void MainWindow::FillRow(int row, const Variable &var) { QTableWidgetItem * item; item = new QTableWidgetItem(var.GetName()); item->setFlags(Qt::ItemIsEnabled); ui->Table->setItem(row,NAME, item); item = new QTableWidgetItem(QString("0x%1").arg(var.GetAddressOffset(),0,16)); item->setFlags(Qt::ItemIsEnabled); ui->Table->setItem(row,ADDRESS,item); item = new QTableWidgetItem(var.GetType()); item->setFlags(Qt::ItemIsEnabled); ui->Table->setItem(row,TYPE,item); item = new QTableWidgetItem(QString("%1 ms").arg(var.RefreshTime())); item->setFlags(Qt::ItemIsEnabled); ui->Table->setItem(row,PERIOD,item); item = new QTableWidgetItem(""); item->setFlags(Qt::ItemIsEnabled); ui->Table->setItem(row, VALUE, item); item = new QTableWidgetItem(""); item->setFlags(Qt::ItemIsEnabled | Qt::ItemIsEditable); ui->Table->setItem(row, MODIFY, item); item = new QTableWidgetItem(""); item->setFlags(Qt::ItemIsEnabled); ui->Table->setItem(row, FLOAT, item); }
//----------------------------------------------------------------------------- // Sets the value of an existing variable in the script. //----------------------------------------------------------------------------- void Script::SetVariable( char *name, void *value ) { // Find the variable. Variable *variable = NULL; m_variables->Iterate( true ); while( m_variables->Iterate() != NULL ) { if( strcmp( m_variables->GetCurrent()->GetName(), name ) == 0 ) { variable = m_variables->GetCurrent(); break; } } // Ensure the variable was found. if( variable == NULL ) return; // Get the variable's type. char type = variable->GetType(); // Destroy the variable. m_variables->Remove( &variable ); // Add the variable back in with the new value. AddVariable( name, type, value ); }
const CompilerType &Value::GetCompilerType() { if (!m_compiler_type.IsValid()) { switch (m_context_type) { case eContextTypeInvalid: break; case eContextTypeRegisterInfo: break; // TODO: Eventually convert into a compiler type? case eContextTypeLLDBType: { Type *lldb_type = GetType(); if (lldb_type) m_compiler_type = lldb_type->GetForwardCompilerType(); } break; case eContextTypeVariable: { Variable *variable = GetVariable(); if (variable) { Type *variable_type = variable->GetType(); if (variable_type) m_compiler_type = variable_type->GetForwardCompilerType(); } } break; } } return m_compiler_type; }
DLRExpressionTree* ETSemanticsForLambdas::ConvertSymbol ( ILTree::Expression* Input, ExpressionFlags Flags, Type* TargetType ) { ThrowIfNull(Input); ThrowIfFalse(Input->bilop == SX_SYM); Declaration* Symbol = Input->AsSymbolReferenceExpression().pnamed; if(Symbol->IsVariable()) { Variable *Var = Symbol->PVariable(); // IsLocal check also required for Chimayo scenarios. if (Var->IsTemporary() || Var->IsFromScriptScope()) { DLRExpressionTree **TreeNode = NULL; if((TreeNode = m_VariablesMap->HashFind(Var)) && *TreeNode) { return *TreeNode; } if (Var->IsFromScriptScope()) { DLRExpressionTree *VarExprNode = m_ExprTreeGenerator->CreateVariableExpr( Var->GetEmittedName(), Var->GetType(), TargetType, Input->Loc ); // All variables need to be added to the map to ensure uniqueness. m_VariablesMap->HashAdd(Var, VarExprNode); return VarExprNode; } // Non-script scope variable should already exist from the outer block // since user lambdas in VB cannot result in creation of new locals. ThrowIfFalse(false); } } // fall back to the base implementation return ExpressionTreeSemantics<DLRExpressionTree>::ConvertSymbol( Input, Flags, TargetType ); }
static void PrivateAutoComplete (StackFrame *frame, const std::string &partial_path, const std::string &prefix_path, // Anything that has been resolved already will be in here const CompilerType& compiler_type, StringList &matches, bool &word_complete) { // printf ("\nPrivateAutoComplete()\n\tprefix_path = '%s'\n\tpartial_path = '%s'\n", prefix_path.c_str(), partial_path.c_str()); std::string remaining_partial_path; const lldb::TypeClass type_class = compiler_type.GetTypeClass(); if (partial_path.empty()) { if (compiler_type.IsValid()) { switch (type_class) { default: case eTypeClassArray: case eTypeClassBlockPointer: case eTypeClassBuiltin: case eTypeClassComplexFloat: case eTypeClassComplexInteger: case eTypeClassEnumeration: case eTypeClassFunction: case eTypeClassMemberPointer: