asnp,v_len);
+
+ q_len = 0;
+ while (v_len-- > 0) {
+ q_len *= 256;
+ q_len += *asnp->abp++;
+ }
+ }
+ else {
+ q_len = *asnp->abp++ & 0x7f;
+ }
+
+ asnp->abp = read_asn_dest(asnp, q_len, oct_str, o_len);
+
+ oct_str[min(q_len,o_len)]='\0';
+
+ asnp->abp += 2; /* skip characters and NULL's */
+ }
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_seqinst(struct asn_bstruct *asnp,
+ unsigned char **query,
+ int *nq) {
+
+ int end_seq=0, tmp;
+
+ /* get sequence '0' */
+ /* get 160/128/10/len/val - repr enum raw val */
+ /* get 161/128/10/len/val - mol enum aa val */
+ /* get 162/128/02/len/val - length int val */
+ /* get 166/128 - topology (empty) */
+ /* get 167/128 - seq-data */
+ /* get 65/len+128/len/octet_string */
+ /* pop nulls */
+
+ asnp->abp = chk_asn_buf(asnp,12);
+
+ if (*asnp->abp == ASN_SEQ) {
+ end_seq++;
+ asnp->abp += 2;
+ }
+ else {
+ fprintf(stderr, " missing ASN_SEQ '0': %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_INST_REPR && *(asnp->abp+1) == 128) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_enum(asnp, &tmp);
+ }
+ else {
+ fprintf(stderr, " missing ASN_BIOSEQ_INST_REPR 160: %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_INST_MOL && *(asnp->abp+1) == 128) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_enum(asnp, &tmp);
+ }
+ else {
+ fprintf(stderr, " missing ASN_BIOSEQ_INST_MOL 161: %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_INST_LEN) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, nq);
+ }
+ else {
+ fprintf(stderr, " missing ASN_BIOSEQ_INST_LEN 161: %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+
+ if ((*query = (unsigned char *)calloc(*nq + 1, sizeof(char)))==NULL) {
+ fprintf(stderr, " cannot read %d char query\n", *nq+1);
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_INST_TOPOL && *(asnp->abp+1) == 128 ) {
+ asnp->abp += 2;
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_INST_SEQD) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_octstr(asnp, *query, *nq );
+ }
+ else {
+ fprintf(stderr, " missing ASN_BIOSEQ_INST_SEQD 166: %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+
+ asnp->abp += 4; /* skip over nulls */
+
+ return asnp->abp;
+}
+
+
+unsigned char *
+get_astr_textid( struct asn_bstruct *asnp,
+ char *name,
+ char *acc) {
+ int end_seq = 0;
+ int ver;
+
+ chk_asn_buf(asnp,16);
+
+ if (*asnp->abp != ASN_SEQ) {
+ fprintf(stderr, " Expected ASN_SEQ: %0x %0x\n",*asnp->abp, asnp->abp[1]);
+ }
+ else {asnp->abp += 2; end_seq++;}
+
+ name[0] = acc[0] = '\0';
+
+ while (*asnp->abp != '\0') {
+ if (*asnp->abp == ASN_BIOSEQ_TEXTID_NAME) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_str(asnp, name, MAX_SSTR);
+ }
+ if (*asnp->abp == ASN_BIOSEQ_TEXTID_ACC) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_str(asnp, acc, MAX_SSTR);
