bool CBioseq_Handle::ContainsSegment(CSeq_id_Handle id,
size_t resolve_depth,
EFindSegment limit_flag) const
{
CBioseq_Handle h = GetScope().GetBioseqHandle(id);
CConstRef<CSynonymsSet> syns;
if ( h ) {
syns = h.GetSynonyms();
}
SSeqMapSelector sel;
sel.SetFlags(CSeqMap::fFindRef);
if ( limit_flag == eFindSegment_LimitTSE ) {
sel.SetLimitTSE(GetTopLevelEntry());
}
sel.SetResolveCount(resolve_depth);
CSeqMap_CI it = GetSeqMap().BeginResolved(&GetScope(), sel);
for ( ; it; ++it) {
if ( syns ) {
if ( syns->ContainsSynonym(it.GetRefSeqid()) ) {
return true;
}
}
else {
if (it.GetRefSeqid() == id) {
return true;
}
}
}
return false;
}
void CSeqMap_CI::x_Push(const CConstRef<CSeqMap>& seqMap,
const CTSE_Handle& tse,
TSeqPos from, TSeqPos length,
bool minusStrand,
TSeqPos pos)
{
TSegmentInfo push;
push.m_SeqMap = seqMap;
push.m_TSE = tse;
push.m_LevelRangePos = from;
push.m_LevelRangeEnd = from + length;
if (push.m_LevelRangeEnd < push.m_LevelRangePos) {
// Detect (from + length) overflow
NCBI_THROW(CSeqMapException, eDataError,
"Sequence position overflow");
}
push.m_MinusStrand = minusStrand;
TSeqPos findOffset = !minusStrand? pos: length - 1 - pos;
push.m_Index = seqMap->x_FindSegment(from + findOffset, GetScope());
if ( push.m_Index == size_t(-1) ) {
if ( !m_Stack.empty() ) {
return;
}
push.m_Index = !minusStrand?
seqMap->x_GetLastEndSegmentIndex():
seqMap->x_GetFirstEndSegmentIndex();
}
else {
_ASSERT(push.m_Index > seqMap->x_GetFirstEndSegmentIndex() &&
push.m_Index < seqMap->x_GetLastEndSegmentIndex());
if ( pos >= length ) {
if ( !minusStrand ) {
if ( seqMap->x_GetSegmentPosition(push.m_Index, 0) <
push.m_LevelRangeEnd ) {
++push.m_Index;
_ASSERT(seqMap->x_GetSegmentPosition(push.m_Index, 0) >=
push.m_LevelRangeEnd);
}
}
else {
if ( seqMap->x_GetSegmentEndPosition(push.m_Index, 0) >
push.m_LevelRangePos ) {
--push.m_Index;
_ASSERT(seqMap->x_GetSegmentEndPosition(push.m_Index, 0) <=
push.m_LevelRangePos);
}
}
}
}
// update length of current segment
seqMap->x_GetSegmentLength(push.m_Index, GetScope());
m_Stack.push_back(push);
// update position
m_Selector.m_Position += x_GetTopOffset();
// update length
m_Selector.m_Length = push.x_CalcLength();
}
void CamShiftPlugin::OnOK()
{
wxBeginBusyCursor();
if (!GetScope())
ProcessImage(cm->book[cm->GetPos()], cm->GetPos());
else{
FetchParams();
ImagePlus *oimg;
CvRect orect, searchwin;
CvPoint ocenter;
oimg = cm->book[0];
int numContours = (int) oimg->contourArray.size();
for (int i=1; i<cm->GetFrameCount(); i++)
cm->book[i]->CloneContours(oimg);
int frameCount = cm->GetFrameCount();
CreateProgressDlg(numContours*frameCount);
bool cont=true;
for (int j=0; j<numContours && cont; j++){
for (int i=1; i<frameCount && (cont=progressDlg->Update(j*frameCount+i, wxString::Format("Cell %d of %d, Frame %d of %d", j+1,numContours, i+1, frameCount))); i++){
ProcessStatic(j, cm->book[i], cm->book[useFirst ? 0 : i-1], hsizes, criteria,
planes, hist, backproject, orect, ocenter, searchwin, rotation, shift, i>1);
}
}
DestroyProgressDlg();