case eTypeClassReference: case eTypeClassTypedef: case eTypeClassVector: { matches.AppendString (prefix_path); word_complete = matches.GetSize() == 1; } break; case eTypeClassClass: case eTypeClassStruct: case eTypeClassUnion: if (prefix_path.back() != '.') matches.AppendString (prefix_path + '.'); break; case eTypeClassObjCObject: case eTypeClassObjCInterface: break; case eTypeClassObjCObjectPointer: case eTypeClassPointer: { bool omit_empty_base_classes = true; if (compiler_type.GetNumChildren (omit_empty_base_classes) > 0) matches.AppendString (prefix_path + "->"); else { matches.AppendString (prefix_path); word_complete = true; } } break; } } else { if (frame) { const bool get_file_globals = true; VariableList *variable_list = frame->GetVariableList(get_file_globals); if (variable_list) { const size_t num_variables = variable_list->GetSize(); for (size_t i=0; i<num_variables; ++i) { Variable *variable = variable_list->GetVariableAtIndex(i).get(); matches.AppendString (variable->GetName().AsCString()); } } } } } else { const char ch = partial_path[0]; switch (ch) { case '*': if (prefix_path.empty()) { PrivateAutoComplete (frame, partial_path.substr(1), std::string("*"), compiler_type, matches, word_complete); } break; case '&': if (prefix_path.empty()) { PrivateAutoComplete (frame, partial_path.substr(1), std::string("&"), compiler_type, matches, word_complete); } break; case '-': if (partial_path[1] == '>' && !prefix_path.empty()) { switch (type_class) { case lldb::eTypeClassPointer: { CompilerType pointee_type(compiler_type.GetPointeeType()); if (partial_path[2]) { // If there is more after the "->", then search deeper PrivateAutoComplete (frame, partial_path.substr(2), prefix_path + "->", pointee_type.GetCanonicalType(), matches, word_complete); } else { // Nothing after the "->", so list all members PrivateAutoCompleteMembers (frame, std::string(), std::string(), prefix_path + "->", pointee_type.GetCanonicalType(), matches, word_complete); } } break; default: break; } } break; case '.': if (compiler_type.IsValid()) { switch (type_class) { case lldb::eTypeClassUnion: case lldb::eTypeClassStruct: case lldb::eTypeClassClass: if (partial_path[1]) { // If there is more after the ".", then search deeper PrivateAutoComplete (frame, partial_path.substr(1), prefix_path + ".", compiler_type, matches, word_complete); } else { // Nothing after the ".", so list all members PrivateAutoCompleteMembers (frame, std::string(), partial_path, prefix_path + ".", compiler_type, matches, word_complete); } break; default: break; } } break; default: if (isalpha(ch) || ch == '_' || ch == '$') { const size_t partial_path_len = partial_path.size(); size_t pos = 1; while (pos < partial_path_len) { const char curr_ch = partial_path[pos]; if (isalnum(curr_ch) || curr_ch == '_' || curr_ch == '$') { ++pos; continue; } break; } std::string token(partial_path, 0, pos); remaining_partial_path = partial_path.substr(pos); if (compiler_type.IsValid()) { PrivateAutoCompleteMembers (frame, token, remaining_partial_path, prefix_path, compiler_type, matches, word_complete); } else if (frame) { // We haven't found our variable yet const bool get_file_globals = true; VariableList *variable_list = frame->GetVariableList(get_file_globals); if (!variable_list) break; const size_t num_variables = variable_list->GetSize(); for (size_t i=0; i<num_variables; ++i) { Variable *variable = variable_list->GetVariableAtIndex(i).get(); if (!variable) continue; const char *variable_name = variable->GetName().AsCString(); if (strstr(variable_name, token.c_str()) == variable_name) { if (strcmp (variable_name, token.c_str()) == 0) { Type *variable_type = variable->GetType(); if (variable_type) { CompilerType variable_compiler_type (variable_type->GetForwardCompilerType ()); PrivateAutoComplete (frame, remaining_partial_path, prefix_path + token, // Anything that has been resolved already will be in here variable_compiler_type.GetCanonicalType(), matches, word_complete); } else { matches.AppendString (prefix_path + variable_name); } } else if (remaining_partial_path.empty()) { matches.AppendString (prefix_path + variable_name); } } } } } break; } } }
