// read delta file
void read_commands (FILE* fi, int file_id) {
unsigned char buf[4];
command_count = 0;
chunks = NULL;
size_t fo_pos = 0;
delta_chunk t_chunk;
size_t parm1, parm2;
fread(&buf, 4, 1, fi); // header
while ( fread(&buf, 1, 1, fi) > 0 ) {
cmd = buf[0];
rs_prototab_ent cmd_data = rs_prototab[cmd];
t_chunk.c_type = cmd_data.kind;
t_chunk.start = fo_pos;
t_chunk.len = 0;
t_chunk.sf_id = 0;
t_chunk.sf_pos = 0;
switch (cmd_data.kind) {
case RS_KIND_LITERAL:
parm1 = read_parm(fi, cmd_data.len_1);
trace("%i LITERAL %i | ", (int) fo_pos, (int) parm1);
t_chunk.len = parm1;
t_chunk.sf_id = file_id;
t_chunk.sf_pos = ftell(fi);
fseek(fi, parm1, SEEK_CUR);
fo_pos += t_chunk.len;
break;
case RS_KIND_COPY:
parm1 = read_parm(fi, cmd_data.len_1);
parm2 = read_parm(fi, cmd_data.len_2);
trace("%i COPY %i %i | ", (int) fo_pos, (int) parm1, (int) parm2);
t_chunk.sf_pos = parm1;
t_chunk.len = parm2;
fo_pos += t_chunk.len;
break;
case RS_KIND_END:
trace("%i END", (int) fo_pos);
break;
default: // unknown
fprintf(stderr, "ERROR: unknown command %i\n", cmd);
throw new int;
}
add_chunk(t_chunk);
}
};
void PrepinReader::do_water(Water * w)
{
read_prep("opls_uni.in");
compare(w->getAtoms());
read_parm("parm94.dat");
set_parameters(w->getAtoms());
}
void PrepinReader::do_molecule(Molecule * m, string soup_name)
{
string guess = soup_name+"and-bcc.prepi";
printf("Guessing that the name of the prepin file is: %s\n",guess.c_str());
read_prep(guess);
compare(m->getAtoms());
read_parm("gaff.dat");
set_parameters(m->getAtoms());
}
void PrepinReader::do_proteinChain(ProteinChain * p)
{
/*** N-terminus ***/
read_prep("all_aminont94.in");
compare(p->getResidues()[0]->getAtoms());
/*** everything between ***/
read_prep("all_amino94.in");
for(unsigned int i=1; i<p->getResidues().size()-1; i++)
compare(p->getResidues()[i]->getAtoms());
/*** C-terminus ***/
read_prep("all_aminoct94.in");
compare(p->getResidues()[p->getResidues().size()-1]->getAtoms());
/*** setting parameters ***/
read_parm("parm94.dat");
set_parameters(p->getAtoms());
}
void Dorade::sweepread(const char swp_fname[],struct sswb_info *ssptr, struct vold_info *vptr,
struct radd_info *rptr,struct celv_info *cptr,
struct cfac_info *cfptr,struct parm_info *pptr,
struct swib_info *sptr,struct ryib_info *ryptr,
struct asib_info *aptr, struct rdat_info **dptr)
{
/****************************************************/
/* THIS SUBROUTINE READS THE DESCRIPTORS FROM A */
/* SWEEP FILE & PASSES THE VOLD, RADD, CFAC, PARM, */
/* SWIB BACK TO THE FORTRAN PROGRAM */
/* swp_fname=name of sweep file */
/* *vptr=pointer to vold descriptor */
/* *rptr=pointer to radd descriptor */
/* *cptr=pointer to cfac descriptor */
/* *pptr=pointer to parm descriptor */
/* *sptr=pointer to swib descriptor */
/* *ryptr=pointer to ryib descriptor */
/* *aptr=pointer to asib descriptor */
/* *dptr=pointer to rdat descriptor */
/* tot_gates=total number of gates */
/* arr=array to hold gate spacing */
/* *sptr=pointer of swib descriptor */
/****************************************************/
FILE *fp;
int i=0;
char identifier[IDENT_LEN]; //defined in read_dorade.h (RV)
int desc_len;
int fld_num=0;
int match;
int found=false;
int beam=-1;
i = 0;
/* ADD NULL CHARACTER TO END OF STRING
for (unsigned int i=0;i<strlen(swp_fname);i++) {
if (isspace(swp_fname[i])) {break;}
else {len++;}
}
swp_fname[len]='\0'; */
/* READ THE SWEEP FILE */
/* OPEN THE SWEEP FILE */
if ( (fp = fopen(swp_fname,"rb"))==NULL) {
printf("Can't open %s\n",swp_fname);
}
while ( !feof(fp) ) {
/* READ THE DESCRIPTOR IDENTIFIER */
//printf ("at %d\n",ftell(fp));
if ( (fread(identifier,sizeof(char),IDENT_LEN,fp)) != IDENT_LEN) {
printf("sweep file read error..can't read identifier\n");
exit(-1);
}
/* READ THE DESCRIPTOR LENGTH */
desc_len=read_int(fp);