}
cm->ReloadCurrentFrameContours(true, false);
wxEndBusyCursor();
}
bool TagEntry::IsConstructor() const
{
if(GetKind() != wxT("function") && GetKind() != wxT("prototype"))
return false;
return GetName() == GetScope();
}
void CSeqMap_CI::x_Select(const CConstRef<CSeqMap>& seqMap,
const SSeqMapSelector& selector,
TSeqPos pos)
{
m_Selector = selector;
if ( m_Selector.m_Length == kInvalidSeqPos ) {
TSeqPos len = seqMap->GetLength(GetScope());
len -= min(len, m_Selector.m_Position);
m_Selector.m_Length = len;
}
if ( pos < m_Selector.m_Position ) {
pos = m_Selector.m_Position;
}
else if ( pos > m_Selector.m_Position + m_Selector.m_Length ) {
pos = m_Selector.m_Position + m_Selector.m_Length;
}
x_Push(seqMap, m_Selector.m_TopTSE,
m_Selector.m_Position,
m_Selector.m_Length,
m_Selector.m_MinusStrand,
pos - m_Selector.m_Position);
while ( !x_Found() && GetPosition() < m_SearchEnd ) {
if ( !x_Push(pos - m_Selector.m_Position) ) {
x_SettleNext();
break;
}
}
}
void PHPEntityVariable::Store(wxSQLite3Database& db)
{
// we keep only the function arguments in the databse and globals
if(IsFunctionArg() || IsMember()) {
try {
wxSQLite3Statement statement =
db.PrepareStatement("INSERT OR REPLACE INTO VARIABLES_TABLE VALUES (NULL, "
":SCOPE_ID, :FUNCTION_ID, :NAME, :FULLNAME, :SCOPE, :TYPEHINT, "
":FLAGS, :DOC_COMMENT, :LINE_NUMBER, :FILE_NAME)");
statement.Bind(statement.GetParamIndex(":SCOPE_ID"), IsMember() ? Parent()->GetDbId() : wxLongLong(-1));
statement.Bind(statement.GetParamIndex(":FUNCTION_ID"),
IsFunctionArg() ? Parent()->GetDbId() : wxLongLong(-1));
statement.Bind(statement.GetParamIndex(":NAME"), GetShortName());
statement.Bind(statement.GetParamIndex(":FULLNAME"), GetFullName());
statement.Bind(statement.GetParamIndex(":SCOPE"), GetScope());
statement.Bind(statement.GetParamIndex(":TYPEHINT"), GetTypeHint());
statement.Bind(statement.GetParamIndex(":FLAGS"), (int)GetFlags());
statement.Bind(statement.GetParamIndex(":DOC_COMMENT"), GetDocComment());
statement.Bind(statement.GetParamIndex(":LINE_NUMBER"), GetLine());
statement.Bind(statement.GetParamIndex(":FILE_NAME"), GetFilename().GetFullPath());
statement.ExecuteUpdate();
SetDbId(db.GetLastRowId());
} catch(wxSQLite3Exception& exc) {
wxUnusedVar(exc);
}
}
}
CConstRef<CSynonymsSet> CBioseq_Handle::GetSynonyms(void) const
{
if ( !*this ) {
return CConstRef<CSynonymsSet>();
}
return GetScope().GetSynonyms(*this);
}
void NewScalar(const char *scope, const char *lval, const char *rval, enum cfdatatype dt)
{
Rval rvald;
Scope *ptr;
CfDebug("NewScalar(%s,%s,%s)\n", scope, lval, rval);
ptr = GetScope(scope);
if (ptr == NULL)
{
CfOut(cf_error, "", "!! Attempt to add variable \"%s\" to non-existant scope \"%s\" - ignored", lval, scope);
return;
}
// Newscalar allocates memory through NewAssoc
if (GetVariable(scope, lval, &rvald) != cf_notype)
{
DeleteScalar(scope, lval);
}
/*
* We know AddVariableHash does not change passed Rval structure or its
* contents, but we have no easy way to express it in C type system, hence cast.