bool Address::Dump(Stream *s, ExecutionContextScope *exe_scope, DumpStyle style, DumpStyle fallback_style, uint32_t addr_size) const { // If the section was nullptr, only load address is going to work unless we // are // trying to deref a pointer SectionSP section_sp(GetSection()); if (!section_sp && style != DumpStyleResolvedPointerDescription) style = DumpStyleLoadAddress; ExecutionContext exe_ctx(exe_scope); Target *target = exe_ctx.GetTargetPtr(); // If addr_byte_size is UINT32_MAX, then determine the correct address // byte size for the process or default to the size of addr_t if (addr_size == UINT32_MAX) { if (target) addr_size = target->GetArchitecture().GetAddressByteSize(); else addr_size = sizeof(addr_t); } Address so_addr; switch (style) { case DumpStyleInvalid: return false; case DumpStyleSectionNameOffset: if (section_sp) { section_sp->DumpName(s); s->Printf(" + %" PRIu64, m_offset); } else { s->Address(m_offset, addr_size); } break; case DumpStyleSectionPointerOffset: s->Printf("(Section *)%p + ", static_cast<void *>(section_sp.get())); s->Address(m_offset, addr_size); break; case DumpStyleModuleWithFileAddress: if (section_sp) { ModuleSP module_sp = section_sp->GetModule(); if (module_sp) s->Printf("%s[", module_sp->GetFileSpec().GetFilename().AsCString( "<Unknown>")); else s->Printf("%s[", "<Unknown>"); } LLVM_FALLTHROUGH; case DumpStyleFileAddress: { addr_t file_addr = GetFileAddress(); if (file_addr == LLDB_INVALID_ADDRESS) { if (fallback_style != DumpStyleInvalid) return Dump(s, exe_scope, fallback_style, DumpStyleInvalid, addr_size); return false; } s->Address(file_addr, addr_size); if (style == DumpStyleModuleWithFileAddress && section_sp) s->PutChar(']'); } break; case DumpStyleLoadAddress: { addr_t load_addr = GetLoadAddress(target); /* * MIPS: * Display address in compressed form for MIPS16 or microMIPS * if the address belongs to eAddressClassCodeAlternateISA. */ if (target) { const llvm::Triple::ArchType llvm_arch = target->GetArchitecture().GetMachine(); if (llvm_arch == llvm::Triple::mips || llvm_arch == llvm::Triple::mipsel || llvm_arch == llvm::Triple::mips64 || llvm_arch == llvm::Triple::mips64el) load_addr = GetCallableLoadAddress(target); } if (load_addr == LLDB_INVALID_ADDRESS) { if (fallback_style != DumpStyleInvalid) return Dump(s, exe_scope, fallback_style, DumpStyleInvalid, addr_size); return false; } s->Address(load_addr, addr_size); } break; case DumpStyleResolvedDescription: case DumpStyleResolvedDescriptionNoModule: case DumpStyleResolvedDescriptionNoFunctionArguments: case DumpStyleNoFunctionName: if (IsSectionOffset()) { uint32_t pointer_size = 4; ModuleSP module_sp(GetModule()); if (target) pointer_size = target->GetArchitecture().GetAddressByteSize(); else if (module_sp) pointer_size = module_sp->GetArchitecture().GetAddressByteSize(); bool showed_info = false; if (section_sp) { SectionType sect_type = section_sp->GetType(); switch (sect_type) { case eSectionTypeData: if (module_sp) { SymbolVendor *sym_vendor = module_sp->GetSymbolVendor(); if (sym_vendor) { Symtab *symtab = sym_vendor->GetSymtab(); if (symtab) { const addr_t file_Addr = GetFileAddress(); Symbol *symbol = symtab->FindSymbolContainingFileAddress(file_Addr); if (symbol) { const char *symbol_name = symbol->GetName().AsCString(); if (symbol_name) { s->PutCString(symbol_name); addr_t delta = file_Addr - symbol->GetAddressRef().GetFileAddress(); if (delta) s->Printf(" + %" PRIu64, delta); showed_info = true; } } } } } break; case eSectionTypeDataCString: // Read the C string from memory and display it showed_info = true; ReadCStringFromMemory(exe_scope, *this, s); break; case eSectionTypeDataCStringPointers: if (ReadAddress(exe_scope, *this, pointer_size, so_addr)) { #if VERBOSE_OUTPUT s->PutCString("(char *)"); so_addr.Dump(s, exe_scope, DumpStyleLoadAddress, DumpStyleFileAddress); s->PutCString(": "); #endif showed_info = true; ReadCStringFromMemory(exe_scope, so_addr, s); } break; case eSectionTypeDataObjCMessageRefs: if (ReadAddress(exe_scope, *this, pointer_size, so_addr)) { if (target && so_addr.IsSectionOffset()) { SymbolContext func_sc; target->GetImages().ResolveSymbolContextForAddress( so_addr, eSymbolContextEverything, func_sc); if (func_sc.function != nullptr || func_sc.symbol != nullptr) { showed_info = true; #if VERBOSE_OUTPUT s->PutCString("(objc_msgref *) -> { (func*)"); so_addr.Dump(s, exe_scope, DumpStyleLoadAddress, DumpStyleFileAddress); #else s->PutCString("{ "); #endif Address cstr_addr(*this); cstr_addr.SetOffset(cstr_addr.GetOffset() + pointer_size); func_sc.DumpStopContext(s, exe_scope, so_addr, true, true, false, true, true); if (ReadAddress(exe_scope, cstr_addr, pointer_size, so_addr)) { #if VERBOSE_OUTPUT s->PutCString("), (char *)"); so_addr.Dump(s, exe_scope, DumpStyleLoadAddress, DumpStyleFileAddress); s->PutCString(" ("); #else s->PutCString(", "); #endif ReadCStringFromMemory(exe_scope, so_addr, s); } #if VERBOSE_OUTPUT s->PutCString(") }"); #else s->PutCString(" }"); #endif } } } break; case eSectionTypeDataObjCCFStrings: { Address cfstring_data_addr(*this); cfstring_data_addr.SetOffset(cfstring_data_addr.GetOffset() + (2 * pointer_size)); if (ReadAddress(exe_scope, cfstring_data_addr, pointer_size, so_addr)) { #if VERBOSE_OUTPUT s->PutCString("(CFString *) "); cfstring_data_addr.Dump(s, exe_scope, DumpStyleLoadAddress, DumpStyleFileAddress); s->PutCString(" -> @"); #else s->PutChar('@'); #endif if (so_addr.Dump(s, exe_scope, DumpStyleResolvedDescription)) showed_info = true; } } break; case eSectionTypeData4: // Read the 4 byte data and display it showed_info = true; s->PutCString("(uint32_t) "); DumpUInt(exe_scope, *this, 4, s); break; case eSectionTypeData8: // Read the 8 byte data and display it showed_info = true; s->PutCString("(uint64_t) "); DumpUInt(exe_scope, *this, 8, s); break; case eSectionTypeData16: // Read the 16 byte data and display it showed_info = true; s->PutCString("(uint128_t) "); DumpUInt(exe_scope, *this, 16, s); break; case eSectionTypeDataPointers: // Read the pointer data and display it if (ReadAddress(exe_scope, *this, pointer_size, so_addr)) { s->PutCString("(void *)"); so_addr.Dump(s, exe_scope, DumpStyleLoadAddress, DumpStyleFileAddress); showed_info = true; if (so_addr.IsSectionOffset()) { SymbolContext pointer_sc; if (target) { target->GetImages().ResolveSymbolContextForAddress( so_addr, eSymbolContextEverything, pointer_sc); if (pointer_sc.function != nullptr || pointer_sc.symbol != nullptr) { s->PutCString(": "); pointer_sc.DumpStopContext(s, exe_scope, so_addr, true, false, false, true, true); } } } } break; default: break; } } if (!showed_info) { if (module_sp) { SymbolContext sc; module_sp->ResolveSymbolContextForAddress( *this, eSymbolContextEverything, sc); if (sc.function || sc.symbol) { bool show_stop_context = true; const bool show_module = (style == DumpStyleResolvedDescription); const bool show_fullpaths = false; const bool show_inlined_frames = true; const bool show_function_arguments = (style != DumpStyleResolvedDescriptionNoFunctionArguments); const bool show_function_name = (style != DumpStyleNoFunctionName); if (sc.function == nullptr && sc.symbol != nullptr) { // If we have just a symbol make sure it is in the right section if (sc.symbol->ValueIsAddress()) { if (sc.symbol->GetAddressRef().GetSection() != GetSection()) { // don't show the module if the symbol is a trampoline symbol show_stop_context = false; } } } if (show_stop_context) { // We have a function or a symbol from the same // sections as this address. sc.DumpStopContext(s, exe_scope, *this, show_fullpaths, show_module, show_inlined_frames, show_function_arguments, show_function_name); } else { // We found a symbol but it was in a different // section so it isn't the symbol we should be // showing, just show the section name + offset Dump(s, exe_scope, DumpStyleSectionNameOffset); } } } } } else { if (fallback_style != DumpStyleInvalid) return Dump(s, exe_scope, fallback_style, DumpStyleInvalid, addr_size); return false; } break; case DumpStyleDetailedSymbolContext: if (IsSectionOffset()) { ModuleSP module_sp(GetModule()); if (module_sp) { SymbolContext sc; module_sp->ResolveSymbolContextForAddress( *this, eSymbolContextEverything | eSymbolContextVariable, sc); if (sc.symbol) { // If we have just a symbol make sure it is in the same section // as our address. If it isn't, then we might have just found // the last symbol that came before the address that we are // looking up that has nothing to do with our address lookup. if (sc.symbol->ValueIsAddress() && sc.symbol->GetAddressRef().GetSection() != GetSection()) sc.symbol = nullptr; } sc.GetDescription(s, eDescriptionLevelBrief, target); if (sc.block) { bool can_create = true; bool get_parent_variables = true; bool stop_if_block_is_inlined_function = false; VariableList variable_list; sc.block->AppendVariables(can_create, get_parent_variables, stop_if_block_is_inlined_function, [](Variable *) { return true; }, &variable_list); const size_t num_variables = variable_list.GetSize(); for (size_t var_idx = 0; var_idx < num_variables; ++var_idx) { Variable *var = variable_list.GetVariableAtIndex(var_idx).get(); if (var && var->LocationIsValidForAddress(*this)) { s->Indent(); s->Printf(" Variable: id = {0x%8.8" PRIx64 "}, name = \"%s\"", var->GetID(), var->GetName().GetCString()); Type *type = var->GetType(); if (type) s->Printf(", type = \"%s\"", type->GetName().GetCString()); else s->PutCString(", type = <unknown>"); s->PutCString(", location = "); var->DumpLocationForAddress(s, *this); s->PutCString(", decl = "); var->GetDeclaration().DumpStopContext(s, false); s->EOL(); } } } } } else { if (fallback_style != DumpStyleInvalid) return Dump(s, exe_scope, fallback_style, DumpStyleInvalid, addr_size); return false; } break; case DumpStyleResolvedPointerDescription: { Process *process = exe_ctx.GetProcessPtr(); if (process) { addr_t load_addr = GetLoadAddress(target); if (load_addr != LLDB_INVALID_ADDRESS) { Error memory_error; addr_t dereferenced_load_addr = process->ReadPointerFromMemory(load_addr, memory_error); if (dereferenced_load_addr != LLDB_INVALID_ADDRESS) { Address dereferenced_addr; if (dereferenced_addr.SetLoadAddress(dereferenced_load_addr, target)) { StreamString strm; if (dereferenced_addr.Dump(&strm, exe_scope, DumpStyleResolvedDescription, DumpStyleInvalid, addr_size)) { s->Address(dereferenced_load_addr, addr_size, " -> ", " "); s->Write(strm.GetData(), strm.GetSize()); return true; } } } } } if (fallback_style != DumpStyleInvalid) return Dump(s, exe_scope, fallback_style, DumpStyleInvalid, addr_size); return false; } break; } return true; }
void CodeGenerator::ProcessVarTerm(int flags) { infunc(CodeGenerator::ProcessVarTerm); char name[MAX_LABEL_SIZE]; VarType type; if ((flags & FLAGS_IN_STATE) && !(flags & FLAGS_IN_FUNCTION)) throw CompileError("(Line %d) Not allowed variable declarations inside states, but outside of functions", CUR_TOKEN.line); // Grab the type GetTypeInfo(type, 0); // Loop until the declaration has ended while (CUR_TOKEN.type != TOKEN_END_OF_LINE) { Variable *var; if (CUR_TOKEN.type != TOKEN_NAME) throw CompileError("(Line %d) No name after type declaration", CUR_TOKEN.line); // Get the current variable name IsolateTokenString(CUR_TOKEN); strcpy(name, token_string); INC_TOKEN; // Grab the array dimensions if it's an array if (CUR_TOKEN.type == TOKEN_ARRAY_OPEN) GetArrayInfo(type); if (g_Object == NULL) { if (flags & FLAGS_IN_FUNCTION) { var = cur_class->cur_function->AddLocal(type, name); } else { // Create a new variable if ((var = new Variable) == NULL) throw CError("Couldn't allocate variable structure"); var->SetType(type); var->SetScope(VARIABLE_SCOPE_MEMBER); if (type.array) { var->SetAddress(cur_class->NewAddress(4 + (type.elements << 2), 0)); var->SetArrayElements(type.elements); } else var->SetAddress(cur_class->NewAddress(4, 1)); // Add it to the class list of variables cur_class->variables.Add(name, var); } } else { // Variable already defined, get it from the class var = cur_class->GetVariable(name, flags); // Check for invalid custom variable types if (var->GetType().id == VARIABLE_TYPEID_CUSTOM) if (g_Env->GetClass(var->GetType().name) == NULL) throw CompileError("(Line %d) Undefined variable type", CUR_TOKEN.line); // Local variables that are arrays need to be prepared if (flags & FLAGS_IN_FUNCTION && var->GetType().array) g_Object->WriteOp(OPCODE_ARRAYP, var->GetAddress()); } // Check for initial values if (CUR_TOKEN.type == TOKEN_ASSIGN) { if (type.id == VARIABLE_TYPEID_CUSTOM) throw CompileError("(Line %d) Not allowed immediate assignments on custom variable types", CUR_TOKEN.line); INC_TOKEN; // Is this an array? if (var->GetArrayElements()) { int x = 0, neg; dynamic num; neg = 0; if (CUR_TOKEN.type != TOKEN_BLOCK_OPEN) throw CompileError("(Line %d) Expecting block open for