+ }
+ if (*asnp->abp == ASN_BIOSEQ_TEXTID_VER) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, &ver);
+ }
+ }
+ asnp->abp += 4;
+ while (end_seq-- > 0) { asnp->abp += 4; }
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_query(struct asn_bstruct *asnp,
+ int *gi,
+ char *name,
+ char *acc,
+ char *descr,
+ unsigned char **query,
+ int *nq
+ ) {
+
+ int end_seq = 0;
+
+ asnp->abp = chk_asn_buf(asnp,32);
+
+ if (*asnp->abp != ASN_BIOSEQ_SEQ) {
+ fprintf(stderr, "Bioseq - missing SEQ 1: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else { asnp->abp += 2;}
+
+ if (*asnp->abp != ASN_SEQ && *asnp->abp != ASN_SEQOF ) {
+ fprintf(stderr, "Bioseq - missing SEQUENCE tag 1: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else {
+ end_seq++;
+ asnp->abp += 2;
+ }
+
+ if (*asnp->abp != ASN_BIOSEQ_ID) {
+ fprintf(stderr, "Bioseq - missing ID tag: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else {
+ asnp->abp += 2;
+ if (*asnp->abp != ASN_SEQOF) {
+ fprintf(stderr, "missing bioseq/id/SEQOF tag: %d\n",*asnp->abp);
+ return asnp->abp;
+ }
+ else {
+ asnp->abp += 2;
+ if (*asnp->abp == ASN_BIOSEQ_ID_VAL && *(asnp->abp+1)==128) { asnp->abp += 2;}
+
+ if (*asnp->abp == ASN_BIOSEQ_ID_GI ) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, gi);
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_ID_LOCAL) {
+ *gi = 0;
+ acc[0] = '\0';
+
+ asnp->abp+=2;
+ asnp->abp = get_astr_str(asnp, name, MAX_SSTR);
+ asnp->abp += 2;
+ }
+ else if (*asnp->abp == ASN_BIOSEQ_ID_SP || *asnp->abp == ASN_BIOSEQ_ID_EMBL ||
+ *asnp->abp == ASN_BIOSEQ_ID_GB || *asnp->abp == ASN_BIOSEQ_ID_PIR ||
+ *asnp->abp == ASN_BIOSEQ_ID_OTHER ) {
+
+ asnp->abp+=2;
+ asnp->abp = get_astr_textid(asnp, name, acc);
+ }
+ }
+ }
+
+ while (*asnp->abp == 0) asnp->abp += 2;
+
+ if (*asnp->abp == ASN_BIOSEQ_DESCR) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_seqdescr(asnp, descr);
+ asnp->abp += 2; /* skip nulls */
+ }
+ else { descr[0] = '\0';}
+
+ if (*asnp->abp != ASN_BIOSEQ_INST) {
+ fprintf(stderr, "Bioseq - missing ID tag: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else {
+ asnp->abp += 2;
+ asnp->abp = get_astr_seqinst(asnp, query, nq);
+ asnp->abp += 2; /* skip nulls */
+ }
+ return asnp->abp;
+}
+
+unsigned char *
+get_astr_query2(struct asn_bstruct *asnp,
+ int *gi,
+ char *name,
+ char *acc,
+ char *descr,
+ unsigned char **query,
+ int *nq
+ ) {
+
+ int end_seq = 0;
+
+ asnp->abp = chk_asn_buf(asnp,32);
+
+ if (*asnp->abp != ASN_BIOSEQ_SEQ) {
+ fprintf(stderr, "Bioseq - missing SEQ 1: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else { asnp->abp += 2;}
+
+ if (*asnp->abp != ASN_SEQOF ) {
+ fprintf(stderr, "Bioseq2 - missing SEQOF tag 1: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else {
