static void global_add( HMODULE hModule )
{
global_object *pobject;
global_object *nobject;
if( hModule == NULL )
return;
pobject = global_search( hModule );
/* Do not add object again if it's already on the list */
if( pobject )
return;
for( pobject = &first_object; pobject->next ; pobject = pobject->next );
nobject = malloc( sizeof(global_object) );
/* Should this be enough to fail global_add, and therefore also fail
* dlopen?
*/
if( !nobject )
return;
pobject->next = nobject;
nobject->previous = pobject;
nobject->hModule = hModule;
}
static void
global_add(HMODULE module)
{
global_object *pobject;
global_object *nobject;
if (module == NULL)
return;
pobject = global_search(module);
/* Do not add object again if it's already on the list */
if(pobject)
return;
for (pobject = &first_object; pobject->next ; pobject = pobject->next);
nobject = malloc( sizeof(global_object) );
if( !nobject )
return;
pobject->next = nobject;
nobject->next = NULL;
nobject->previous = pobject;
nobject->hModule = module;
}
static void edit_find_ok_callback(read_direction_t direction, Widget w, XtPointer context, XtPointer info)
{ /* "Find" is the label here */
char *str = NULL, *buf = NULL;
XmString s1;
XEN proc;
str = XmTextGetString(edit_find_text);
if ((str) && (*str))
{
clear_global_search_procedure(true);
ss->search_expr = mus_strdup(str);
redirect_errors_to(errors_to_find_text, NULL);
proc = snd_catch_any(eval_str_wrapper, str, str);
redirect_errors_to(NULL, NULL);
if ((XEN_PROCEDURE_P(proc)) && (procedure_arity_ok(proc, 1)))
{
ss->search_proc = proc;
ss->search_proc_loc = snd_protect(proc);
#if HAVE_SCHEME
if (optimization(ss) > 0)
ss->search_tree = mus_run_form_to_ptree_1_b(XEN_PROCEDURE_SOURCE(proc));
#endif
buf = (char *)calloc(PRINT_BUFFER_SIZE, sizeof(char));
mus_snprintf(buf, PRINT_BUFFER_SIZE, "find: %s", str);
set_label(edit_find_label, buf);
/* XmTextSetString(edit_find_text, NULL); */
free(buf);
}
}
else
{
if (ss->search_expr == NULL)
{
char *temp = NULL;
/* using global search_proc set by user */
buf = (char *)calloc(PRINT_BUFFER_SIZE, sizeof(char));
mus_snprintf(buf, PRINT_BUFFER_SIZE, "find: %s", temp = (char *)XEN_AS_STRING(ss->search_proc));
#if HAVE_SCHEME
if (temp) free(temp);
#endif
set_label(edit_find_label, buf);
/* XmTextSetString(edit_find_text, NULL); */
free(buf);
}
}
if (str) XtFree(str);
if ((XEN_PROCEDURE_P(ss->search_proc)) || (ss->search_tree))
{
s1 = XmStringCreateLocalized((char *)"Stop");
XtVaSetValues(cancelB, XmNlabelString, s1, NULL);
XmStringFree(s1);
redirect_xen_error_to(stop_search_if_error, NULL);
str = global_search(direction);
redirect_xen_error_to(NULL, NULL);
s1 = XmStringCreateLocalized((char *)"Go Away");
XtVaSetValues(cancelB, XmNlabelString, s1, NULL);
XmStringFree(s1);
if ((str) && (*str)) set_label(edit_find_label, str);
}
}
Solution *Solver::solve(){
std::ofstream out_file (file_out.c_str());
if (!out_file.is_open()) {
std::cout << "Unable to open file";
}
init();
// ------ print solution -------
print_solution(current_solution);
//print_file_solution(0, current_solution, out_file);
// ------ print solution -------
clock_t start, end, total;
start = clock();
for(unsigned int i=0;i<max_iterations;i++){
iter_cost_time = 0;
std::cout << "----- iteration "<< i << " ------" << std::endl;
local_search();
// ------ print solution -------
std::cout << "local search ";
print_solution(current_solution);
print_file_solution(i, current_solution, out_file);
// ------ print solution -------
global_search();
// ------ print solution -------
std::cout << "global search ";
print_solution(current_solution);
//print_file_solution(i, current_solution, out_file);
// ------ print solution -------
tabu_list->update_tabu();
total_cost_time += iter_cost_time;
if(global_best_cost == 0)
break;
}
end = clock();
total = end - start;
printf("\nTotal OpenCL Kernel time in milliseconds = %0.3f ms\n", (total_cost_time / 1000000.0) );
printf("Total CPU time in milliseconds = %0.3f ms\n", total /1000.0);
return global_best;
}
/**
* get_starts
*
* Create a list of starting points for EM.
