void ParserImpl::handle(const std::string& json)
{
if (!_allowNullByte && json.find("\\u0000") != json.npos)
throw JSONException("Null bytes in strings not allowed.");
try
{
json_open_buffer(_pJSON, json.data(), json.size());
checkError();
//////////////////////////////////
// Underlying parser is capable of parsing multiple consecutive JSONs;
// we do not currently support this feature; to force error on
// excessive characters past valid JSON end, this MUST be called
// AFTER opening the buffer - otherwise it is overwritten by
// json_open*() call, which calls internal init()
json_set_streaming(_pJSON, false);
/////////////////////////////////
handle(); checkError();
if (JSON_DONE != json_next(_pJSON))
throw JSONException("Excess characters found after JSON end.");
json_close(_pJSON);
}
catch (std::exception&)
{
json_close(_pJSON);
throw;
}
}
void display_close(time_t now)
{
switch(DisplayMode) {
case DisplayReport:
report_close();
break;
case DisplayTXT:
txt_close();
break;
case DisplayXML:
xml_close();
break;
case DisplayJSON:
json_close();
break;
case DisplayCSV:
csv_close(now);
break;
case DisplayCurses:
#ifdef IPINFO
if (ipinfo_no >= 0)
asn_close();
#endif
mtr_curses_close();
break;
case DisplaySplit:
split_close();
break;
case DisplayGTK:
gtk_close();
break;
}
}
Scene *loadScene(char *aFilename)
{
Scene *t = new Scene;
json_stream json;
FILE * f = fopen(aFilename, "rb");
json_open_stream(&json, f);
json_type type = json_next(&json);
assert(type == JSON_OBJECT);
while (json_peek(&json) != JSON_OBJECT_END && json_peek(&json) != JSON_ERROR)
{
type = json_next(&json);
assert(type == JSON_STRING);
const char *otype = json_get_string(&json, 0);
if (strcmp(otype, "material") == 0)
{
const char *name = "[untitled]";
glm::vec3 diffuse(1);
glm::vec3 specular(0);
glm::vec3 ambient(0);
float opacity = 1;
float reflection = 0;
type = json_next(&json);
assert(type == JSON_OBJECT);
while (json_peek(&json) != JSON_OBJECT_END)
{
type = json_next(&json);
assert(type == JSON_STRING);
otype = json_get_string(&json, 0);
if (!getJSONString(&json, "name", otype, (char**)&name))
if (!getJSONVec3(&json, "diffuse", otype, diffuse))
if (!getJSONVec3(&json, "ambient", otype, ambient))
if (!getJSONVec3(&json, "specular", otype, specular))
if (!getJSONNumber(&json, "opacity", otype, opacity))
if (!getJSONNumber(&json, "reflection", otype, reflection))
assert(0 && "error parsing material");
}
type = json_next(&json);
assert(type == JSON_OBJECT_END);
Material *m = new Material();
m->mName = (char*)name;
m->mDiffuse = diffuse;
m->mAmbient = ambient;
m->mSpecular = specular;
m->mOpacity = opacity;
m->mReflection = reflection;
m->mNext = t->mMaterial;
t->mMaterial = m;
}
else
if (strcmp(otype, "box") == 0)
{
const char *name = "[untitled]";
const char *material = "default";
glm::vec3 center;
glm::vec3 size;
float dynamic = 0;
type = json_next(&json);
assert(type == JSON_OBJECT);
while (json_peek(&json) != JSON_OBJECT_END)
{
type = json_next(&json);
assert(type == JSON_STRING);
otype = json_get_string(&json, 0);
if (!getJSONString(&json, "name", otype, (char**)&name))
if (!getJSONString(&json, "material", otype, (char**)&material))
if (!getJSONNumber(&json, "dynamic", otype, dynamic))