+ end_seq++;
+ asnp->abp += 2;
+ }
+
+ if (*asnp->abp != ASN_BIOSEQ_ID) {
+ fprintf(stderr, "Bioseq - missing ID tag: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else {
+ asnp->abp += 2;
+ if (*asnp->abp == ASN_SEQOF) {
+ asnp->abp += 2;
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_ID_VAL && *(asnp->abp+1)==128) { asnp->abp += 2;}
+
+ if (*asnp->abp == ASN_BIOSEQ_ID_GI ) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, gi);
+ }
+
+ if (*asnp->abp == ASN_BIOSEQ_ID_LOCAL) {
+ *gi = 0;
+ acc[0] = '\0';
+
+ asnp->abp+=2;
+ asnp->abp = get_astr_str(asnp, name, MAX_SSTR);
+ asnp->abp += 2;
+ }
+ else if (*asnp->abp == ASN_BIOSEQ_ID_SP || *asnp->abp == ASN_BIOSEQ_ID_EMBL ||
+ *asnp->abp == ASN_BIOSEQ_ID_GB || *asnp->abp == ASN_BIOSEQ_ID_PIR ||
+ *asnp->abp == ASN_BIOSEQ_ID_OTHER ) {
+
+ asnp->abp+=2;
+ asnp->abp = get_astr_textid(asnp, name, acc);
+ }
+ }
+
+ while (*asnp->abp == 0) asnp->abp += 2;
+
+ if (*asnp->abp == ASN_BIOSEQ_DESCR) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_seqdescr(asnp, descr);
+ asnp->abp += 2; /* skip nulls */
+ }
+ else { descr[0] = '\0';}
+
+ if (*asnp->abp != ASN_BIOSEQ_INST) {
+ fprintf(stderr, "Bioseq - missing ID tag: %2x %2x\n",*asnp->abp, asnp->abp[1]);
+ return asnp->abp;
+ }
+ else {
+ asnp->abp += 2;
+ asnp->abp = get_astr_seqinst(asnp, query, nq);
+ asnp->abp += 2; /* skip nulls */
+ }
+ return asnp->abp;
+}
+
+unsigned char *
+get_pssm_freqs(struct asn_bstruct *asnp,
+ double **freqs,
+ int n_rows,
+ int n_cols,
+ int by_row) {
+
+ int i_rows, i_cols;
+ int in_seq = 0;
+
+ double f_val;
+
+ asnp->abp = chk_asn_buf(asnp,4);
+
+ if (*asnp->abp == ASN_SEQ) {
+ in_seq = 1;
+ asnp->abp += 2;
+ in_seq = 1;
+ }
+
+ if (!by_row) {
+ for (i_cols = 0; i_cols < n_cols; i_cols++) {
+ for (i_rows = 0; i_rows < n_rows; i_rows++) {
+ asnp->abp = get_astr_packedfloat(asnp, &f_val);
+ freqs[i_cols][i_rows] = f_val;
+ }
+ }
+ }
+ else {
+ for (i_rows = 0; i_rows < n_rows; i_rows++) {
+ for (i_cols = 0; i_cols < n_cols; i_cols++) {
+ asnp->abp = get_astr_packedfloat(asnp, &f_val);
+ freqs[i_cols][i_rows] = f_val;
+ }
+ }
+ }
+ if (in_seq) {asnp->abp +=2;} /* skip nulls */
+ asnp->abp += 2;
+ return asnp->abp;
+}
+
+unsigned char *
+get_pssm_intermed(struct asn_bstruct *asnp,
+ double **freqs,
+ int n_rows,
+ int n_cols,
+ int by_row) {
+
+ asnp->abp = chk_asn_buf(asnp,4);
+
+ if (*asnp->abp == ASN_SEQ) {
+ asnp->abp += 2;
+ if (*asnp->abp == ASN_PSSM_FREQS) {
+ asnp->abp+=2;
+ asnp->abp = get_pssm_freqs(asnp, freqs, n_rows, n_cols, by_row);
+ }
+ asnp->abp +=2; /* skip nulls */
+ }
+ asnp->abp += 2;
+ return asnp->abp;
+}
+
+
+#define ASN_PSSM_PARAMS 161
+#define ASN_PSSM_PARAMS_PSEUDOCNT 160
+#define ASN_PSSM_PARAMS_RPSPARAMS 161