*/
AddVariableHash(scope, lval, (Rval) {(char *) rval, CF_SCALAR}, dt, NULL, 0);
}
TAstNode::ValueReturned TAstNodeForSentence::Execute() const
{
auto secondChild = m_firstChild->GetSibling();
auto thirdChild = secondChild->GetSibling();
auto firstValue = m_firstChild->Execute();
auto sencondValue = secondChild->Execute();
//auto thirdValue = thirdChild->Execute();
auto scope = GetScope();
auto name = m_firstChild->GetFirstChild()->GetToken()->Name();
auto type = TVariateManager::GetInstance()->GetVariateSrollUp(scope, name)->GetType();
UpdateValue(type, scope, name, firstValue.value);
if (GetValue(type, scope, name)<sencondValue.value)
{
Context::interpreterContext.SetNextNode(thirdChild->GetSibling().get());
}
else
{
Context::interpreterContext.SetNextNode(FindNextValidNode());
}
return ValueReturned{ 0, SYMBOL_TYPE::TYPE_VOID };
}
int TagEntry::Store(wxSQLite3Statement& insertPerepareStmnt)
{
// If this node is a dummy, (IsOk() == false) we dont insert it to database
if( !IsOk() )
return TagOk;
try
{
// see TagsDatabase::GetInsertOneStatement() for the order of binding
insertPerepareStmnt.Bind(1, GetParentId());
insertPerepareStmnt.Bind(2, GetName());
insertPerepareStmnt.Bind(3, GetFile());
insertPerepareStmnt.Bind(4, GetLine());
insertPerepareStmnt.Bind(5, GetKind());
insertPerepareStmnt.Bind(6, GetAccess());
insertPerepareStmnt.Bind(7, GetSignature());
insertPerepareStmnt.Bind(8, GetPattern());
insertPerepareStmnt.Bind(9, GetParent());
insertPerepareStmnt.Bind(10, GetInherits());
insertPerepareStmnt.Bind(11, GetPath());
insertPerepareStmnt.Bind(12, GetTyperef());
insertPerepareStmnt.Bind(13, GetScope());
insertPerepareStmnt.ExecuteUpdate();
insertPerepareStmnt.Reset();
}
catch(wxSQLite3Exception& exc)
{
if(exc.ErrorCodeAsString(exc.GetErrorCode()) == wxT("SQLITE_CONSTRAINT"))
return TagExist;
wxLogMessage(exc.GetMessage());
return TagError;
}
return TagOk;
}
int TagEntry::Update(wxSQLite3Statement& updatePerepareStmnt)
{
// If this node is a dummy, (IsOk() == false) we dont update it to database
if( !IsOk() )
return TagOk;
try
{
// see TagsDatabase::GetUpdateOneStatement() function for the order of binding
updatePerepareStmnt.Bind(1, GetParentId());
updatePerepareStmnt.Bind(2, GetName());
updatePerepareStmnt.Bind(3, GetFile());
updatePerepareStmnt.Bind(4, GetLine());
updatePerepareStmnt.Bind(5, GetAccess());
updatePerepareStmnt.Bind(6, GetPattern());
updatePerepareStmnt.Bind(7, GetParent());
updatePerepareStmnt.Bind(8, GetInherits());
updatePerepareStmnt.Bind(9, GetTyperef());
updatePerepareStmnt.Bind(10, GetScope());
updatePerepareStmnt.Bind(11, GetKind());
updatePerepareStmnt.Bind(12, GetSignature());
updatePerepareStmnt.Bind(13, GetPath());
updatePerepareStmnt.ExecuteUpdate();
updatePerepareStmnt.Reset();
}
catch(wxSQLite3Exception& exc)
{
wxLogMessage(exc.GetMessage());
return TagError;
}
return TagOk;
}