array default value definition", CUR_TOKEN.line); INC_TOKEN; while (1) { // Check for exit if (CUR_TOKEN.type == TOKEN_BLOCK_CLOSE) { INC_TOKEN; break; } // Check for too many variables if (x == var->GetArrayElements()) throw CompileError("(Line %d) Too many initialisers for array", CUR_TOKEN.line); // Read the value ReadConstant(&num, type, TOKEN_COMMA, TOKEN_BLOCK_CLOSE); if (g_Object == NULL) var->SetElementValue(x, &num); x++; // Check for the comma if (CUR_TOKEN.type != TOKEN_BLOCK_CLOSE) { if (CUR_TOKEN.type != TOKEN_COMMA) throw CompileError("(Line %d) Expecting comma seperator", CUR_TOKEN.line); INC_TOKEN; // Check for situations like = { 4, }; if (CUR_TOKEN.type == TOKEN_BLOCK_CLOSE) throw CompileError("(Line %d) Expecting array element", CUR_TOKEN.line); } } } // No else { dynamic num; ReadConstant(&num, type, TOKEN_END_OF_LINE, TOKEN_COMMA); if (g_Object == NULL) var->SetDefaultValue(&num); } } // Check for multiple variable declarations if (CUR_TOKEN.type == TOKEN_COMMA) { INC_TOKEN; if (CUR_TOKEN.type == TOKEN_END_OF_LINE) throw CompileError("(Line %d) Unexpected end of line", CUR_TOKEN.line); } else if (CUR_TOKEN.type != TOKEN_END_OF_LINE) throw CompileError("(Line %d) Illegal token after variable declaration", CUR_TOKEN.line); } outfunc; }
void Module::LoadSBML(const SBMLDocument* sbmldoc) { //m_sbml = *sbmldoc; const Model* sbml = sbmldoc->getModel(); string sbmlname = ""; //Function Definitions //This is a bit weird, since functions exist outside of modules, since they can be used in any model. So we have to go to the registry to save them. for (unsigned int func=0; func<sbml->getNumFunctionDefinitions(); func++) { const FunctionDefinition* function = sbml->getFunctionDefinition(func); sbmlname = getNameFromSBMLObject(function, "_F"); g_registry.NewUserFunction(&sbmlname); for (unsigned int arg=0; arg<function->getNumArguments(); arg++) { string argument(parseASTNodeToString(function->getArgument(arg))); Variable* expvar = g_registry.AddVariableToCurrent(&argument); g_registry.AddVariableToCurrentExportList(expvar); } string formulastring(parseASTNodeToString(function->getBody())); Formula* formula = g_registry.NewBlankFormula(); setFormulaWithString(formulastring, formula, this); g_registry.SetUserFunction(formula); g_registry.GetNthUserFunction(g_registry.GetNumUserFunctions()-1)->FixNames(); } set<string> defaultcompartments; //Compartments for (unsigned int comp=0; comp<sbml->getNumCompartments(); comp++) { const Compartment* compartment = sbml->getCompartment(comp); sbmlname = getNameFromSBMLObject(compartment, "_C"); if (compartment->getSBOTerm() == 410) { //The 'implicit compartment' defaultcompartments.insert(sbmlname); continue; } if (sbmlname == DEFAULTCOMP && compartment->getConstant() && compartment->isSetSize() && compartment->getSize() == 1.0) { defaultcompartments.insert(sbmlname); continue; //LS NOTE: we assume this was created with Antimony, and ignore the auto-generated 'default compartment' // Later versions of antimony now set the SBO terms to 410, so we might not need this code very long. } Variable* var = AddOrFindVariable(&sbmlname); if (compartment->isSetName()) { var->SetDisplayName(compartment->getName()); } var->SetType(varCompartment); Formula* formula = g_registry.NewBlankFormula(); if (compartment->isSetSize()) { formula->AddNum(compartment->getSize()); var->SetFormula(formula); } if (compartment->isSetUnits()) { var->SetUnits(compartment->getUnits()); } } //Species for (unsigned int spec=0; spec<sbml->getNumSpecies(); spec++) { const Species* species = sbml->getSpecies(spec); sbmlname = getNameFromSBMLObject(species, "_S"); Variable* var = AddOrFindVariable(&sbmlname); if (species->isSetName()) { var->SetDisplayName(species->getName()); } var->SetType(varSpeciesUndef); //Setting the formula Formula* formula = g_registry.NewBlankFormula(); if (species->isSetInitialAmount()) { double amount = species->getInitialAmount(); formula->AddNum(amount); if (amount != 0 && defaultcompartments.find(species->getCompartment()) == defaultcompartments.end()) { Variable* compartment = AddOrFindVariable(&(species->getCompartment())); Formula* compform = compartment->GetFormula(); if (!compform->IsOne()) { formula->AddMathThing('/'); formula->AddVariable(compartment); } } var->SetFormula(formula); } else