+#define ASN_PSSM_RPSPARAMS_MATRIX 160
+#define ASN_PSSM_RPSPARAMS_GAPOPEN 161
+#define ASN_PSSM_RPSPARAMS_GAPEXT 162
+
+unsigned char *
+get_pssm_rpsparams(struct asn_bstruct *asnp,
+ char *matrix,
+ int *gap_open,
+ int *gap_ext) {
+
+ int end_seq=0;
+
+ asnp->abp = chk_asn_buf(asnp,4);
+
+ if (*asnp->abp == ASN_SEQ) {
+ asnp->abp += 2;
+ end_seq++;
+ }
+
+ if (*asnp->abp == ASN_PSSM_RPSPARAMS_MATRIX) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_str(asnp, matrix, MAX_SSTR);
+ }
+
+ if (*asnp->abp == ASN_PSSM_RPSPARAMS_GAPOPEN) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, gap_open);
+ }
+
+ if (*asnp->abp == ASN_PSSM_RPSPARAMS_GAPEXT) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, gap_ext);
+ }
+
+ if (end_seq) { chk_asn_buf(asnp,end_seq * 2); }
+ while (end_seq-- > 0) { asnp->abp += 2; }
+ return asnp->abp;
+}
+
+unsigned char *
+get_pssm_params(struct asn_bstruct *asnp,
+ int *pseudo_cnts,
+ char *matrix,
+ int *gap_open,
+ int *gap_ext) {
+
+ int end_seq=0;
+
+ asnp->abp = chk_asn_buf(asnp,6);
+
+ if (*asnp->abp == ASN_SEQ) {
+ asnp->abp += 2;
+ end_seq++;
+ }
+
+ if (*asnp->abp == ASN_PSSM_PARAMS_PSEUDOCNT) {
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, pseudo_cnts);
+ }
+
+ if (*asnp->abp == ASN_PSSM_PARAMS_RPSPARAMS) {
+ asnp->abp+=2;
+ asnp->abp = get_pssm_rpsparams(asnp, matrix, gap_open, gap_ext);
+ asnp->abp += 2;
+ }
+ while (end_seq-- > 0) { asnp->abp+=2; }
+ return asnp->abp;
+}
+
+
+unsigned char *
+get_pssm2_intermed(struct asn_bstruct *asnp,
+ double ***freqs,
+ int n_rows,
+ int n_cols) {
+
+ int i;
+ double **my_freqs;
+
+ if ((my_freqs = (double **) calloc(n_cols, sizeof(double *)))==NULL) {
+ fprintf(stderr, " cannot allocate freq cols - %d\n", n_cols);
+ exit(1);
+ }
+
+ if ((my_freqs[0] = (double *) calloc(n_cols * n_rows, sizeof(double)))==NULL) {
+ fprintf(stderr, " cannot allocate freq rows * cols - %d * %d\n", n_rows, n_cols);
+ exit(1);
+ }
+
+ for (i=1; i < n_cols; i++) {
+ my_freqs[i] = my_freqs[i-1] + n_rows;
+ }
+
+ *freqs = my_freqs;
+
+ chk_asn_buf(asnp, 8);
+
+ return get_pssm_freqs(asnp, my_freqs, n_rows, n_cols, 0);
+}
+
+int
+parse_pssm2_asn(struct asn_bstruct *asnp,
+ int *gi,
+ char *name,
+ char *acc,
+ char *descr,
+ unsigned char **query,
+ int *nq,
+ int *n_rows,
+ int *n_cols,
+ double ***freqs,
+ int *pseudo_cnts,
+ char *matrix,
+ double *lambda_p) {
+
+ int is_protein;
+ int have_rows, have_cols;
+
+ chk_asn_buf(asnp, 32);
+
+ if (memcmp(asnp->abp, "\241\2000\200",4) != 0) {
+ fprintf(stderr, "improper PSSM2 start\n");
+ return -1;
+ }
+ else {asnp->abp+=4;}
+
+ if (*asnp->abp == ASN_BIOSEQ_SEQ ) {
+ asnp->abp = get_astr_query2(asnp, gi, name, acc, descr, query, nq);
+ }
+
+ /* finish up the nulls */