// printf ("reading %s at %d\n",identifier,ftell(fp));
// printf("desc_len: %d\n",desc_len);
if ( (strncmp(identifier,"SSWB",IDENT_LEN)) == 0) {
/* READ THE SSWB DESCRIPTOR */
/*printf ("reading vold\n");*/
read_sswb(fp,ssptr);
} else if ( (strncmp(identifier,"VOLD",IDENT_LEN)) == 0) {
/* READ THE VOLUME DESCRIPTOR */
/*printf ("reading vold\n");*/
read_vold(fp,vptr);
} else if ( (strncmp(identifier,"RADD",IDENT_LEN)) == 0) {
/* READ THE RADAR DESCRIPTOR */
/*printf ("reading radd\n");*/
read_radd(fp,rptr);
if (rptr->num_param_desc > MAX_NUM_PARMS) {
printf ("WARNING: NUMBER OF PARAMETERS ");
printf ("GREATER THAN MAX_NUM_PARMS\n");
printf ("NUMBER OF PARAMETERS: %d\n",rptr->num_param_desc);
printf ("MAX_NUM_PARMS: %d\n",MAX_NUM_PARMS);
printf ("SEE READ_DORADE.H\n");
}
} else if ( (strncmp(identifier,"CFAC",IDENT_LEN)) == 0) {
/* READ THE CFAC DESCRIPTOR */
/*printf ("reading cfac\n");*/
read_cfac(fp,cfptr);
} else if ( (strncmp(identifier,"PARM",IDENT_LEN)) == 0) {
/* READ THE PARAMETER DESCRIPTOR */
/*printf ("reading parm\n");*/
read_parm(fp,pptr);
*pptr++;
} else if ( (strncmp(identifier,"CELV",IDENT_LEN)) == 0) {
/*printf ("reading CELV\n");*/
/* CHECK & MAKE SURE NUMBER OF GATES DOESN'T
EXCEED LIMIT */
read_celv(fp,cptr,desc_len);
if (cptr->total_gates>MAX_GATES) {
printf ("WARNING: NUMBER OF GATES ");
printf ("GREATER THAN MAX_GATES\n");
printf ("SEE READ_DORADE.H\n");
printf ("NUMBER OF GATES: %d\n",(int)cptr->total_gates);
printf ("MAX_GATES: %d\n",MAX_GATES);
}
} else if ( (strncmp(identifier,"SWIB",IDENT_LEN)) == 0) {
/* READ THE SWEEP INFO DESCRIPTOR */
/*printf ("reading swib\n");*/
read_swib(fp,sptr);
if (sptr->num_rays > MAX_BEAMS) {
printf ("WARNING: NUMBER OF BEAMS ");
printf ("GREATER THAN MAX_BEAMS\n");
printf ("SEE READ_DORADE.H\n");
printf ("NUMBER OF BEAMS: %d\n",(int)sptr->num_rays);
printf ("MAX_BEAMS: %d\n",MAX_BEAMS);
}
} else if ( (strncmp(identifier,"RYIB",IDENT_LEN)) == 0) {
/* READ THE RAY INFO DESCRIPTOR */
/*printf ("reading ryib\n");*/
beam++;
read_ryib(fp,&ryptr[beam]);
fld_num=0;
/* GO BACK TO FIRST PARAMETER DESCRIPTOR */
for (i=0;i<rptr->num_param_desc;i++) {*pptr--;}
/* DID WE FIND THE FIELD??
if (beam==2 && found==FALSE) {
printf ("%s NOT FOUND..\n",fld_name);
printf ("VALID FIELD NAMES:\n");
for (i=0;i<rptr->num_param_desc;i++) {
printf ("%s\n",pptr->parm_name);
*pptr++;
}
printf ("EXITING..\n");
exit(-1);
}
*/
} else if ( (strncmp(identifier,"ASIB",IDENT_LEN)) == 0) {
/* READ THE PLATFORM INFO DESCRIPTOR */
/*printf ("reading asib\n");*/
read_asib(fp,&aptr[beam]);
//*aptr++;
} else if ( (strncmp(identifier,"RDAT",IDENT_LEN)) == 0) {
/* READ THE DATA DESCRIPTOR */
// printf ("reading rdat %s %d:\n", fld_name, desc_len);
match=false;
read_rdat(fp,fld_num,desc_len,&match,
pptr->parm_type,beam,cptr->total_gates,
rptr->compress_flag,pptr->baddata_flag,
pptr->scale_fac,&dptr[fld_num][beam]);
fld_num++;
*pptr++;
if (match==true) {
// *dptr++;
found=match;
}
} else if ( (strncmp(identifier,"NULL",IDENT_LEN)) == 0) {
skip_bytes(fp,desc_len-(IDENT_LEN+sizeof(int)));
} else if ( (strncmp(identifier,"RKTB",IDENT_LEN)) == 0) {
/* READ THE ROTATION ANGLE DESCRIPTOR */
/*printf ("reading rktb\n");*/
rktb_size = desc_len;
read_rktb(fp);
// That should be the end
break;
} else {
// printf ("Dorade.cpp HOLA1\n");
// printf("Identifier: %s\n",identifier);
// printf("desc_len: %d\n",desc_len);
// // printf("ftell: %s\n",ftell(fp)); // <-- segmentation fault with ftell(fp) (RV)
// printf ("Dorade.cpp HOLA2\n");
// exit(1);
skip_bytes(fp,desc_len-(IDENT_LEN+sizeof(int))); //<--"Seek Error..aborting" (RV)
} /* endif */
} /* endwhile */
fclose(fp);
if (rptr->scan_mode == 9) {
// Airborne data, need to calculate ground relative azimuth and elevation
for (int i=0; i < sptr->num_rays; i++) {
calcAirborneAngles(&aptr[i], cfptr, &ryptr[i], &rangles[i]);
}
}
}
