void ESolver::BindType(const string& TypeName, const ESFixedTypeBase* Type)
{
if (LookupType(TypeName) != nullptr) {
throw TypeException((string)"Error: Attempted to rebind previously bound type name \"" +
TypeName + "\"");
}
TypeMgr->BindType(TypeName, Type);
}
BOOL Binder::IsType(TypeHandle th, BinderTypeID id)
{
if (RawGetType(id) == th)
return TRUE;
if (!m_pTypeHandles[id-1].IsNull())
return FALSE;
else
return LookupType(id, FALSE) == th;
}
TypeHandle Binder::FetchType(BinderTypeID id)
{
THROWSCOMPLUSEXCEPTION();
_ASSERTE(id != TYPE__NIL);
_ASSERTE(id <= m_cTypeHandles);
TypeHandle th = m_pTypeHandles[id-1];
if (th.IsNull())
th = LookupType(id);
return th;
}
bool
SymbolTable::AddType(const char *name, const Type *type, SourcePos pos) {
const Type *t = LookupType(name);
if (t != NULL && CastType<UndefinedStructType>(t) == NULL) {
// If we have a previous declaration of anything other than an
// UndefinedStructType with this struct name, issue an error. If
// we have an UndefinedStructType, then we'll fall through to the
// code below that adds the definition to the type map.
Error(pos, "Ignoring redefinition of type \"%s\".", name);
return false;
}
types[name] = type;
return true;
}
/** Tokenize data. */
TokenNode *Tokenize(const char *line, const char *fileName)
{
AttributeNode *ap;
TokenNode *current;
char *temp;
unsigned int x;
unsigned int offset;
unsigned int lineNumber;
char inElement;
char found;
head = NULL;
current = NULL;
inElement = 0;
lineNumber = 1;
x = 0;
/* Skip any initial white space. */
while(IsSpace(line[x], &lineNumber)) {
x += 1;
}
/* Skip any XML stuff. */
if(!strncmp(line + x, "<?", 2)) {
while(line[x]) {
if(line[x] == '\n') {
lineNumber += 1;
}
if(!strncmp(line + x, "?>", 2)) {
x += 2;
break;
}
x += 1;
}
}
/* Process the XML data. */
while(line[x]) {
/* Skip comments and white space. */
do {
/* Skip white space. */
while(IsSpace(line[x], &lineNumber)) {
x += 1;
}
/* Skip comments */
found = 0;
if(!strncmp(line + x, "<!--", 4)) {
while(line[x]) {
if(line[x] == '\n') {
lineNumber += 1;
}
if(!strncmp(line + x, "-->", 3)) {
x += 3;
found = 1;
break;
}
x += 1;
}
}
} while(found);
switch(line[x]) {
case '<':
x += 1;
if(line[x] == '/') {
/* Close tag. */
x += 1;
temp = ReadElementName(line + x);
if(current) {
if(JLIKELY(temp)) {
if(JUNLIKELY(current->type != LookupType(temp, NULL))) {
Warning(_("%s[%u]: close tag \"%s\" does not "
"match open tag \"%s\""),
fileName, lineNumber, temp,
GetTokenName(current));
}
} else {
Warning(_("%s[%u]: unexpected and invalid close tag"),
fileName, lineNumber);
}
current = current->parent;
} else {
if(temp) {
Warning(_("%s[%u]: close tag \"%s\" without open tag"),
fileName, lineNumber, temp);
} else {
Warning(_("%s[%u]: invalid close tag"), fileName, lineNumber);
}
}
if(temp) {
x += strlen(temp);
Release(temp);
}
} else {
/* Open tag. */
current = CreateNode(current, fileName, lineNumber);
temp = ReadElementName(line + x);
if(JLIKELY(temp)) {
x += strlen(temp);
LookupType(temp, current);
Release(temp);
} else {
Warning(_("%s[%u]: invalid open tag"), fileName, lineNumber);
}
}
inElement = 1;
break;
case '/':
/* End of open/close tag. */
if(inElement) {
x += 1;
if(JLIKELY(line[x] == '>' && current)) {
x += 1;
current = current->parent;
inElement = 0;
} else {
Warning(_("%s[%u]: invalid tag"), fileName, lineNumber);
}
} else {
goto ReadDefault;
}
break;
case '>':
/* End of open tag. */
x += 1;
inElement = 0;
break;
default:
ReadDefault:
if(inElement) {
/* In the open tag; read attributes. */
ap = CreateAttribute(current);
ap->name = ReadElementName(line + x);
if(ap->name) {
x += strlen(ap->name);
if(line[x] == '=') {
x += 1;
}
if(line[x] == '\"') {
x += 1;
}
ap->value = ReadAttributeValue(line + x, fileName,
&offset, &lineNumber);
x += offset;
if(line[x] == '\"') {
x += 1;
}
}
} else {
/* In tag body; read text. */
temp = ReadElementValue(line + x, fileName, &offset, &lineNumber);
x += offset;
if(temp) {
if(current) {
if(current->value) {
current->value = Reallocate(current->value,