if (species->isSetInitialConcentration()) { formula->AddNum(species->getInitialConcentration()); var->SetFormula(formula); } //Anything more complicated is set in a Rule, which we'll get to later. if (species->getConstant() || species->getBoundaryCondition()) { //Since all species are variable by default, we only set this explicitly if true. var->SetIsConst(true); } if (defaultcompartments.find(species->getCompartment()) == defaultcompartments.end()) { Variable* compartment = AddOrFindVariable(&(species->getCompartment())); compartment->SetType(varCompartment); var->SetCompartment(compartment); } if (species->isSetUnits()) { var->SetUnits(species->getUnits()); } } //Events: for (unsigned int ev=0; ev<sbml->getNumEvents(); ev++) { const Event* event = sbml->getEvent(ev); sbmlname = getNameFromSBMLObject(event, "_E"); Variable* var = AddOrFindVariable(&sbmlname); if (event->isSetName()) { var->SetDisplayName(event->getName()); } var->SetType(varEvent); //Set the trigger: string triggerstring(parseASTNodeToString(event->getTrigger()->getMath())); Formula trigger; setFormulaWithString(triggerstring, &trigger, this); Formula delay; const Delay* sbmldelay = event->getDelay(); if (sbmldelay != NULL) { string delaystring(parseASTNodeToString(sbmldelay->getMath())); setFormulaWithString(delaystring, &delay, this); } AntimonyEvent antevent(delay, trigger,var); var->SetEvent(&antevent); //Set the assignments: for (unsigned int asnt=0; asnt<event->getNumEventAssignments(); asnt++) { const EventAssignment* assignment = event->getEventAssignment(asnt); string name = assignment->getVariable(); Variable* asntvar = AddOrFindVariable(&name); Formula* asntform = g_registry.NewBlankFormula(); setFormulaWithString(parseASTNodeToString(assignment->getMath()), asntform, this); var->GetEvent()->AddResult(asntvar, asntform); } } //LS DEBUG: Add constraints? //Parameters for (unsigned int param=0; param<sbml->getNumParameters(); param++) { const Parameter* parameter = sbml->getParameter(param); sbmlname = getNameFromSBMLObject(parameter, "_P"); Variable* var = AddOrFindVariable(&sbmlname); if (parameter->isSetName()) { var->SetDisplayName(parameter->getName()); } if (parameter->isSetValue()) { Formula* formula = g_registry.NewBlankFormula(); formula->AddNum(parameter->getValue()); var->SetFormula(formula); //LS NOTE: If a parameter has both a value and an 'initial assignment', the initial assignment will override the value. } if (parameter->isSetUnits()) { var->SetUnits(parameter->getUnits()); } } //Initial Assignments: can override 'getValue' values. for (unsigned int ia=0; ia<sbml->getNumInitialAssignments(); ia++) { const InitialAssignment* initasnt = sbml->getInitialAssignment(ia); if (initasnt->isSetSymbol()) { sbmlname = initasnt->getSymbol(); Variable* var = AddOrFindVariable(&sbmlname); if (initasnt->isSetName()) { var->SetDisplayName(initasnt->getName()); } Formula* formula = g_registry.NewBlankFormula(); string formulastring(parseASTNodeToString(initasnt->getMath())); setFormulaWithString(formulastring, formula, this); var->SetFormula(formula); } else { //LS DEBUG: error? The 'symbol' is supposed to be required. } } //Rules: for (unsigned int rulen=0; rulen<sbml->getNumRules(); rulen++) { const Rule* rule = sbml->getRule(rulen); if (rule->isAlgebraic()) { //LS DEBUG: error message? Unable to process algebraic rules continue; } sbmlname = rule->getVariable(); assert(sbmlname != ""); if (sbmlname == "") { sbmlname = getNameFromSBMLObject(rule, "_R"); } Variable* var = AddOrFindVariable(&sbmlname); if (rule->isSetName()) { var->SetDisplayName(rule->getName()); } Formula* formula = g_registry.NewBlankFormula(); string formulastring(parseASTNodeToString(rule->getMath())); setFormulaWithString(formulastring, formula, this); if (IsSpecies(var->GetType())) { //Any species in any rule must be 'const' (in Antimony), because this means it's a 'boundary species' var->SetIsConst(true); } else { //For other parameters, assignment and rate rules always mean the variable in question is not constant. var->SetIsConst(false); } if (rule->isAssignment()) { var->SetAssignmentRule(formula); } else if (rule->isRate()) { var->SetRateRule(formula); } else { assert(false); //should