if (!getJSONVec3(&json, "position", otype, center))
if (!getJSONVec3(&json, "center", otype, center))
if (!getJSONVec3(&json, "size", otype, size))
assert(0 && "error parsing box");
}
type = json_next(&json);
assert(type == JSON_OBJECT_END);
SceneObject *so;
t->insert(so = new Box((char*)name, center, size, t->getMaterialByName((char*)material)));
so->mDynamic = dynamic != 0;
}
else
if (strcmp(otype, "plane") == 0)
{
const char *name = "[untitled]";
const char *material = "default";
glm::vec3 point;
glm::vec3 normal;
float dynamic = 0;
type = json_next(&json);
assert(type == JSON_OBJECT);
while (json_peek(&json) != JSON_OBJECT_END)
{
type = json_next(&json);
assert(type == JSON_STRING);
otype = json_get_string(&json, 0);
if (!getJSONString(&json, "name", otype, (char**)&name))
if (!getJSONString(&json, "material", otype, (char**)&material))
if (!getJSONNumber(&json, "dynamic", otype, dynamic))
if (!getJSONVec3(&json, "point", otype, point))
if (!getJSONVec3(&json, "normal", otype, normal))
assert(0 && "error parsing box");
}
type = json_next(&json);
assert(type == JSON_OBJECT_END);
SceneObject *so;
t->insert(so = new Plane((char*)name, point, normal, t->getMaterialByName((char*)material)));
so->mDynamic = dynamic != 0;
}
else
if (strcmp(otype, "sphere") == 0)
{
const char *name = "[untitled]";
const char *material = "default";
glm::vec3 center;
float radius = 5;
float dynamic = 0;
type = json_next(&json);
assert(type == JSON_OBJECT);
while (json_peek(&json) != JSON_OBJECT_END)
{
type = json_next(&json);
assert(type == JSON_STRING);
otype = json_get_string(&json, 0);
if (!getJSONString(&json, "name", otype, (char**)&name))
if (!getJSONString(&json, "material", otype, (char**)&material))
if (!getJSONNumber(&json, "dynamic", otype, dynamic))
if (!getJSONVec3(&json, "center", otype, center))
if (!getJSONVec3(&json, "position", otype, center))
if (!getJSONNumber(&json, "radius", otype, radius))
assert(0 && "error parsing sphere");
}
type = json_next(&json);
assert(type == JSON_OBJECT_END);
SceneObject *so;
t->insert(so = new Sphere((char*)name, center, radius, t->getMaterialByName((char*)material)));
so->mDynamic = dynamic != 0;
}
else
if (strcmp(otype, "light") == 0)
{
const char *name = "[untitled]";
const char *material = "default";
glm::vec3 position;
type = json_next(&json);
assert(type == JSON_OBJECT);
while (json_peek(&json) != JSON_OBJECT_END)
{
type = json_next(&json);
assert(type == JSON_STRING);
otype = json_get_string(&json, 0);
if (!getJSONString(&json, "name", otype, (char**)&name))
if (!getJSONString(&json, "material", otype, (char**)&material))
if (!getJSONVec3(&json, "position", otype, position))
assert(0 && "error parsing light");
}
type = json_next(&json);
assert(type == JSON_OBJECT_END);
t->insert(new Light((char*)name, position, t->getMaterialByName((char*)material)));
}
else
{
assert(0);
}
}
type = json_next(&json);
if (type == JSON_ERROR)
{
const char * err = json_get_error(&json);
err = err;
}
assert(type == JSON_OBJECT_END);
type = json_next(&json);
assert(type == JSON_DONE);
json_close(&json);
setupScene(t);
t->optimize();
return t;
};
int main (int argc, char* argv[]) {
char filename1[200];
char filename2[200];
char pairs_file[200];
char fileout[200];