+ while (*asnp->abp == '\0') { asnp->abp += 2;}
+
+ if (*asnp->abp == ASN_PSSM2_QUERY &&
+ asnp->abp[2] != ASN_SEQ ) {
+ fprintf(stderr, "improper PSSM2 start\n");
+ return -1;
+ }
+ else {asnp->abp += 4;}
+
+ while (*asnp->abp != '\0' ) {
+
+ switch (*asnp->abp) {
+ case ASN_PSSM_IS_PROT :
+ asnp->abp+=2;
+ asnp->abp = get_astr_bool(asnp, &is_protein);
+ break;
+
+ case ASN_PSSM2_MATRIX :
+ asnp->abp+=2;
+ asnp->abp = get_astr_str(asnp, matrix, MAX_SSTR);
+ break;
+
+ case ASN_PSSM2_NROWS :
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, n_rows);
+
+ if (*n_rows > 0) { have_rows = 1; }
+ else {
+ fprintf(stderr, " bad n_row count\n");
+ exit(1);
+ }
+ break;
+
+ case ASN_PSSM2_NCOLS :
+ asnp->abp+=2;
+ asnp->abp = get_astr_int(asnp, n_cols);
+ if (*n_cols > 0) {
+ have_cols = 1;
+ }
+ else {
+ fprintf(stderr, " bad n_row count\n");
+ exit(1);
+ }
+ break;
+
+ case ASN_PSSM2_FREQS :
+ asnp->abp += 4;
+ if (*asnp->abp == '\0') { asnp->abp += 4;}
+ break;
+
+ case ASN_PSSM2_LAMBDA :
+ asnp->abp += 2;
+ asnp->abp = get_astr_packedfloat(asnp,lambda_p);
+ asnp->abp +=2; /* skip over end of ASN_PSSM2_LAMBDA */
+ break;
+
+ case ASN_PSSM_INTERMED_DATA :
+ asnp->abp += 2;
+ asnp->abp = get_pssm2_intermed(asnp, freqs, *n_rows, *n_cols);
+ asnp->abp += 4;
+ break;
+
+ default: asnp->abp += 2;
+ }
+ }
+
+
+ return 1;
+}
+
+int
+parse_pssm_asn(FILE *afd,
+ int *gi,
+ char *name,
+ char *acc,
+ char *descr,
+ unsigned char **query,
+ int *nq,
+ int *n_rows,
+ int *n_cols,
+ double ***freqs,
+ int *pseudo_cnts,
+ char *matrix,
+ int *gap_open,
+ int *gap_ext,
+ double *lambda_p) {
+
+ int is_protein, pssm_version;
+ int i;
+ int have_rows, have_cols, by_col;
+ double **my_freqs;
+
+ struct asn_bstruct asn_str;
+
+ if ((asn_str.buf = (unsigned char *)calloc(ASN_BUF, sizeof(char))) == NULL ) {
+ fprintf(stderr, " cannot allocate asn_buf (%d)\n",ASN_BUF);
+ exit(1);
+ }
+
+ asn_str.fd = afd;
+ asn_str.len = ASN_BUF;
+ asn_str.abp = asn_str.buf_max = asn_str.buf + ASN_BUF;
+
+ chk_asn_buf(&asn_str, 32);
+
+ if (memcmp(asn_str.abp, "0\200\240\200",4) != 0) {
+ fprintf(stderr, "improper PSSM header -");
+ return -1;
+ }
+ else {asn_str.abp+=4;}
+
+ if (*asn_str.abp == ASN_IS_INT) {
+ asn_str.abp = get_astr_int(&asn_str, &pssm_version);
+ if (pssm_version != 2) {
+ fprintf(stderr, "PSSM2 version mismatch: %d\n",pssm_version);
+ return -1;
+ }
+ *gap_open = *gap_ext = 0;
+ return parse_pssm2_asn(&asn_str, gi, name, acc, descr,
+ query, nq,
+ n_rows, n_cols, freqs,
+ pseudo_cnts, matrix,
+ lambda_p);
+ }
+
+ if (*asn_str.abp == ASN_SEQ) { asn_str.abp += 2; }
+
+ if (*asn_str.abp == ASN_PSSM_IS_PROT ) {
+ asn_str.abp+=2;
+ asn_str.abp = get_astr_bool(&asn_str, &is_protein);
+ }
+
+ if (*asn_str.abp == ASN_PSSM_NROWS ) {