*
* If dataset->prob > 0, samples subsequences in the input dataset for good
* starting points. Otherwise, e_cons is specified as the starting point.
*
* In order to generate starting points for EM, get_starts either performs
* a "global search", or else uses a specified consensus string. Global search
* always includes substring search, but several other algorithms ("branching"
* searches) can optionally be run after substring search in order to improve
* the starting points from which EM shall be run.
*
* Returns number of starting points in list.
*/
extern S_POINT *get_starts(
DATASET *dataset, ///< the dataset
MODEL *model, ///< the model
char *e_cons, ///< encoded consensus sequence
int *n_starts ///< number of starting points
)
{
S_POINT *s_points = NULL; // array of starting points to perform EM from
BOOLEAN pal = dataset->pal; /* force DNA palindromes */
int min_w = model->min_w; // minimum width
int max_w = model->max_w; // maximum width
double min_nsites = model->min_nsites; // min. allowed sites
double max_nsites = model->max_nsites; // max. allowed sites
double sample_prob = dataset->prob; // sampling probability for subsequences
// Generate geometric progressions over width and nsites. Make these
// progressions identical to those used in original meme:
int n_ns;
int *central_ns = make_geometric_prog(min_nsites, max_nsites, 2, &n_ns);
int n_ws;
int *central_ws =
make_width_prog(min_w, max_w, sqrt(2), &n_ws, pal, model->all_widths);
// Create a matrix of S_POINTS over which global search will be performed.
// Each S_POINT corresponds to a separate combination of n and w:
SP_MATRIX *sp_matrix =
create_spoint_matrix(central_ws, n_ws, central_ns, n_ns, dataset);
// Fill in the starting points with the subsequence to use
if (!e_cons && sample_prob != 0) { // sample subsequences (and do branching)
// Perform "global search" in order to find starting points for EM.
// global_search() will establish a string, from which EM will be
// performed, for a number of S_POINT objects in the matrix (one string per
// S_POINT). This process results in S_POINTS in the matrix being filled
// in:
global_search(sp_matrix, dataset, model);
} else { // don't sample subsequences
// Use the specified consensus sequence, "e_cons", in order to fill in
// the sp_matrix:
use_input_cons(sp_matrix, e_cons);
}
// Choose (from the matrix) which S_POINTS em will be executed from:
s_points = choose_em_starts(sp_matrix, dataset, model, n_starts);
// Free memory associated with the sp_matrix, as we no longer need it:
free_sp_matrix(sp_matrix);
return s_points;
} // get_starts
static void global_rem( HMODULE hModule )
{
global_object *pobject;
if( hModule == NULL )
return;
pobject = global_search( hModule );
if( !pobject )
return;
if( pobject->next )
pobject->next->previous = pobject->previous;
if( pobject->previous )
pobject->previous->next = pobject->next;
free( pobject );
}
static GList*
node_symbol_list_member (IJsSymbol *obj)
{
NodeSymbol* self = NODE_SYMBOL (obj);
NodeSymbolPrivate *priv = NODE_SYMBOL_PRIVATE(self);
gchar *name = get_complex_node_type (priv->node, priv->my_cx);
if (!name)
return NULL;
GList *t = js_context_get_member_list (priv->my_cx, name);
if (t)
return t;
IJsSymbol *sym = global_search (name);
if (sym)
return ijs_symbol_list_member (sym);
return NULL;
}
static gchar*
get_complex_node_type (JSNode *node, JSContext *my_cx)
{
Type *name = js_context_get_node_type (my_cx, node);
if (!name)
return NULL;
if (!name->isFuncCall)
return name->name;
IJsSymbol* sym = global_search (name->name);
if (sym && ijs_symbol_get_base_type (sym) == BASE_FUNC)
{
GList *ret = ijs_symbol_get_func_ret_type (sym);
if (ret)
{
g_assert (ret->data != NULL);
return (gchar*)ret->data;
}
}
return NULL;
}
static IJsSymbol*
node_symbol_get_member (IJsSymbol *obj, const gchar * name)
{
NodeSymbol* self = NODE_SYMBOL (obj);
NodeSymbolPrivate *priv = NODE_SYMBOL_PRIVATE(self);
gchar *tname = get_complex_node_type (priv->node, priv->my_cx);
if (!tname)
return NULL;
if (js_context_get_member_list (priv->my_cx, tname)) //TODO:Fix mem leak
{
return IJS_SYMBOL (
node_symbol_new (js_context_get_member (priv->my_cx, tname, name),
name, priv->my_cx));
}
IJsSymbol *t = global_search (tname);
if (t)
return ijs_symbol_get_member (t, name);
return NULL;
}
void *dlopen( const char *file, int mode )
{
HMODULE hModule;
UINT uMode;
current_error = NULL;
/* Do not let Windows display the critical-error-handler message box */
uMode = SetErrorMode( SEM_FAILCRITICALERRORS );
if( file == 0 )
{
/* POSIX says that if the value of file is 0, a handle on a global
* symbol object must be provided. That object must be able to access
* all symbols from the original program file, and any objects loaded
* with the RTLD_GLOBAL flag.