FILE* query_fp = 0;
FILE* reference_fp = 0;
FILE* fp_pairs = 0;
FILE* fpout = stdout;
int total_pairs = 0;
pair_struct* pairs = 0;
extern FILE *scaninfo_file;
setup_match_types();
/* Set Default Parameter Values*/
length_5p_for_weighting = 8; /* The 5' sequence length to be weighted except for the last residue */
scale = 4.0; /* The 5' miRNA scaling parameter */
strict = 0; /* Strict seed model on/off*/
debug = 0; /* Debugging mode on/off*/
key_value_pairs = 0;
gap_open = -9.0; /* Gap-open Penalty*/
gap_extend = -4.0; /* Gap-extend Penalty*/
score_threshold = 140.0; /* SW Score Threshold for reporting hits*/
score_ceiling = 0; /* Default upper limit to score. If zero, this is not used. */
energy_threshold = 1.0; /* Energy Threshold (DG) for reporting hits*/
verbosity = 1; /* Verbose mode on/off*/
brief_output = 0; /* Brief output off by default */
rusage_output = 0; /* rusage output off by default */
outfile = 0; /* Dump to file on/off*/
truncated = 0; /* Truncate sequences on/off*/
no_energy = 1; /* Turn off Energy Calcs - FASTER*/
restricted = 0; /* Perform restricted search space*/
parse_command_line(argc, argv, filename1, filename2, fileout, pairs_file);
if (gap_open > 0.0 || gap_extend > 0.0) {
fprintf(stderr, "Error: gap penalties may not be greater than 0\n");
return 1;
}
if (truncated < 0) {
fprintf(stderr, "Error: negative value give for UTR truncation\n");
return 1;
}
if ((query_fp = fopen(filename1, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename1);
return 1;
}
if ((reference_fp = fopen(filename2, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename2);
return 1;
}
fclose(reference_fp);
if ((outfile) && ((fpout = fopen(fileout, "w")) == NULL)) {
fprintf(stderr, "Error: Cannot create output file %s\n", fileout);
return 1;
}
if (restricted) {
if ((fp_pairs = fopen(pairs_file, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open restrict pairs file %s\n", pairs_file);
return 1;
}
/* Initialize the pairs list for restriced searches*/
total_pairs = load_pairs(fp_pairs, &pairs);
fclose(fp_pairs);
}
fflush(fpout);
initialize_globals();
if(!brief_output)
print_parameters(filename1, filename2, fpout);
if (restricted && verbosity) {
printf("Performing Restricted Scan on:%d pairs\n", total_pairs);
}
find_targets(query_fp, fpout, pairs, total_pairs, filename2);
#ifdef USE_RUSAGE
if(rusage_output)
{
struct rusage ru;
if(getrusage(RUSAGE_SELF,&ru) != 0)
{
fprintf(stderr,"Could not get rusage data\n");
if(errno)
fprintf(stderr,"Reason: %s",strerror(errno));
}
else
{
printf("User CPU time: %ld.%06ld\n",ru.ru_utime.tv_sec,ru.ru_utime.tv_usec);
printf("Max RSS: %ld KB\n",ru.ru_maxrss);
}
}
#endif // RUSAGE
destroy_globals();
if (outfile) fclose(fpout);
if (scaninfo_file != stdout && scaninfo_file != stderr && scaninfo_file != NULL)
fclose(scaninfo_file);
json_close();
fclose(query_fp);
return 0;
}
static void linda_store_handler(void *p1, const uuid *u, const void *_s, int len)
{
linda *l = (linda*)p1;
const char *s = (const char*)_s;
if (len > 0) // add
{
json *j = json_open(s);
json *j1 = json_get_object(j);
json *jid = json_find(j1, LINDA_ID);
if (!jid)
return;
if (json_is_integer(jid))
{
long long k = json_get_integer(jid);
if (l->sl && !l->is_int)