CSeq_id_Handle CBioseq_Handle::GetAccessSeq_id_Handle(void) const
{
CSeq_id_Handle id = GetSeq_id_Handle();
// First try original id
if ( id ) {
return id;
}
// Then try to find gi
ITERATE ( TId, it, GetId() ) {
if ( it->IsGi() ) {
CBioseq_Handle bh =
GetScope().GetBioseqHandleFromTSE(*it, GetTSE_Handle());
if ( bh == *this ) {
id = *it;
_ASSERT(id);
return id;
}
}
}
// Then try to find accession
ITERATE ( TId, it, GetId() ) {
if ( !it->IsGi() && it->GetSeqId()->GetTextseq_Id() ) {
CBioseq_Handle bh =
GetScope().GetBioseqHandleFromTSE(*it, GetTSE_Handle());
if ( bh == *this ) {
id = *it;
_ASSERT(id);
return id;
}
}
}
// Then try to find any other id
ITERATE ( TId, it, GetId() ) {
if ( !it->IsGi() && !it->GetSeqId()->GetTextseq_Id() ) {
CBioseq_Handle bh =
GetScope().GetBioseqHandleFromTSE(*it, GetTSE_Handle());
if ( bh == *this ) {
id = *it;
_ASSERT(id);
return id;
}
}
}
NCBI_THROW(CObjMgrException, eOtherError,
"CBioseq_Handle::GetAccessSeq_id_Handle "
"can not find seq-id to access this bioseq");
}
NS_IMETHODIMP
HTMLTableCellElement::GetScope(nsAString& aScope)
{
DOMString scope;
GetScope(scope);
scope.ToString(aScope);
return NS_OK;
}
NS_IMETHODIMP
HTMLTableCellElement::GetScope(nsAString& aScope)
{
nsString scope;
GetScope(scope);
aScope = scope;
return NS_OK;
}
bool CSeqMap_CI::x_RefTSEMatch(const CSeqMap::CSegment& seg) const
{
_ASSERT(m_Selector.x_HasLimitTSE());
_ASSERT(CSeqMap::ESegmentType(seg.m_SegType) == CSeqMap::eSeqRef);
CSeq_id_Handle id = CSeq_id_Handle::
GetHandle(x_GetSeqMap().x_GetRefSeqid(seg));
return m_Selector.x_GetLimitTSE(GetScope()).GetBioseqHandle(id);
}
// The aln_id_map argument is required because TScopeAlnStat keeps const
// reference to the id-map. So, the map needs to be returned to the caller.
CRef<TScopeAlnStats> InitAlnStats(const CAlnContainer& aligns,
auto_ptr<TScopeAlnIdMap>& aln_id_map)
{
TScopeAlnSeqIdConverter id_conv(&GetScope());
TScopeIdExtract id_extract(id_conv);
aln_id_map.reset(new TScopeAlnIdMap(id_extract, aligns.size()));
ITERATE(CAlnContainer, aln_it, aligns) {
aln_id_map->push_back(**aln_it);
}
TSeqPos CBioseq_Handle::GetBioseqLength(void) const
{
if ( IsSetInst_Length() ) {
return GetInst_Length();
}
else {
return GetSeqMap().GetLength(&GetScope());
}
}
bool CSeqMap_CI::x_TopPrev(void)
{
TSegmentInfo& top = x_GetSegmentInfo();
if ( !top.x_Move(!top.m_MinusStrand, GetScope()) ) {
m_Selector.m_Length = 0;
return false;
}
else {
m_Selector.m_Length = x_GetSegmentInfo().x_CalcLength();
m_Selector.m_Position -= m_Selector.m_Length;
return true;
}
}
void DeleteScalar(const char *scope_name, const char *lval)
{
Scope *scope = GetScope(scope_name);
if (scope == NULL)
{
return;
}
if (HashDeleteElement(scope->hashtable, lval) == false)
{
CfDebug("Attempt to delete non-existent variable %s in scope %s\n", lval, scope_name);
}
}
CRef<CDense_seg> CAlnVec::CreateConsensus(int& consensus_row,
const CSeq_id& consensus_id) const
