bool SxeEdit::operator<(const SxeEdit &other) const {
// Can't compare edits to different records
if(rid() != other.rid()) {
qDebug(QString("Comparing SxeEdits to %1 an %2.").arg(rid()).arg(other.rid()).toAscii());
return false;
}
if(type() == other.type()) {
// Only Record edits can be unequal with other edits of the same type
if(type() == SxeEdit::Record) {
const SxeRecordEdit* thisp = dynamic_cast<const SxeRecordEdit*>(this);
const SxeRecordEdit* otherp = dynamic_cast<const SxeRecordEdit*>(&other);
return (thisp->version() < otherp->version());
}
return false;
} else {
// New < Record, Record < Remove
if(type() == SxeEdit::New) return true;
if(other.type() == SxeEdit::Remove) return true;
return false;
}
}
std::wstring Hyperlink::GetPathFromId(OOX::IFileContainer* pRels, const std::wstring & rId)const
{
if (rId.empty()) return L"";
OOX::RId rid(rId);
std::wstring sLink = L"";
if (pRels != NULL)
{
smart_ptr<OOX::HyperLink> p = pRels->Get<OOX::HyperLink>(rid);
if (p.is_init())
sLink = p->Uri().m_strFilename;
}
if(sLink.empty())
{
if(parentFileIs<FileContainer>())
sLink = parentFileAs<FileContainer>().GetLinkFromRId(rid);
}
XmlUtils::replace_all(sLink, L"\\", L"/");
XmlUtils::replace_all(sLink, L"//", L"/");
XmlUtils::replace_all(sLink, L"http:/", L"http://");
XmlUtils::replace_all(sLink, L"https:/",L"https://");
XmlUtils::replace_all(sLink, L"ftp:/", L"ftp://");
XmlUtils::replace_all(sLink, L"file:/", L"file://");
return sLink;
}
bool ridc( FILE *fp,uchar correctID )
{
uchar id=rid(fp);
if(id!=correctID)
error("Expected id %i, read %i\n",correctID,id);
return id==correctID;
}
StringData ObjectWrapper::Key::toStringData(JSContext* cx, JSStringWrapper* jsstr) {
if (_type == Type::Field) {
return _field;
}
if (_type == Type::Index) {
*jsstr = JSStringWrapper(_idx);
return jsstr->toStringData();
}
JS::RootedId rid(cx);
if (_type == Type::Id) {
rid.set(_id);
} else {
InternedStringId id(cx, _internedString);
rid.set(id);
}
if (JSID_IS_INT(rid)) {
*jsstr = JSStringWrapper(JSID_TO_INT(rid));
return jsstr->toStringData();
}
if (JSID_IS_STRING(rid)) {
*jsstr = JSStringWrapper(cx, JSID_TO_STRING(rid));
return jsstr->toStringData();
}
uasserted(ErrorCodes::BadValue, "Couldn't convert key to String");
}
CString Hyperlink::GetFullHyperlinkName()const
{
if(id.IsInit() && *id != _T(""))
{
OOX::RId rid(*id);
CString sLink = _T("");
if(parentFileIs<Slide>())
sLink = parentFileAs<Slide>().GetFullHyperlinkNameFromRId(rid);
else if(parentFileIs<SlideLayout>())
sLink = parentFileAs<SlideLayout>().GetFullHyperlinkNameFromRId(rid);
else if(parentFileIs<SlideMaster>())
sLink = parentFileAs<SlideMaster>().GetFullHyperlinkNameFromRId(rid);
else if(parentFileIs<Theme>())
sLink = parentFileAs<Theme>().GetFullHyperlinkNameFromRId(rid);
sLink.Replace(TCHAR('\\'), TCHAR('/'));
sLink.Replace(_T("//"), _T("/"));
sLink.Replace(_T("http:/"), _T("http://"));
sLink.Replace(_T("https:/"), _T("https://"));
sLink.Replace(_T("ftp:/"), _T("ftp://"));
sLink.Replace(_T("file:/"), _T("file://"));
return sLink;
}
return _T("");
}
void MeterSML::_parse(sml_list *entry, Reading *rd) {