* The return value from GetModuleHandle( ) allows us to retrieve
* symbols only from the original program file. For objects loaded with
* the RTLD_GLOBAL flag, we create our own list later on.
*/
hModule = GetModuleHandle( NULL );
if( !hModule )
save_err_ptr_str( file );
}
else
{
char lpFileName[MAX_PATH];
int i;
/* MSDN says backslashes *must* be used instead of forward slashes. */
for( i = 0 ; i < sizeof(lpFileName)-1 ; i++ )
{
if( !file[i] )
break;
else if( file[i] == '/' )
lpFileName[i] = '\\';
else
lpFileName[i] = file[i];
}
lpFileName[i] = '\0';
/* POSIX says the search path is implementation-defined.
* LOAD_WITH_ALTERED_SEARCH_PATH is used to make it behave more closely
* to UNIX's search paths (start with system folders instead of current
* folder).
*/
hModule = LoadLibraryEx( (LPSTR) lpFileName, NULL,
LOAD_WITH_ALTERED_SEARCH_PATH );
/* If the object was loaded with RTLD_GLOBAL, add it to list of global
* objects, so that its symbols may be retrieved even if the handle for
* the original program file is passed. POSIX says that if the same
* file is specified in multiple invocations, and any of them are
* RTLD_GLOBAL, even if any further invocations use RTLD_LOCAL, the
* symbols will remain global.
*/
if( !hModule )
save_err_str( lpFileName );
else if( (mode & RTLD_GLOBAL) )
global_add( hModule );
else if( (mode & RTLD_NOLOAD) )
{
global_object *pobject = global_search( hModule );
// when RLTD_NOLOAD is set, POSIX says that the module handle
// returned is NULL when the object was not previously loaded.
if(!pobject)
hModule = NULL;
}
}
/* Return to previous state of the error-mode bit flags. */
SetErrorMode( uMode );
return (void *) hModule;
}
void search_in_wc(const char *what)
{
global_search(what, what);
}
static IJsSymbol*
find (const gchar* name, IJsSymbol *sym)
{
gchar *vname = NULL, *left = NULL;
if (!sym)
return NULL;
if (!name)
return NULL;
int i;
for (i = 0; i < strlen (name); i++)
{
if (name[i] != '.')
continue;
vname = g_strndup (name, i);
left = g_strdup (name + i + 1);
break;
}
if (!vname)
vname = g_strdup (name);
if (strlen (vname) == 0)
{
g_free (vname);
g_free (left);
return NULL;
}
gboolean is_func_call = *((vname + strlen (vname)) - 1) == ')';
if (is_func_call)
vname [strlen (vname) - 2] = '\0';
GList *j;////TODO
for (j = ijs_symbol_list_member (sym); j; j = g_list_next (j))
{
gchar *t = (gchar*)j->data;
//puts (t);
if (strcmp (vname, t) != 0 )
continue;
if (!is_func_call)
{
if (!left)
return ijs_symbol_get_member (sym, t);
IJsSymbol *tjs = ijs_symbol_get_member (sym, t);
IJsSymbol *ret = find (left, tjs);
g_object_unref (tjs);
return ret;
}
else
{
IJsSymbol *s = ijs_symbol_get_member (sym, t);
if (!s)
return NULL;
if (ijs_symbol_get_base_type (s) != BASE_FUNC)
{
g_object_unref (s);
return NULL;
}
GList* rets = ijs_symbol_get_func_ret_type (s);
g_object_unref (s);
if (rets == NULL)
{
return NULL;
}
//TODO: Fix
IJsSymbol *ret = global_search (rets->data);
if (!ret)
return NULL;
if (!left)
return ret;
s = find (left, ret);
g_object_unref (ret);
return s;
}
}
return NULL;
}
