text: /* 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;
  }
  