/* ToDo make sure position of vlen and klen are at the right place */
fint F77_FUNC(ipaddstroption,IPADDSTROPTION)
(fptr* FProblem,
char* KEYWORD,
char* VALUE,
int klen,
int vlen)
{
char* keyword;
char* val;
FUserData* fuser_data = (FUserData*) *FProblem;
fint retval;
keyword = f2cstr(KEYWORD, klen);
val = f2cstr(VALUE, vlen);
retval = AddIpoptStrOption(fuser_data->Problem, keyword, val);
free(val);
free(keyword);
if (retval) {
return OKRetVal;
}
else {
return NotOKRetVal;
}
}
fint F77_FUNC(ipaddnumoption,IPADDNUMOPTION)
(fptr* FProblem,
char* KEYWORD,
fdouble* VALUE,
int klen)
{
char* keyword;
FUserData* fuser_data = (FUserData*) *FProblem;
fint retval;
keyword = f2cstr(KEYWORD, klen);
retval = AddIpoptNumOption(fuser_data->Problem, keyword, *VALUE);
free(keyword);
if (retval) {
return OKRetVal;
}
else {
return NotOKRetVal;
}
}
fint F77_FUNC(ipopenoutputfile,IPOPENOUTPUTFILE)
(fptr* FProblem,
char* FILENAME,
fint* PRINTLEVEL,
int flen)
{
char* filename;
FUserData* fuser_data = (FUserData*) *FProblem;
Int printlevel = *PRINTLEVEL;
fint retval;
filename = f2cstr(FILENAME, flen);
retval = OpenIpoptOutputFile(fuser_data->Problem, filename, printlevel);
free(filename);
if (retval) {
return OKRetVal;
}
else {
return NotOKRetVal;
}
}
fint F77_FUNC(ipaddintoption,IPADDINTOPTION)
(fptr* FProblem,
char* KEYWORD,
fint* VALUE,
int klen)
{
char* keyword;
FUserData* fuser_data = (FUserData*) *FProblem;
Int value = *VALUE;
fint retval;
keyword = f2cstr(KEYWORD, klen);
retval = AddIpoptIntOption(fuser_data->Problem, keyword, value);
free(keyword);
if (retval) {
return OKRetVal;
}
else {
return NotOKRetVal;
}
}
List *xdap_late_read_gel_data(void)
{
List *gel_details;
if (cur_gel_index > io.num_gels)
gel_details = nil;
else {
bap_ar_file_rec ar_line;
bap_rl_file_rec rl_line;
bap_sq_file_rec sq_line;
bap_tg_file_rec tg_line;
int index;
char name[17];
char *seq;
int length;
int comp;
int pos;
int l_nbr;
int r_nbr;
sq_line = (char *) malloc(io.max_gel_length+1);
bap_read_ar(&io,cur_gel_index,&ar_line);
bap_read_rl(&io,cur_gel_index,&rl_line);
bap_read_tg(&io,cur_gel_index,&tg_line);
bap_read_sq(&io,cur_gel_index,sq_line);
index = cur_gel_index;
f2cstr(ar_line.lines.name,BAP_FILE_NAME_LENGTH,name,
(size_t)BAP_FILE_NAME_LENGTH);
length = abs(rl_line.lines.length);
comp = (rl_line.lines.length < 0);
seq = sq_line;
seq[length] = '\0';
pos = rl_line.lines.rel_pos;
l_nbr = rl_line.lines.left_nbr;
r_nbr = rl_line.lines.right_nbr;
gel_details =
build_list(
atom_str(gel_rec),
build_list(
atom_str(gel_index),
atom_int(index),
nil),
build_list(
atom_str(gel_name),
atom_str(name),
nil),
build_list(
atom_str(gel_length),
atom_int(length),
nil),
build_list(
atom_str(gel_comp),
atom_int(comp),
nil),
build_list(
atom_str(gel_seq),
atom_str(seq),
nil),
build_list(
atom_str(gel_pos),
atom_int(pos),
nil),
build_list(
atom_str(gel_l_nbr),
atom_int(l_nbr),
nil),
build_list(
atom_str(gel_r_nbr),
atom_int(r_nbr),
nil),
nil);