//int unit = (entry->unit) ? *entry->unit : 0;
int scaler = (entry->scaler) ? *entry->scaler : 1;
rd->value(sml_value_to_double(entry->value) * pow(10, scaler));
Obis obis((unsigned char)entry->obj_name->str[0],
(unsigned char)entry->obj_name->str[1],
(unsigned char)entry->obj_name->str[2],
(unsigned char)entry->obj_name->str[3],
(unsigned char)entry->obj_name->str[4],
(unsigned char)entry->obj_name->str[5]);
ReadingIdentifier *rid(new ObisIdentifier(obis));
rd->identifier(rid);
// TODO handle SML_TIME_SEC_INDEX or time by SML File/Message
struct timeval tv;
if (entry->val_time) { /* use time from meter */
tv.tv_sec = *entry->val_time->data.timestamp;
tv.tv_usec = 0;
}
else {
gettimeofday(&tv, NULL); /* use local time */
}
rd->time(tv);
}
void RepeatingBulkRound::ProcessDataBase(const Id &from, const QByteArray &data)
{
QByteArray payload;
if(!Verify(from, data, payload)) {
throw QRunTimeError("Invalid signature or data");
}
if(_state == Offline) {
throw QRunTimeError("Should never receive a message in the bulk"
" round while offline.");
}
QDataStream stream(payload);
int mtype;
QByteArray round_id;
uint phase;
stream >> mtype >> round_id >> phase;
MessageType msg_type = (MessageType) mtype;
Id rid(round_id);
if(rid != GetRoundId()) {
throw QRunTimeError("Not this round: " + rid.ToString() + " " +
GetRoundId().ToString());
}
if(_state == Shuffling) {
_log.Pop();
_offline_log.Append(data, from);
return;
}
if(_phase != phase) {
if(_phase == phase - 1 && _state == DataSharing) {
_log.Pop();
_offline_log.Append(data, from);
return;
} else {
throw QRunTimeError("Received a message for phase: " +
QString::number(phase) + ", while in phase: " +
QString::number(_phase));
}
} else if(_state == PhasePreparation) {
_log.Pop();
_offline_log.Append(data, from);
return;
}
switch(msg_type) {
case BulkData:
HandleBulkData(stream, from);
break;
default:
throw QRunTimeError("Unknown message type");
}
}
void SxeRecord::apply(QDomDocument &doc, SxeEdit* edit, bool importing) {
if(edit->rid() == rid()) {
if((edit->type() == SxeEdit::New && applySxeNewEdit(doc, dynamic_cast<const SxeNewEdit*>(edit)))
|| (edit->type() == SxeEdit::Remove && applySxeRemoveEdit(dynamic_cast<const SxeRemoveEdit*>(edit)))
|| (edit->type() == SxeEdit::Record && applySxeRecordEdit(dynamic_cast<const SxeRecordEdit*>(edit), importing))) {
edits_ += edit;
}
} else {
qDebug(QString("Tried to apply an edit meant for %1 to %2.").arg(edit->rid()).arg(rid()).toAscii());
}
}
void SxeRecord::apply(QDomDocument &doc, SxeEdit* edit) {
if(edit->rid() == rid()) {
if(edit->type() == SxeEdit::New)
applySxeNewEdit(doc, dynamic_cast<SxeNewEdit*>(edit));
else if (edit->type() == SxeEdit::Remove)
applySxeRemoveEdit(dynamic_cast<SxeRemoveEdit*>(edit));
else if (edit->type() == SxeEdit::Record)
applySxeRecordEdit(dynamic_cast<SxeRecordEdit*>(edit));
} else {
qDebug("Tried to apply an edit meant for %s to %s.", qPrintable(edit->rid()), qPrintable(rid()));
}
}
bool SxeEdit::overridenBy(const SxeEdit &e) const {
if(e.rid() == rid()) {
if(e.type() == SxeEdit::Remove)
return true;