{
printf("linda_store_handler: expected integer id\n");
return;
}
if (!l->sl)
{
l->sl = sb_int_uuid_create2();
l->is_int = 1;
}
sb_int_uuid_set(l->sl, k, u);
}
else if (json_is_string(jid))
{
const char *k = json_get_string(jid);
if (l->sl && !l->is_string)
{
printf("linda_store_handler: expected string id\n");
return;
}
if (!l->sl)
{
l->sl = sb_string_uuid_create2();
l->is_string = 1;
}
sb_string_uuid_set(l->sl, k, u);
}
json_close(j);
}
else if (len < 0) // remove (with hint)
{
json *j = json_open(s);
json *j1 = json_get_object(j);
json *jid = json_find(j1, LINDA_ID);
if (!jid)
return;
if (json_is_integer(jid))
{
long long k = json_get_integer(jid);
if (l->sl && !l->is_int)
{
printf("linda_out: expected integer id\n");
return;
}
if (!l->sl)
{
l->sl = sb_int_uuid_create2();
l->is_int = 1;
}
sb_int_uuid_erase(l->sl, k, u);
}
else if (json_is_string(jid))
{
const char *k = json_get_string(jid);
if (l->sl && !l->is_string)
{
printf("linda_out: expected string id\n");
return;
}
if (!l->sl)
{
l->sl = sb_string_uuid_create2();
l->is_string = 1;
}
sb_string_uuid_erase(l->sl, k, u);
}
json_close(j);
}
else // remove (brute search)
{
sb_uuid_efface(l->sl, u);
}
}
int linda_rm(hlinda *h, const char *s)
{
json *j = json_open(s);
json *j1 = json_get_object(j);
int is_int = 0, is_string = 0;
const char *string_id = NULL;
long long int_id = 0;
uuid u;
json *joid = json_find(j1, LINDA_OID);
if (!joid)
{
json_close(j);
return 0;
}
uuid_from_string(json_get_string(joid), &u);
json *jid = json_find(j1, LINDA_ID);
if (jid)
{
if (h->l->is_int && !json_is_integer(jid))
{
printf("linda_read: expected integer id\n");
json_close(j);
return 0;
}
else if (h->l->is_string && !json_is_string(jid))
{
printf("linda_read: expected string id\n");
json_close(j);
return 0;
}
if (json_is_integer(jid))
{
int_id = json_get_integer(jid);
is_int = 1;
}
else if (json_is_string(jid))
{
string_id = json_get_string(jid);
json_close(h->jquery);
is_string = 1;
}
else
{
json_close(j);
return 0;
}
}
json_close(j);
if (is_int)
{
char tmpbuf[1024];
int tmplen = sprintf(tmpbuf, "{\"%s\":%lld}\n", LINDA_ID, int_id);
store_hrem2(h->hst, &u, tmpbuf, tmplen);
sb_int_uuid_erase(h->l->sl, int_id, &u);
}
else if (is_string)
{
char tmpbuf[1024], tmpbuf2[1024];
json_format_string(string_id, tmpbuf2, sizeof(tmpbuf2));
int tmplen = sprintf(tmpbuf, "{\"%s\":\"%s\"}\n", LINDA_ID, tmpbuf2);
store_hrem2(h->hst, &u, tmpbuf, tmplen);
sb_string_uuid_erase(h->l->sl, string_id, &u);
}
else
{
store_rem(h->l->st, &u);
sb_uuid_efface(h->l->sl, &u);
}
return 1;
}
int linda_out(hlinda *h, const char *s)
{
if (!h)
return 0;
json *j = json_open(s);
json *j1 = json_get_object(j);
json *joid = json_find(j1, LINDA_OID);
uuid u;
if (joid)
{
uuid_from_string(json_get_string(joid), &u);
}
else
uuid_gen(&u);
json *jid = json_find(j1, LINDA_ID);
if (jid)
{
if (json_is_integer(jid))
{
long long k = json_get_integer(jid);
if (h->l->sl && !h->l->is_int)
{
printf("linda_out: expected integer id\n");
return 0;
}
if (!h->l->sl)
{
h->l->sl = sb_int_uuid_create2();
h->l->is_int = 1;
}
sb_int_uuid_set(h->l->sl, k, &u);
}
else if (json_is_string(jid))
{
const char *k = json_get_string(jid);
if (h->l->sl && !h->l->is_string)
{
printf("linda_out: expected string id\n");