/* Get raw data details */
if (tg_line.lines.comment) {
List *raw_data_details;
char *rd;
int rd_length;
int rd_cut;
int rd_ulen;
char rd_type[5];
char rd_file[19];
rd = bap_read_comment(&io, tg_line.lines.comment);
sscanf(rd,"%6d%6d%6d%*s",&rd_length, &rd_cut, &rd_ulen);
f2cstr(&rd[18],4,rd_type,(size_t)4);
f2cstr(&rd[22],18,rd_file,(size_t)18);
raw_data_details =
build_list(
build_list(
atom_str(gel_rd_length),
atom_int(rd_length),
nil),
build_list(
atom_str(gel_rd_cut),
atom_int(rd_cut),
nil),
build_list(
atom_str(gel_rd_ulen),
atom_int(rd_ulen),
nil),
build_list(
atom_str(gel_rd_type),
atom_str(rd_type),
nil),
build_list(
atom_str(gel_rd_file),
atom_str(rd_file),
nil),
nil);
join_list (gel_details, raw_data_details, nil);
}
/*
** Process tags, maintaining separate lists for
** (a) special tags
** (b) annotation
** (c) edits
*/
{
List *specials;
List *notes;
List *edits;
int_4 next;
specials = nil;
notes =
build_list(
atom_str(gel_annotation),
nil);
edits =
build_list(
atom_str(gel_edits),
nil);
while (tg_line.lines.next) {
next = tg_line.lines.next;
bap_read_tg(&io,next,&tg_line);
if (strncmp(tg_line.lines.type.c,"*LC*",4)==0) {
if (tg_line.lines.comment) {
List *lc;
lc = build_list(
atom_str(gel_l_cut_seq),
atom_str(bap_read_comment(&io,tg_line.lines.comment)),
nil);
if (isNil(specials))
specials = build_list(lc,nil);
else
specials = join_list(specials,build_list(lc,nil),nil);
}
} else if (strncmp(tg_line.lines.type.c,"*RC*",4)==0) {
if (tg_line.lines.comment) {
List *rc;
rc = build_list(
atom_str(gel_r_cut_seq),
atom_str(bap_read_comment(&io,tg_line.lines.comment)),
nil);
if (isNil(specials))
specials = build_list(rc,nil);
else
specials = join_list(specials,build_list(rc,nil),nil);
}
} else if (strncmp(tg_line.lines.type.c,"*",1)==0) {
List *ed;
char base[2];
base[0] = tg_line.lines.type.c[3];
base[1] = '\0';
ed = build_list(
build_list(
atom_str(gel_ed_op),
atom_str( (strncmp(tg_line.lines.type.c,"*IN",3))==0
? gel_ed_insert : gel_ed_delete),
nil),
build_list(
atom_str(gel_ed_base),
atom_str(base),
nil),
build_list(
atom_str(gel_ed_base_pos),
atom_int( tg_line.lines.position ),
nil),
nil);
edits = join_list(edits, build_list(ed,nil),nil);
} else {
List *an;
char type[5];
char *com;
strncpy(type,tg_line.lines.type.c,4);
type[4]='\0';
com = bap_read_comment(&io,tg_line.lines.comment);
an = build_list(
build_list(
atom_str(gel_an_pos),
atom_int(tg_line.lines.position),
nil),
build_list(
atom_str(gel_an_len),
atom_int(tg_line.lines.length),
nil),
build_list(
atom_str(gel_an_type),
atom_str(type),
nil),
(com == NULL) ? nil :
build_list(
atom_str(gel_an_comment),
atom_str(com),
nil),
nil);
notes = join_list(notes,build_list(an,nil),nil);
}
}
if (isNil(specials))
gel_details = join_list(gel_details,build_list(edits,nil),build_list(notes,nil),nil);
else
gel_details = join_list(gel_details,specials,build_list(edits,nil),build_list(notes,nil),nil);
}
cur_gel_index++;
free(sq_line);
}
return gel_details;
}