strlen(current->value) +
strlen(temp) + 1);
strcat(current->value, temp);
Release(temp);
} else {
current->value = temp;
}
} else {
if(JUNLIKELY(temp[0])) {
Warning(_("%s[%u]: unexpected text: \"%s\""),
fileName, lineNumber, temp);
}
Release(temp);
}
}
}
break;
}
}
return head;
}
bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &bv)
{
if (!_init)
Init();
OBAtom *a1,*a2;
OBResidue *r1,*r2;
vector<OBAtom*>::iterator i,j;
vector3 v;
int bo;
string skipres = ""; // Residue Number to skip
string rname = "";
//assign residue bonds
for (a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i))
{
r1 = a1->GetResidue();
if (r1 == NULL) // atoms may not have residues
continue;
if (skipres.length() && r1->GetNumString() == skipres)
continue;
if (r1->GetName() != rname)
{
skipres = SetResName(r1->GetName()) ? "" : r1->GetNumString();
rname = r1->GetName();
}
//assign bonds for each atom
for (j=i,a2 = mol.NextAtom(j);a2;a2 = mol.NextAtom(j))
{
r2 = a2->GetResidue();
if (r2 == NULL) // atoms may not have residues
continue;
if (r1->GetNumString() != r2->GetNumString())
break;
if (r1->GetName() != r2->GetName())
break;
if (r1->GetChain() != r2->GetChain())
break; // Fixes PR#2889763 - Fabian
if ((bo = LookupBO(r1->GetAtomID(a1),r2->GetAtomID(a2))))
{
// Suggested by Liu Zhiguo 2007-08-13
// for predefined residues, don't perceive connection
// by distance
// v = a1->GetVector() - a2->GetVector();
// if (v.length_2() < 3.5) //check by distance
mol.AddBond(a1->GetIdx(),a2->GetIdx(),bo);
}
}
}
int hyb;
string type;
//types and hybridization
rname = ""; // name of current residue
skipres = ""; // don't skip any residues right now
for (a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i))
{
if (a1->GetAtomicNum() == OBElements::Oxygen && !a1->GetValence())
{
a1->SetType("O3");
continue;
}
if (a1->GetAtomicNum() == OBElements::Hydrogen)
{
a1->SetType("H");
continue;
}
//***valence rule for O-
if (a1->GetAtomicNum() == OBElements::Oxygen && a1->GetValence() == 1)
{
OBBond *bond;
bond = (OBBond*)*(a1->BeginBonds());
if (bond->GetBO() == 2)
{
a1->SetType("O2");
a1->SetHyb(2);
}
else if (bond->GetBO() == 1)
{
// Leave the protonation/deprotonation to phmodel.txt
a1->SetType("O3");
a1->SetHyb(3);
// PR#3203039 -- Fix from Magnus Lundborg
// a1->SetFormalCharge(0);
}
continue;
}
r1 = a1->GetResidue();
if (r1 == NULL) continue; // atoms may not have residues
if (skipres.length() && r1->GetNumString() == skipres)
continue;
if (r1->GetName() != rname)
{
// if SetResName fails, skip this residue
skipres = SetResName(r1->GetName()) ? "" : r1->GetNumString();
rname = r1->GetName();
}
if (LookupType(r1->GetAtomID(a1),type,hyb))
{
a1->SetType(type);
a1->SetHyb(hyb);
}
else // try to figure it out by bond order ???
{}
}
return(true);
}
/** Tokenize a data. */
TokenNode *Tokenize(const char *line, const char *fileName) {
TokenNode *np;
AttributeNode *ap;
char *temp;
int inElement;
int x;
int found;
int lineNumber;
head = NULL;
current = NULL;
inElement = 0;
lineNumber = 1;
x = 0;
/* Skip any initial white space */
while(IsSpace(line[x], &lineNumber)) ++x;
/* Skip any XML stuff */
if(!strncmp(line + x, "<?", 2)) {
while(line[x]) {
if(line[x] == '\n') {
++lineNumber;
}
if(!strncmp(line + x, "?>", 2)) {
x += 2;
break;
}
++x;
}
}
while(line[x]) {
do {
while(IsSpace(line[x], &lineNumber)) ++x;
/* Skip comments */
found = 0;
if(!strncmp(line + x, "<!--", 4)) {
while(line[x]) {
if(line[x] == '\n') {
++lineNumber;
}
if(!strncmp(line + x, "-->", 3)) {
x += 3;
found = 1;
break;
}
++x;
}
}
} while(found);
switch(line[x]) {
case '<':
++x;
if(line[x] == '/') {
++x;
temp = ReadElementName(line + x);
if(current) {
if(temp) {
if(current->type != LookupType(temp, NULL)) {
Warning("%s[%d]: close tag \"%s\" does not "
"match open tag \"%s\"",
fileName, lineNumber, temp,
GetTokenName(current));
}
} else {
Warning("%s[%d]: unexpected and invalid close tag",
fileName, lineNumber);
}
current = current->parent;
} else {
if(temp) {
