/** amino acid 3-letter to 1-letter code conversion */
__inline__ static char aacode(char *code3)
{
char residue = ' '; /* 1-letter residue name */
/* three-letter code of amino acid residues, exception HET -> X */
char *aa3[] = {"ALA","---","CYS","ASP","GLU","PHE","GLY","HIS","ILE","---","LYS","LEU","MET","ASN","---","PRO","GLN","ARG","SER","THR","UNL","VAL","TRP","HET","TYR","UNK"};
/* nucleotide residues */
char *nuc[] = {" A"," DA"," C"," DC","---","---"," G"," DG"," I"," DI","---","---","---"," N"," DN","---","---","---"," DT"," T"," U"," DU","---","---","---","---"};
/* match against amino acid residues */
residue = scan_array(code3, aa3, 65);
/* match against nucleotide residues */
if (residue == ' ')
residue = scan_array(code3, nuc, 97);
/* residue not found */
if (residue == ' ') {
Warning("Check the format of the PDB file: might be non-standard. See examples in the README file.");
ErrorSpec("Unknown standard residue type in protein structure:", code3);
}
/*else
fprintf(stderr, "%s:%d: %c ", __FILE__, __LINE__, residue);*/
return residue;
}
void Parser::scan_value(void) {
int c = read_byte();
switch (c) {
case trace::TYPE_NULL:
case trace::TYPE_FALSE:
case trace::TYPE_TRUE:
break;
case trace::TYPE_SINT:
scan_sint();
break;
case trace::TYPE_UINT:
scan_uint();
break;
case trace::TYPE_FLOAT:
scan_float();
break;
case trace::TYPE_DOUBLE:
scan_double();
break;
case trace::TYPE_STRING:
scan_string();
break;
case trace::TYPE_ENUM:
scan_enum();
break;
case trace::TYPE_BITMASK:
scan_bitmask();
break;
case trace::TYPE_ARRAY:
scan_array();
break;
case trace::TYPE_STRUCT:
scan_struct();
break;
case trace::TYPE_BLOB:
scan_blob();
break;
case trace::TYPE_OPAQUE:
scan_opaque();
break;
case trace::TYPE_REPR:
scan_repr();
break;
case trace::TYPE_WSTRING:
scan_wstring();
break;
default:
std::cerr << "error: unknown type " << c << "\n";
exit(1);
case -1:
break;
}
}
void mark_recursive(Managed_Object_Handle ref, bool ref_is_compressed)
{
// If ref_is_compressed, ref is a compressed reference: the uint32 offset to an object in the heap.
// ref_is_compressed => (GC::compressing_references && is_compressed_reference(ref))
assert(!ref_is_compressed || (GC::compressing_references && is_compressed_reference((COMPRESSED_REFERENCE)ref)));
uint64 null_ref = (GC::compressing_references? GC::heap_base : NULL);
if (ref_is_compressed) {
if (ref == 0) {
return;
}
} else {
if ((uint64)ref == null_ref) {
return;
}
}
Object_With_Header *obj;
if (ref_is_compressed) {
Managed_Object_Handle ref2 = (Managed_Object_Handle)(GC::heap_base + (COMPRESSED_REFERENCE)ref);
obj = (Object_With_Header *)(((Byte *)ref2) - sizeof(GC_Overhead));
} else {
obj = (Object_With_Header *)(((Byte *)ref) - sizeof(GC_Overhead));
}
unsigned space = obj->header.semispace;
validate_object(obj);
if(false && GC::verbosegc) {
#ifdef GC_STATS
printf("Marking object: %s%p [id=%I64d]\n", (ref_is_compressed? "compressed " : ""), ref, obj->header.id);
#endif //GC_STATS
}
if(is_marked(obj)) {
return;
}
set_marked(obj);
Vtable_GC *vt = obj->vt();
if(false && GC::verbosegc) {
printf("\tObject of type %s\n", class_get_name(vt->gcvt->ch));
}
if(vt->gcvt->is_scannable_array) {
scan_array(obj);
} else {
uint16 *offsets = vt->gcvt->offsets;
Managed_Object_Handle ref2 = ref;
if (ref_is_compressed) {
ref2 = (Managed_Object_Handle)(GC::heap_base + (COMPRESSED_REFERENCE)ref);
}
if (GC::compressing_references) {
while(*offsets) {
COMPRESSED_REFERENCE *slot = (COMPRESSED_REFERENCE *)(((Byte *)ref2) + (*offsets));
COMPRESSED_REFERENCE val_offset = (COMPRESSED_REFERENCE)(*slot);
assert(is_compressed_reference(val_offset));
Managed_Object_Handle val = (Managed_Object_Handle)(GC::heap_base + val_offset);
push_on_mark_stack(val);
offsets++;
}
} else {
while(*offsets) {
Managed_Object_Handle *slot = (Managed_Object_Handle *)(((Byte *)ref2) + *offsets);
push_on_mark_stack(*slot);
offsets++;
}
}
}
} //mark_recursive