be caught above } } //Reactions for (unsigned int rxn=0; rxn<sbml->getNumReactions(); rxn++) { const Reaction* reaction = sbml->getReaction(rxn); sbmlname = getNameFromSBMLObject(reaction, "_J"); Variable* var = AddOrFindVariable(&sbmlname); if (reaction->isSetName()) { var->SetDisplayName(reaction->getName()); } //reactants ReactantList reactants; for (unsigned int react=0; react<reaction->getNumReactants(); react++) { const SpeciesReference* reactant = reaction->getReactant(react); double stoichiometry = 1; if (reactant->isSetStoichiometryMath()) { //LS DEBUG: error message? } else { stoichiometry = reactant->getStoichiometry(); } sbmlname = reactant->getSpecies(); if (sbmlname == "") { sbmlname = getNameFromSBMLObject(reactant, "_S"); } Variable* rvar = AddOrFindVariable(&sbmlname); reactants.AddReactant(rvar, stoichiometry); } //products ReactantList products; for (unsigned int react=0; react<reaction->getNumProducts(); react++) { const SpeciesReference* product = reaction->getProduct(react); double stoichiometry = 1; if (product->isSetStoichiometryMath()) { //LS DEBUG: error message? } else { stoichiometry = product->getStoichiometry(); } sbmlname = product->getSpecies(); if (sbmlname == "") { sbmlname = getNameFromSBMLObject(product, "_S"); } Variable* rvar = AddOrFindVariable(&sbmlname); products.AddReactant(rvar, stoichiometry); } //formula string formulastring = ""; Formula formula; if (reaction->isSetKineticLaw()) { const KineticLaw* kl = reaction->getKineticLaw(); var->SetUnits(kl->getSubstanceUnits() + "/(" + kl->getTimeUnits() + ")"); formulastring = parseASTNodeToString(kl->getMath()); setFormulaWithString(formulastring, &formula, this); for (unsigned int localp=0; localp<kl->getNumParameters(); localp++) { const Parameter* localparam = kl->getParameter(localp); vector<string> fullname; //Find the variable with the original name: string origname = getNameFromSBMLObject(localparam, "_P"); fullname.push_back(origname); Variable* origvar = GetVariable(fullname); //Create a new variable with a new name: fullname.clear(); sbmlname = var->GetNameDelimitedBy('_') + "_" + origname; fullname.push_back(sbmlname); Variable* foundvar = GetVariable(fullname); while (foundvar != NULL) { //Just in case something weird happened and there was another one of *this* name, too. sbmlname = var->GetNameDelimitedBy('_') + "_" + sbmlname; fullname.clear(); fullname.push_back(sbmlname); foundvar = GetVariable(fullname); } Variable* localvar = AddOrFindVariable(&sbmlname); //Replace the variable in the formula: if(origvar != NULL) { formula.ReplaceWith(origvar, localvar); } else { //If origvar is NULL, nothing needs to be replaced: if the original formula had included the parameter, the earlier setFormulaWithString would have created one. But since there wasn't one, this means the original formula didn't include the parameter at all! Meaning this local parameter has no use whatsoever! What the heck, dude. Oh, well. //cout << "Unused local variable for reaction " << var->GetNameDelimitedBy('.') << ": " << origname << endl; } //Set the value for the new variable: Formula localformula; localformula.AddNum(localparam->getValue()); localvar->SetFormula(&localformula); } } else if (reaction->getNumModifiers() > 0) { //If the kinetic law is empty, we can set some interactions, if there are any Modifiers. ReactantList right; right.AddReactant(var); ReactantList left; for (unsigned int mod=0; mod<reaction->getNumModifiers(); mod++) { const ModifierSpeciesReference* msr = reaction->getModifier(mod); string species = msr->getSpecies(); Variable* specvar = AddOrFindVariable(&species); left.AddReactant(specvar); sbmlname = getNameFromSBMLObject(msr, "_I"); } Variable* interaction = AddOrFindVariable(&sbmlname); Formula blankform; AddNewReaction(&left, rdInfluences, &right, &blankform, interaction); } rd_type rxntype = rdBecomes; if (!reaction->getReversible()) { rxntype = rdBecomesIrreversibly; } //Put reactants, products, and the formula together: AddNewReaction(&reactants, rxntype, &products, &formula, var); } //Finally, fix the fact that 'time' used to be OK in functions (l2v1), but is no longer (l2v2). g_registry.FixTimeInFunctions(); //And that some SBML-OK names are not OK in Antimony FixNames(); }