{
CRef<CBioseq> bioseq(new CBioseq);
CRef<CDense_seg> ds = CreateConsensus(consensus_row,
*bioseq, consensus_id);
// add bioseq to the scope
CRef<CSeq_entry> entry(new CSeq_entry());
entry->SetSeq(*bioseq);
GetScope().AddTopLevelSeqEntry(*entry);
return ds;
}
void DeleteVariable(char *scope, char *id)
{
Scope *ptr = GetScope(scope);
if (ptr == NULL)
{
return;
}
if (HashDeleteElement(ptr->hashtable, id) == false)
{
CfDebug("No variable matched %s\n", id);
}
}
void ProjectVariatesXmlManager::WriteScopeVariates(QXmlStreamWriter& writer, const QString& scope, QVector<QByteArray>& variatesArray) const
{
writer.writeStartElement(scope);
for (auto& variateBytes : variatesArray)
{
auto variate = TVariateFactory::GetVariate(variateBytes);
if (variate->GetScope() == scope)
{
WriteVariate(writer, variate);
}
}
writer.writeEndElement();
}
void GUICursor::Build()
{
m_elements.clear();
BuildElements(m_elements);
SpriteRect rect;
GetScope(rect);
rect.GetFourBorders(m_renderer, m_fourBorders);
matrix4x4 mat;
Matrix4x4_set_one(&mat);
GetMatrix(&mat);
m_fourBorders.ApplyTranform(&mat);
}
void
XPCWrappedNativeProto::JSProtoObjectFinalized(js::FreeOp *fop, JSObject *obj)
{
NS_ASSERTION(obj == mJSProtoObject, "huh?");
// Map locking is not necessary since we are running gc.
// Only remove this proto from the map if it is the one in the map.
ClassInfo2WrappedNativeProtoMap* map =
GetScope()->GetWrappedNativeProtoMap(ClassIsMainThreadOnly());
if (map->Find(mClassInfo) == this)
map->Remove(mClassInfo);
GetRuntime()->GetDetachedWrappedNativeProtoMap()->Remove(this);
GetRuntime()->GetDyingWrappedNativeProtoMap()->Add(this);
mJSProtoObject.finalize(js::CastToJSFreeOp(fop)->runtime());
}
//_____________________________________________________________________________
//
void AUScope::SetNumberOfElements(UInt32 numElements)
{
if (mDelegate)
return mDelegate->SetNumberOfElements(numElements);
if (numElements > mElements.size()) {
mElements.reserve(numElements);
while (numElements > mElements.size()) {
AUElement *elem = mCreator->CreateElement(GetScope(), mElements.size());
mElements.push_back(elem);
}
} else
while (numElements < mElements.size()) {
AUElement *elem = mElements.back();
mElements.pop_back();
delete elem;
}
}
const CBioseq_Handle& CAlnVec::GetBioseqHandle(TNumrow row) const
{
TBioseqHandleCache::iterator i = m_BioseqHandlesCache.find(row);
if (i != m_BioseqHandlesCache.end()) {
return i->second;
} else {
CBioseq_Handle bioseq_handle =
GetScope().GetBioseqHandle(GetSeqId(row));
if (bioseq_handle) {
return m_BioseqHandlesCache[row] = bioseq_handle;
} else {
string errstr = string("CAlnVec::GetBioseqHandle(): ")
+ "Seq-id cannot be resolved: "
+ GetSeqId(row).AsFastaString();
NCBI_THROW(CAlnException, eInvalidSeqId, errstr);
}
}
}
void PHPEntityFunctionAlias::Store(wxSQLite3Database& db)
{
try {
wxSQLite3Statement statement = db.PrepareStatement(