return 0;
}
if (!h->l->sl)
{
h->l->sl = sb_string_uuid_create2();
h->l->is_string = 1;
}
sb_string_uuid_set(h->l->sl, k, &u);
}
}
store_hadd(h->hst, &u, s, strlen(s));
h->last_oid = u;
json_close(j);
return 0;
}
static int linda_read(hlinda *h, const char *s, const char **buf, int rm, int nowait)
{
json *j = json_open(s);
json *j1 = json_get_object(j);
h->oid.u1 = h->oid.u2 = 0;
int is_int = 0, is_string = 0;
json *jid = json_find(j1, LINDA_ID);
if (jid)
{
if (h->l->is_int && !json_is_integer(jid))
{
printf("linda_read: expected integer id\n");
json_close(j);
return 0;
}
else if (h->l->is_string && !json_is_string(jid))
{
printf("linda_read: expected string id\n");
json_close(j);
return 0;
}
if (json_is_integer(jid))
{
h->int_id = json_get_integer(jid);
h->jquery = json_open(s);
sb_int_uuid_find(h->l->sl, h->int_id, &read_int_handler, h);
json_close(h->jquery);
is_int = 1;
}
else if (json_is_string(jid))
{
h->string_id = json_get_string(jid);
h->jquery = json_open(s);
sb_string_uuid_find(h->l->sl, h->string_id, &read_string_handler, h);
json_close(h->jquery);
is_string = 1;
}
else
{
json_close(j);
return 0;
}
}
else
{
h->jquery = json_open(s);
sb_iter(h->l->sl, &read_handler, h);
json_close(h->jquery);
}
json_close(j);
if (!h->oid.u1 && !h->oid.u2)
return 0;
if (rm)
{
if (is_int)
{
char tmpbuf[1024];
int tmplen = sprintf(tmpbuf, "{\"%s\":%lld}\n", LINDA_ID, h->int_id);
store_hrem2(h->hst, &h->oid, tmpbuf, tmplen);
sb_int_uuid_erase(h->l->sl, h->int_id, &h->oid);
}
else if (is_string)
{
char tmpbuf[1024], tmpbuf2[1024];
json_format_string(h->string_id, tmpbuf2, sizeof(tmpbuf2));
int tmplen = sprintf(tmpbuf, "{\"%s\":\"%s\"}\n", LINDA_ID, tmpbuf2);
store_hrem2(h->hst, &h->oid, tmpbuf, tmplen);
sb_string_uuid_erase(h->l->sl, h->string_id, &h->oid);
}
else
{
store_hrem(h->hst, &h->oid);
sb_uuid_efface(h->l->sl, &h->oid);
}
}
*buf = h->dst;
return 1;
}
static int read_handler(void *arg, void *k, void *v)
{
hlinda *h = (hlinda*)arg;
uuid *u = (uuid*)v;
if (!store_get(h->l->st, u, (void**)&h->dst, &h->len))
return 0;
int match = 1;
json *j1 = json_get_object(h->jquery);
json *jdst = json_open(h->dst);
json *j2 = json_get_object(jdst);
size_t i, cnt = json_count(j1);
for (i = 0; i < cnt; i++)
{
json *j1it = json_index(j1, i);
const char *name = json_get_string(j1it);
if (name[0] == '$')
continue;
json *j2it = json_find(j2, name);
if (!j2it)
{
match = 0;
continue;
}
if (json_is_integer(j1it))
{
if (!json_is_integer(j2it))
{
match = 0;
break;
}
if (json_get_integer(j1it) != json_get_integer(j2it))
{
match = 0;
break;
}
}
else if (json_is_real(j1it))
{
if (!json_is_real(j2it))
{
match = 0;
break;
}
if (json_get_real(j1it) != json_get_real(j2it))
{
match = 0;
break;
}
}
else if (json_is_string(j1it))
{
if (!json_is_string(j2it))
{
match = 0;
break;
}
if (strcmp(json_get_string(j1it), json_get_string(j2it)))
{
match = 0;
break;
}
}
else if (json_is_true(j1it))
{
if (!json_is_true(j2it))
{
match = 0;
break;
}
}
else if (json_is_false(j1it))
{
if (!json_is_false(j2it))
{
match = 0;
break;
}
}
else if (json_is_null(j1it))
{
if (!json_is_null(j2it))
{
match = 0;
break;
}
}
}
json_close(jdst);
if (!match)
return 1;
h->oid.u1 = u->u1;
h->oid.u2 = u->u2;
return 0;
}
