void write_PDB_dstring
(JNIEnv *env, jobject graph, jobject elementRule,
void *nGraph, int dimension, dstring *encoding)
{
char buffer [100], *element;
int i, size;
void *iterator;
g_float *coord;
jclass elementRuleClass;
jmethodID getElement, getBytes;
prepare_get_element
(env, elementRule, &elementRuleClass, &getElement, &getBytes);
clear_dstring (encoding);
size = get_graph_size (nGraph);
for (i = 1; i <= size; ++i)
{
coord = get_3d_coordinates (nGraph, i);
element = get_element
(env, elementRule, elementRuleClass, getElement, getBytes, graph, i);
if (element == NULL) element = "X";
sprintf (buffer,
"ATOM %5d %3s %8.3f%8.3f%8.3f \n",
i, element, coord [0], coord [1], coord [2]);
add_string (encoding, buffer);
}
for (i = 1; i <= size; ++i)
{
void *iterator;
int k = 0;
iterator = get_edge_iterator (nGraph, i);
while (has_next_edge (iterator))
{
int j;
if (k % 6 == 0) {
if (k > 0) add_char (encoding, '\n');
add_string (encoding, "CONECT");
sprintf (buffer, "%5d", i);
add_string (encoding, buffer);
}
++k;
j = get_next_edge (iterator);
sprintf (buffer, "%5d", j);
add_string (encoding, buffer);
}
free (iterator);
add_char (encoding, '\n');
}
add_string (encoding, "END\n");
}
void * run_program(void * program_stat)
{
graph_t c_graph;
int memkey, i;
status client_program;
process_t process_type;
mstack_t instruction_stack;
thread_status_t thread_info = (thread_status_t)program_stat;
instruction_stack = parse_file((char*)thread_info->file);
if (instruction_stack != NULL){
c_graph = build_graph(instruction_stack);
if (c_graph != NULL)
{
create_sh_graph(c_graph, get_graph_size(c_graph),
&memkey, &client_program.g_header);
client_program.cursor = 0;
client_program.flag = FALSE;
client_program.client_id = thread_info->client_id;
for(i = 0; i < MEM_SIZE; i++){
client_program.mem[i] = 0;
}
process_type = c_graph->first->instruction_process->instruction_type;
client_program.mtype = process_type->params->unique_mq_id;
free_graph(c_graph);
free_stack(instruction_stack);
printf("Sending first instruction...\n");
ipc_send(process_type->params, &client_program, sizeof(struct status));
}else{
answer_error_to_client(UNABLE_TO_BUILD_GRAPH, thread_info->client_id);
}
}else{
answer_error_to_client(errno, thread_info->client_id);
errno = 0;
}
pthread_exit(NULL);
}
void * run_program(void * program_stat)
{
ipc_params_t client_params;
stack_t c_stack;
graph_t c_graph;
int memkey, i;
status client_program;
process_t process_type;
thread_status_t thread_info = (thread_status_t)program_stat;
c_stack = parse_file((char*)thread_info->file);
c_graph = build_graph(c_stack);
if (c_graph != NULL)
{
create_sh_graph(c_graph, get_graph_size(c_graph),
&memkey, &client_program.g_header);
client_program.cursor = 0;
client_program.flag = FALSE;
for(i = 0; i < MEM_SIZE; i++) {
client_program.mem[i] = 0;
}
process_type = c_graph->first->instruction_process->instruction_type;
client_program.mtype = process_type->params->unique_mq_id;
ipc_send(process_type->params, &client_program, sizeof(struct status));
} else {
printf("Entrada incorrecta\n");
}
while(!ipc_receive(server_receive_params, &client_program,
sizeof(struct status)))
sleep(1);
client_params = get_params_from_pid(thread_info->client_id, PROGRAM_STATUS, sizeof(struct status));
ipc_open(client_params, O_WRONLY);
ipc_send(client_params, &client_program, sizeof(struct status));
ipc_close(client_params);
}
void write_CML_dstring
(JNIEnv *env, jobject graph, jobject elementRule,
void *nGraph, int dimension, dstring *encoding)
{
char buffer [100], *sep, *element;
dstring from, to;
int i, k, n;
void *iterator;
g_float **coordinate;
jclass elementRuleClass;
jmethodID getElement, getBytes;
prepare_get_element
(env, elementRule, &elementRuleClass, &getElement, &getBytes);
clear_dstring (encoding);
n = get_graph_size (nGraph);
add_string (encoding, "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n");
add_string (encoding, "<!DOCTYPE molecule SYSTEM \"cml.dtd\" []>\n");
add_string (encoding, "<molecule convention=\"MathGraph\">\n");
add_string (encoding, " <atomArray>\n");
add_string (encoding, " <stringArray builtin=\"id\">");
sep = "";
for (i = 1; i <= n; ++i)
{
add_string (encoding, sep);
add_string (encoding, "a");
sprintf (buffer, "%d", i);
add_string (encoding, buffer);
sep = " ";
}
add_string (encoding, "</stringArray>\n");
add_string (encoding, " <stringArray builtin=\"elementType\">");
sep = "";
for (i = 1; i <= n; ++i)
{
element = get_element
(env, elementRule, elementRuleClass, getElement, getBytes, graph, i);
if (element == NULL) element = "X";
add_string (encoding, sep);
add_string (encoding, element);
sep = " ";
}
add_string (encoding, "</stringArray>\n");
coordinate = malloc (n * sizeof (*coordinate));
for (i = 0, k = 1; i < n; i = k++)
{
coordinate [i] = dimension == 2 ?
get_2d_coordinates (nGraph, k) : get_3d_coordinates (nGraph, k);
}
for (k = 0; k < dimension; ++k)
{
add_string (encoding, " <floatArray builtin=\"");
add_char (encoding, 'x' + k);
sprintf (buffer, "%d", dimension);
add_string (encoding, buffer);
add_string (encoding, "\">");
sep = "";
for (i = 0; i < n; ++i)
{
add_string (encoding, sep);
if (sizeof (g_float) == sizeof (float)) {
sprintf (buffer, "%-g", coordinate [i][k]);
} else {
sprintf (buffer, "%-lg", coordinate [i][k]);
}
add_string (encoding, buffer);
sep = " ";
}
add_string (encoding, "</floatArray>\n");
}
add_string (encoding, " </atomArray>\n");
add_string (encoding, " <bondArray>\n");
from = new_dstring;
to = new_dstring;
sep = "";
for (i = 1; i <= n; ++i)
{
void *iterator;
iterator = get_edge_iterator (nGraph, i);
while (has_next_edge (iterator))
{
int j = get_next_edge (iterator);
if (j <= i) continue;
sprintf (buffer, "%sa", sep);
add_string (&from, buffer);
add_string (&to, buffer);
sprintf (buffer, "%d", i);
add_string (&from, buffer);
sprintf (buffer, "%d", j);
add_string (&to, buffer);
sep = " ";
}
}
add_string (encoding, " <stringArray builtin=\"atomRef\">");
add_bytes (encoding, from.base, from.length);
add_string (encoding, "</stringArray>\n");
add_string (encoding, " <stringArray builtin=\"atomRef\">");
add_bytes (encoding, to.base, to.length);
add_string (encoding, "</stringArray>\n");
add_string (encoding, " </bondArray>\n");
add_string (encoding, "</molecule>\n");
clear_dstring (&from);
clear_dstring (&to);
}