else if(type() == SxeEdit::Record && e.type() == SxeEdit::Record) {
const SxeRecordEdit* ep = dynamic_cast<const SxeRecordEdit*>(&e);
const SxeRecordEdit* tp = dynamic_cast<const SxeRecordEdit*>(this);
return (ep->version() <= tp->version());
}
}
return false;
}
void ribo_profile::sailfish_parser(const transcript_info& tinfo, const char* sf_fname, double abundance_cutoff)
{
rid_t pid(0);
ifstream ifile(sf_fname);
while(ifile.peek() == '#'){
string line;
getline(ifile,line);
}
string word, tid;
int i(0);
double tpm(0), total_abundance(0);
while(ifile >> word) {
++i;
// 1st column: transcript ID
if (i==1) {
tid = word;
// // parse Gencode transcript ID to get the actural ID
// size_t id(word.find('|'));
// if (id!= word.npos)
// tid = word.substr(0,id);
// else
// tid = word;
}
// 3rd column: transcript abundance (tpm: transcript per million)
else if (i==3) {
try { tpm = std::stod(word); }
catch (const std::out_of_range& oor) { tpm = 0; }
ifile.ignore(numeric_limits<streamsize>::max(), '\n');
i = 0;
if (tpm <= abundance_cutoff) continue;
rid_t rid(tinfo.get_refID(tid));
if (rid == tinfo.total_count()) continue;
int tlen(tinfo.tlen(rid));
// denominator for computing relative transcript abundance per nucleotide
total_abundance += tpm * tlen ;
// initialize profile list
vector<double> count(tlen,0);
profile.emplace_back(tprofile{0, count, tpm});
refID2pID[rid] = pid++;
include_abundant_transcript(rid);
}
}
ifile.close();
// normalize abundance
for (size_t t = 0; t!=profile.size(); ++t)
profile[t].tot_abundance /= total_abundance;
}
RC QL_ProjNode::GetNext(RM_Record &rec) {
RM_Record record;
if (prevNode.GetNext(record) == QL_EOF) {
return QL_EOF;
}
int i;
int base = 0;
char *prevRecord = record.GetContent();
//投影操作
for(i = 0; i < nAttrInfos; i++) {
memcpy(buffer + base, prevRecord + offsetInPrev[i], attrInfos[i].attrLength);
base += attrInfos[i].attrLength;
}
RID rid(-1, -1);
rec = RM_Record(buffer, rid, tupleLength);
return 0;
}
void BulkRound::ProcessDataBase(const Id &from, const QByteArray &data)
{
QByteArray payload;
if(!Verify(from, data, payload)) {
throw QRunTimeError("Invalid signature or data");
}
if(_state == Offline) {
throw QRunTimeError("Should never receive a message in the bulk"
" round while offline.");
}
QDataStream stream(payload);
int mtype;
QByteArray round_id;
stream >> mtype >> round_id;
MessageType msg_type = (MessageType) mtype;
Id rid(round_id);
if(rid != GetRoundId()) {
throw QRunTimeError("Not this round: " + rid.ToString() + " " +
GetRoundId().ToString());
}
if(_state == Shuffling) {
_log.Pop();
_offline_log.Append(data, from);
return;
}
switch(msg_type) {
case BulkData:
HandleBulkData(stream, from);
break;
case LoggedBulkData:
HandleLoggedBulkData(stream, from);
break;
case AggregatedBulkData:
HandleAggregatedBulkData(stream, from);
break;
default:
throw QRunTimeError("Unknown message type");
}
}
void ribo_profile::express_parser(const transcript_info& tinfo, const char* ep_fname, double abundance_cutoff)
{
rid_t pid(0);
ifstream ifile(ep_fname);
// first line is header description, disgarded.
