static bool VariableStateIncrement(PromiseIterator *iter, size_t index)
{
assert(index < SeqLength(iter->var_states));
CfAssoc *var = SeqAt(iter->vars, index);
switch (var->rval.type)
{
case RVAL_TYPE_LIST:
{
Rlist *state = SeqAt(iter->var_states, index);
assert(state);
// find the next valid value, return false if there is none
state = FirstRealEntry(state->next);
SeqSet(iter->var_states, index, state);
return state != NULL;
}
break;
default:
ProgrammingError("Unhandled case in switch");
}
return false;
}
static void RenameMainBundle(EvalContext *ctx, Policy *policy)
{
assert(policy != NULL);
assert(ctx != NULL);
assert(policy->bundles != NULL);
char *const entry_point = GetRealPath(EvalContextGetEntryPoint(ctx));
if (NULL_OR_EMPTY(entry_point))
{
free(entry_point);
return;
}
Seq *bundles = policy->bundles;
int length = SeqLength(bundles);
bool removed = false;
for (int i = 0; i < length; ++i)
{
Bundle *const bundle = SeqAt(bundles, i);
if (StringSafeEqual(bundle->name, "__main__"))
{
char *abspath = GetRealPath(bundle->source_path);
if (StringSafeEqual(abspath, entry_point))
{
Log(LOG_LEVEL_VERBOSE,
"Redefining __main__ bundle from file %s to be main",
abspath);
strncpy(bundle->name, "main", 4+1);
// "__main__" is always big enough for "main"
}
else
{
Log(LOG_LEVEL_VERBOSE,
"Dropping __main__ bundle from file %s (entry point: %s)",
abspath,
entry_point);
removed = true;
SeqSet(bundles, i, NULL); // SeqSet calls destroy function
}
free(abspath);
}
}
if (removed)
{
SeqRemoveNulls(bundles);
}
free(entry_point);
}
int main(int argc,char *argv[])
{
int i,cutoff_score = 200,minimum=0,arg;
char score[100],*DBS_NAME,c=' ';
ss_type P = NULL;
a_type A;
Boolean success=FALSE,DNA=FALSE,xnu=FALSE,query=FALSE,out_stdout=FALSE;
if(argc < 3) print_error(PURGE_USAGE);
DBS_NAME = argv[1];
if(sscanf(argv[2],"%d",&i)!=1) print_error(PURGE_USAGE);
cutoff_score = tMAX(int,1,i);
sprintf(score,".%c%d",c,cutoff_score);
for(arg = 3; arg < argc; arg++){
if(argv[arg][0] != '-') print_error(PURGE_USAGE);
switch(argv[arg][1]) {
case 'b': c = 'b'; break;
case 'e': c = 'e'; break;
case 'f': c = 'f'; break;
case 'q': query=TRUE; break;
case 'x': xnu=TRUE; break;
case 'n': DNA=TRUE; xnu=FALSE; break;
case 'o': out_stdout=TRUE; break;
default: print_error(PURGE_USAGE);
}
}
//if(c=='b' && DNA == TRUE)
// print_error("-b option is not allowed with -n option");
if(xnu==TRUE && DNA == TRUE)
print_error("-x option is not allowed with -n option");
if(DNA) A = MkAlpha("NACGT",DNA_MTRX);
else A = MkAlpha(AMINO_ACIDS,PROT_BLOSUM62);
if(xnu) P = MkXnuSeqSet(DBS_NAME,A);
else P = SeqSet(DBS_NAME,A);
if (c==' ') { if (DNA) c = 'e'; else c = 'b'; }
success = RmHomologs(cutoff_score, c, minimum, query, P, out_stdout);
NilAlpha(A); NilSeqSet(P);
if(success) return 0;
else return 1;
}