Warning("%s[%d]: close tag \"%s\" without open "
"tag", fileName, lineNumber, temp);
} else {
Warning("%s[%d]: invalid close tag", fileName, lineNumber);
}
}
if(temp) {
x += strlen(temp);
Release(temp);
}
} else {
np = current;
current = NULL;
np = CreateNode(np, fileName, lineNumber);
temp = ReadElementName(line + x);
if(temp) {
x += strlen(temp);
LookupType(temp, np);
Release(temp);
} else {
Warning("%s[%d]: invalid open tag", fileName, lineNumber);
}
}
inElement = 1;
break;
case '/':
if(inElement) {
++x;
if(line[x] == '>' && current) {
++x;
current = current->parent;
inElement = 0;
} else {
Warning("%s[%d]: invalid tag", fileName, lineNumber);
}
} else {
goto ReadDefault;
}
break;
case '>':
++x;
inElement = 0;
break;
default:
ReadDefault:
if(inElement) {
ap = CreateAttribute(current);
ap->name = ReadElementName(line + x);
if(ap->name) {
x += strlen(ap->name);
if(line[x] == '=') {
++x;
}
if(line[x] == '\"') {
++x;
}
ap->value = ReadAttributeValue(line + x, fileName,
&lineNumber);
if(ap->value) {
x += strlen(ap->value);
}
if(line[x] == '\"') {
++x;
}
}
} else {
temp = ReadElementValue(line + x, fileName, &lineNumber);
if(temp) {
x += strlen(temp);
if(current) {
if(current->value) {
current->value = Reallocate(current->value,
strlen(current->value) + strlen(temp) + 1);
strcat(current->value, temp);
Release(temp);
} else {
current->value = temp;
}
} else {
if(temp[0]) {
Warning("%s[%d]: unexpected text: \"%s\"",
fileName, lineNumber, temp);
}
Release(temp);
}
}
}
break;
}
}
return head;
}
static void
ScanConflicts(char *path, unsigned inx, int argc, char **argv)
{
DIR *dp;
struct dirent *de;
struct stat sb;
int j;
unsigned k;
#if SYS_MSDOS || SYS_OS2 || SYS_WIN32 || SYS_OS2_EMX
char save_wd[MAXPATHLEN];
#endif
/*
* When scanning a directory, we first chdir to it, mostly to make
* the scan+stat work faster, but also because some systems don't
* scan properly otherwise.
*
* MSDOS and OS/2 are a little more complicated, because each drive
* has its own current directory.
*/
#if SYS_MSDOS || SYS_OS2 || SYS_WIN32 || SYS_OS2_EMX
(void) strcpy(save_wd, dot);
if (!strcmp(".", path)) {
path = dot;
} else if (!same_drive(dot, path)) {
if (!set_drive(path))
return;
getwd(save_wd);
}
#endif
if (v_opt > 2)
printf("ScanConflicts \"%s\"\n", path);
if (set_directory(path)
&& (dp = opendir(path)) != NULL) {
while ((de = readdir(dp)) != NULL) {
register
type_t ok = 0;
int found = FALSE;
char buffer[MAXPATHLEN];
char *the_name;
char *the_NAME;
if (do_blips)
blip('.');
(void) sprintf(buffer, "%.*s", (int) NAMLEN(de), de->d_name);
the_name = MakeString(DOS_upper(buffer));
the_NAME = ToCompare(the_name);
/* If arguments are given, restrict search to them */
if (argc > optind) {
for (j = optind; j < argc; j++) {
if (SameName(argv[j], the_name)) {
found = TRUE;
break;
}
}
if (!found)
continue;
}
/* Verify that the name is a file, and executable */
if (stat(the_name, &sb) < 0)
continue;
if ((sb.st_mode & S_IFMT) != S_IFREG)
continue;
#if SYS_UNIX || SYS_OS2 || SYS_OS2_EMX
if (access(the_name, acc_mask) < 0)
continue;
ok = 1;
#endif
if (FileTypes != 0) {
if ((ok = LookupType(the_name)) == 0)
continue;
}
/* Find the name in our array of all names */
found = FALSE;
for (k = 0; k < total; k++) {
if (SameName(inpath[k].ip_NAME, the_NAME)) {
FoundNode(&inpath[k], inx);
found = TRUE;
break;
}
}
/* If not there, add it */
if (found) {
if (the_NAME != the_name) {
FreeString(the_NAME);
}
} else {
if (!(total & CHUNK)) {
size_t need = (((total * 3) / 2) | CHUNK) + 1;
if (inpath != 0)
inpath = TypeRealloc(INPATH, inpath, need);
else
inpath = TypeAlloc(INPATH, need);
}
j = (int) total++;
inpath[j].ip_name = the_name;
inpath[j].ip_NAME = the_NAME;
inpath[j].node = TypeAlloc(NODE, path_len);
FoundNode(&inpath[j], inx);
}
if (v_opt > 2) {
(void) printf("%c %s%c%s\n",
found ? '+' : '*',
path, PATHNAME_SEP, buffer);
}
}
(void) closedir(dp);
}
#if SYS_MSDOS || SYS_OS2 || SYS_WIN32 || SYS_OS2_EMX
if (strcmp(dot, save_wd)) {
chdir(save_wd);
}
#endif
(void) set_directory(dot);
}