ifile.ignore(numeric_limits<streamsize>::max(), '\n');
string word, tid;
int i(0);
double fpkm(0), total_abundance(0);
while (ifile >> word) {
++i;
// 2nd column: transcript ID
if (i==2) {
tid = word;
// // parse Gencode transcript ID to get the actural ID
// size_t id(word.find('|'));
// if (id!= word.npos)
// tid = word.substr(0,id);
// else
// tid = word;
}
// 11th column: transcript abundance
else if (i==11) {
try { fpkm = std::stod(word); }
catch (const std::out_of_range& oor) { fpkm = 0; }
ifile.ignore(numeric_limits<streamsize>::max(), '\n');
i = 0;
if (fpkm <= abundance_cutoff) continue;
rid_t rid(tinfo.get_refID(tid));
if (rid == tinfo.total_count()) continue;
int tlen(tinfo.tlen(rid));
total_abundance += fpkm;
// initialize profile list
vector<double> count(tlen,0);
profile.emplace_back(tprofile{0, count, fpkm});
refID2pID[rid] = pid++;
include_abundant_transcript(rid);
}
}
ifile.close();
// normalize abundance
for (size_t t = 0; t!=profile.size(); ++t)
profile[t].tot_abundance /= total_abundance;
}
ObjectWrapper::WriteFieldRecursionFrame::WriteFieldRecursionFrame(JSContext* cx,
JSObject* obj,
BSONObjBuilder* parent,
StringData sd)
: thisv(cx, obj), ids(cx, JS::IdVector(cx)) {
bool isArray = false;
if (parent) {
if (!JS_IsArrayObject(cx, thisv, &isArray)) {
throwCurrentJSException(
cx, ErrorCodes::JSInterpreterFailure, "Failure to check object is an array");
}
subbob.emplace(isArray ? parent->subarrayStart(sd) : parent->subobjStart(sd));
}
if (isArray) {
uint32_t length;
if (!JS_GetArrayLength(cx, thisv, &length)) {
throwCurrentJSException(
cx, ErrorCodes::JSInterpreterFailure, "Failure to get array length");
}
if (!ids.reserve(length)) {
throwCurrentJSException(
cx, ErrorCodes::JSInterpreterFailure, "Failure to reserve array");
}
JS::RootedId rid(cx);
for (uint32_t i = 0; i < length; i++) {
rid.set(INT_TO_JSID(i));
ids.infallibleAppend(rid);
}
} else {
if (!JS_Enumerate(cx, thisv, &ids)) {
throwCurrentJSException(
cx, ErrorCodes::JSInterpreterFailure, "Failure to enumerate object");
}
}
if (getScope(cx)->getProto<BSONInfo>().instanceOf(thisv)) {
std::tie(originalBSON, altered) = BSONInfo::originalBSON(cx, thisv);
}
}
void RestraintCache::load_cache(const kernel::ParticlesTemp &particle_ordering,
RMF::HDF5::ConstGroup group) {
ParticleIndex particle_index = get_particle_index(particle_ordering);
base::map<RestraintID, kernel::Restraint *> index;
for (KnownRestraints::const_iterator it = known_restraints_.begin();
it != known_restraints_.end(); ++it) {
index[get_restraint_id(particle_index, it->second,
restraint_index_.find(it->first)->second)] =
it->first;
}
kernel::RestraintsTemp restraints;