+ asn_str.abp+=2;
+ asn_str.abp = get_astr_int(&asn_str, n_rows);
+
+ if (*n_rows > 0) { have_rows = 1; }
+ else {
+ fprintf(stderr, " bad n_row count\n");
+ exit(1);
+ }
+ }
+
+ if (*asn_str.abp == ASN_PSSM_NCOLS ) {
+ asn_str.abp+=2;
+ asn_str.abp = get_astr_int(&asn_str, n_cols);
+ if (*n_cols > 0) {
+ have_cols = 1;
+ }
+ else {
+ fprintf(stderr, " bad n_row count\n");
+ exit(1);
+ }
+ }
+
+ if (*asn_str.abp == ASN_PSSM_BYCOL ) {
+ asn_str.abp+=2;
+ asn_str.abp = get_astr_bool(&asn_str, &by_col);
+ }
+
+ /* we have read everything up to the query
+
+ n_cols gives us the query length, which we can allocate;
+ */
+
+ if (*asn_str.abp == ASN_PSSM_QUERY ) {
+ asn_str.abp+=2;
+ asn_str.abp = get_astr_query(&asn_str, gi, name, acc, descr, query, nq);
+ *nq = *n_cols;
+ }
+
+ /* finish up the nulls */
+ while (*asn_str.abp == '\0') { asn_str.abp += 2;}
+
+ if (*asn_str.abp == ASN_PSSM_INTERMED_DATA) {
+
+ if (!have_rows || !have_cols) {
+ fprintf(stderr, " cannot allocate freq - missing rows/cols - %d/%d\n",
+ have_rows, have_cols);
+ return -1;
+ }
+
+ if ((my_freqs = (double **) calloc(*n_cols, sizeof(double *)))==NULL) {
+ fprintf(stderr, " cannot allocate freq cols - %d\n", *n_cols);
+ return -1;
+ }
+
+ if ((my_freqs[0] = (double *) calloc(*n_cols * *n_rows, sizeof(double)))==NULL) {
+ fprintf(stderr, " cannot allocate freq rows * cols - %d * %d\n", *n_rows, *n_cols);
+ return -1;
+ }
+ for (i=1; i < *n_cols; i++) {
+ my_freqs[i] = my_freqs[i-1] + *n_rows;
+ }
+
+ *freqs = my_freqs;
+
+ asn_str.abp+=2;
+ asn_str.abp = get_pssm_intermed(&asn_str, my_freqs, *n_rows, *n_cols, by_col);
+ asn_str.abp += 4;
+ }
+
+ if (*asn_str.abp == ASN_PSSM_PARAMS ) {
+ asn_str.abp+=2;
+ asn_str.abp = get_pssm_params(&asn_str, pseudo_cnts, matrix, gap_open, gap_ext);
+ }
+ else if (*asn_str.abp == 0) {asn_str.abp+=2;}
+ return 1;
+}
+
+int
+parse_pssm_asn_fa( FILE *fd,
+ int *n_rows_p, int *n_cols_p,
+ unsigned char **query,
+ double ***freq2d,
+ char *matrix,
+ int *gap_open_p,
+ int *gap_extend_p,
+ double *lambda_p) {
+
+ int qi, rj;
+ int gi;
+ double tmp_freqs[COMPO_LARGEST_ALPHABET];
+ char name[MAX_SSTR], acc[MAX_SSTR], descr[MAX_STR];
+ int nq;
+ int pseudo_cnts, ret_val;
+
+ /* parse the file */
+
+ ret_val = parse_pssm_asn(fd, &gi, name, acc, descr, query, &nq,
+ n_rows_p, n_cols_p, freq2d,
+ &pseudo_cnts, matrix, gap_open_p, gap_extend_p,
+ lambda_p);
+
+ if (ret_val <=0) return ret_val;
+
+ /* transform the frequencies */
+
+ for (qi = 0; qi < *n_cols_p; qi++) {
+ for (rj = 0; rj < *n_rows_p; rj++) { tmp_freqs[rj] = (*freq2d)[qi][rj];}
+
+ for (rj = 0; rj < COMPO_NUM_TRUE_AA; rj++) {
+ (*freq2d)[qi][rj] = tmp_freqs[pssm_aa_order[rj]];
+ }
+ }
+ return 1;
+}
git://source.jalview.org / jabaws.git / blobdiff