"INSERT OR REPLACE INTO FUNCTION_ALIAS_TABLE VALUES(NULL, :SCOPE_ID, :NAME, :REALNAME, :FULLNAME, :SCOPE, "
":LINE_NUMBER, :FILE_NAME)");
statement.Bind(statement.GetParamIndex(":SCOPE_ID"), Parent()->GetDbId());
statement.Bind(statement.GetParamIndex(":NAME"), GetShortName());
statement.Bind(statement.GetParamIndex(":REALNAME"), GetRealname());
statement.Bind(statement.GetParamIndex(":FULLNAME"), GetFullName());
statement.Bind(statement.GetParamIndex(":SCOPE"), GetScope());
statement.Bind(statement.GetParamIndex(":LINE_NUMBER"), GetLine());
statement.Bind(statement.GetParamIndex(":FILE_NAME"), GetFilename().GetFullPath());
statement.ExecuteUpdate();
SetDbId(db.GetLastRowId());
} catch(wxSQLite3Exception& exc) {
CL_WARNING("PHPEntityFunctionAlias::Store: %s", exc.GetMessage());
}
}
void CAlnMrgApp::LoadSeqEntry(CNcbiIstream& is)
{
string se_asn_type;
{{
auto_ptr<CObjectIStream> obj_is
(CObjectIStream::Open(eSerial_AsnText, is));
se_asn_type = obj_is->ReadFileHeader();
obj_is->Close();
is.seekg(0);
}}
auto_ptr<CObjectIStream> obj_is
(CObjectIStream::Open(eSerial_AsnText, is));
if (se_asn_type == "Seq-entry") {
CRef<CSeq_entry> se (new CSeq_entry);
*obj_is >> *se;
GetScope().AddTopLevelSeqEntry(*se);
} else {
void
XPCWrappedNativeProto::JSProtoObjectFinalized(JSContext *cx, JSObject *obj)
{
NS_ASSERTION(obj == mJSProtoObject, "huh?");
// Map locking is not necessary since we are running gc.
if(IsShared())
{
// Only remove this proto from the map if it is the one in the map.
ClassInfo2WrappedNativeProtoMap* map =
GetScope()->GetWrappedNativeProtoMap(ClassIsMainThreadOnly());
if(map->Find(mClassInfo) == this)
map->Remove(mClassInfo);
}
GetRuntime()->GetDetachedWrappedNativeProtoMap()->Remove(this);
GetRuntime()->GetDyingWrappedNativeProtoMap()->Add(this);
mJSProtoObject = nsnull;
}
static void XmlExportVariables(Writer *writer, const char *scope)
{
char *filebuffer = NULL;
Rlist *rp = NULL;
Rlist *list = NULL;
/* START XML ELEMENT -- VARIABLE*-SCOPE */
XmlAttribute scope_name_attr = { "name", scope };
XmlStartTag(writer, XMLTAG_VARSCOPE, 1, scope_name_attr);
/* XML ELEMENT -- INTRO */
filebuffer = ReadTexinfoFileF("varcontexts/%s_intro.texinfo", scope);
XmlTag(writer, XMLTAG_INTRO, filebuffer, 0);
free(filebuffer);
HashToList(GetScope(scope), &list);
list = AlphaSortRListNames(list);
for (rp = list; rp != NULL; rp = rp->next)
{
/* START XML ELEMENT -- VARIABLE */
XmlAttribute var_name_attr = { "name", ScalarValue(rp) };
XmlStartTag(writer, XMLTAG_VARIABLE, 1, var_name_attr);
/* XML ELEMENT -- LONG-DESCRIPTION */
filebuffer = ReadTexinfoFileF("vars/%s_%s.texinfo", scope, ScalarValue(rp));
XmlTag(writer, XMLTAG_LONGDESCRIPTION, filebuffer, 0);
free(filebuffer);
/* END XML ELEMENT -- VARIABLE */
XmlEndTag(writer, XMLTAG_VARIABLE);
}
DeleteRlist(list);
/* END XML ELEMENT -- VARIABLE-SCOPE */
XmlEndTag(writer, XMLTAG_VARSCOPE);
}