for (unsigned int i = 0; i < group.get_number_of_children(); ++i) {
RMF::HDF5::ConstGroup ch = group.get_child_group(i);
int restraint_index =
ch.get_attribute<RMF::HDF5::IndexTraits>("restraint")[0];
RMF::HDF5::Indexes particle_indexes =
ch.get_attribute<RMF::HDF5::IndexTraits>("particles");
RestraintID rid(restraint_index,
base::ConstVector<unsigned int>(Ints(
particle_indexes.begin(), particle_indexes.end())));
kernel::Restraint *r = index.find(rid)->second;
restraints.push_back(r);
IMP_LOG_TERSE("Matching " << Showable(r) << " with " << ch.get_name()
<< std::endl);
}
Orders orders = get_orders(known_restraints_, restraints, particle_ordering);
for (unsigned int i = 0; i < group.get_number_of_children(); ++i) {
RMF::HDF5::ConstGroup ch = group.get_child_group(i);
RMF::HDF5::FloatConstDataSet1D scores =
ch.get_child_float_data_set_1d("scores");
RMF::HDF5::IntConstDataSet2D assignments =
ch.get_child_int_data_set_2d("assignments");
for (unsigned int j = 0; j < scores.get_size()[0]; ++j) {
double s = scores.get_value(RMF::HDF5::DataSetIndex1D(j));
RMF::HDF5::Ints rw = assignments.get_row(RMF::HDF5::DataSetIndex1D(j));
Ints psit(rw.begin(), rw.end());
Assignment ass = orders[i].get_subset_ordered(psit);
cache_.insert(Key(restraints[i], ass), s);
}
}
validate();
}
bool
RegisterRawInput(HWND hwnd, bool enable)
{
nsTArray<RAWINPUTDEVICE> rid(ArrayLength(kUsagePages));
rid.SetLength(ArrayLength(kUsagePages));
for (unsigned i = 0; i < rid.Length(); i++) {
rid[i].usUsagePage = kUsagePages[i].usagePage;
rid[i].usUsage = kUsagePages[i].usage;
rid[i].dwFlags =
enable ? RIDEV_EXINPUTSINK | RIDEV_DEVNOTIFY : RIDEV_REMOVE;
rid[i].hwndTarget = hwnd;
}
if (!RegisterRawInputDevices(rid.Elements(), rid.Length(),
sizeof(RAWINPUTDEVICE))) {
return false;
}
return true;
}
rule_matcher::rule_matcher(vm::program *prog)
{
#ifdef USE_RULE_COUNTING
predicate_count.resize(prog->num_predicates());
rules.resize(prog->num_rules());
fill(predicate_count.begin(), predicate_count.end(), 0);
rule_id rid(0);
for(rule_vector::iterator it(rules.begin()), end(rules.end());
it != end;
it++, rid++)
{
rule_matcher_obj& obj(*it);
obj.ignore = prog->get_rule(rid)->as_persistent();
obj.total_have = 0;
obj.total_needed = prog->get_rule(rid)->num_predicates();
}
#endif
}
void EnterJs(){
HandleScope store;
int rt = -1;
if(_env!=0) return;
_env = new JsEnv;
_threadFlag = 1;
*_env->cont = Context::New(NULL,ObjectTemplate::New());
(*_env->cont)->Enter();
Handle<Object> glb = GetGlobal();
LoadBase();
LoadConsole(glb);
LoadAPICall(glb);
//给全局添加stack只读变量.
glb->Set(String::New("Stack"),Object::New(),ReadOnly);
//加载基本的JS库文件
cs::ResID rid(IDR_JS_BASE);
LoadJsRes(rid,L"IDR_JS_BASE");
//加载JS库里面的纯js类或函数, 供C++使用.
LoadLibStruct(glb);
}
RC QL_JoinNode::GetNext(RM_Record &rec) {
RM_Record leftRec;
RM_Record rightRec;
while(true) {
if (bRightNodeEOF) {
if (lSubNode.GetNext(leftRec) == QL_EOF)
return QL_EOF;
memcpy(buffer, leftRec.GetContent(), leftRec.GetRecordSize());
bRightNodeEOF = false;
}
if (rSubNode.GetNext(rightRec) == QL_EOF) {
bRightNodeEOF = true;
rSubNode.Reset();
continue;
}
memcpy(buffer + lSubNode.GetTupleLength(), rightRec.GetContent(), rSubNode.GetTupleLength());
RID rid(-1, -1);
rec = RM_Record(buffer, rid, tupleLength);
return 0;
}
}
CItemTypeDef * CWorld::GetTerrainItemTypeDef( DWORD dwTerrainIndex )
{
ADDTOCALLSTACK("CWorld::GetTerrainItemTypeDef");
CResourceDef * pRes = NULL;
if ( g_World.m_TileTypes.IsValidIndex( dwTerrainIndex ) )
{
pRes = g_World.m_TileTypes[dwTerrainIndex];
}
if ( !pRes )
{
RESOURCE_ID rid( RES_TYPEDEF, 0 );
pRes = g_Cfg.ResourceGetDef( rid );
}
ASSERT( pRes );
CItemTypeDef * pItemTypeDef = dynamic_cast <CItemTypeDef*> (pRes);
ASSERT( pItemTypeDef );
return( pItemTypeDef );
}
bool GTO2Slater::put(xmlNodePtr cur) {
cur = cur->children;
while(cur != NULL) {
string cname((const char*)(cur->name));
if(cname == "grid")
gridPtr = cur;
else if(cname == "basisGroup") {
string rid("invalid");
string rtype("Gaussian");
string norm("no");
int l=0;
OhmmsAttributeSet inAttrib;
inAttrib.add(rid,"rid");
inAttrib.add(l,"l");
inAttrib.add(rtype,"type");
inAttrib.add(norm,"normalized");
inAttrib.put(cur);
if(rtype == "Gaussian" && l == 0) { //pick only S
//if Ngto==1, don't do it
if(norm == "yes")
Normalized=true;
else
Normalized=false;
map<string,xmlNodePtr>::iterator it(sPtr.find(rid));
if(it == sPtr.end()) {
sPtr[rid]=cur;
}
}
}
cur=cur->next;
}
if(sPtr.empty())
return false;
return
true;
}
rule_matcher::rule_matcher(void)
{
predicate_count = mem::allocator<pred_count>().allocate(theProgram->num_predicates());
memset(predicate_count, 0, theProgram->num_predicates() * sizeof(pred_count));
rules = mem::allocator<utils::byte>().allocate(theProgram->num_rules());
memset(rules, 0, sizeof(utils::byte) * theProgram->num_rules());
bitmap::create(active_bitmap, theProgram->num_rules_next_uint());
bitmap::create(dropped_bitmap, theProgram->num_rules_next_uint());
active_bitmap.clear(theProgram->num_rules_next_uint());
dropped_bitmap.clear(theProgram->num_rules_next_uint());
#ifndef NDEBUG
for(rule_id rid(0); rid < theProgram->num_rules(); ++rid)
{
rule *rl(theProgram->get_rule(rid));
assert(rl->num_predicates() <= 255);
}
#endif
bitmap::create(predicates, theProgram->num_predicates_next_uint());
clear_predicates();
}
// MUST BE CUSTOMIZED FOR EACH RuleSet
void construct_ruleset_adm(const simpleString & s,Source & source) {
asStringGB orderName;
list<Polynomial> L;
Source so(source.inputNamedFunction("List"));
so >> orderName;
GBInputSpecial(L,so);
AdmissibleOrder * p;
bool valid = StorageGet(order_storage,orderName.value(),p);
if(valid) {
RuleSet * result = new AdmRuleSet(*p);
typedef list<Polynomial>::const_iterator LI;
LI w = L.begin(), e = L.end();
int i = 1;
while(w!=e) {
RuleID rid(*w,i);
result->insert(rid);
++w;++i;
};
GBStream << "Constructing the ruleset with name " << s << '\n';
result->print(GBStream);
GBStream << "end\n";
ruleset_storage.insert(make_pair(s,result));
} else DBG();
};