From f3914d5dbebd8d242650162251244ef6234fe9a1 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Tue, 14 Aug 2012 12:04:07 +0200
Subject: [PATCH] remove Push/PopFlag
---
modules/conop/src/processor.hh | 83 +++++++-------------
modules/conop/src/rule_based.cc | 2 +-
modules/conop/src/rule_based.hh | 29 ++-----
modules/conop/tests/test_rule_based_conop.cc | 18 +----
4 files changed, 38 insertions(+), 94 deletions(-)
diff --git a/modules/conop/src/processor.hh b/modules/conop/src/processor.hh
index daba929a3..d8e3e6bf6 100644
--- a/modules/conop/src/processor.hh
+++ b/modules/conop/src/processor.hh
@@ -34,27 +34,13 @@ enum ConopAction {
CONOP_FATAL
};
-struct ProcessorOptions {
- ProcessorOptions(): check_bond_feasibility(false), assign_torsions(false),
- connect(true), unk_atom_treatment(CONOP_WARN), unk_res_treatment(CONOP_WARN),
- zero_occ_treatment(CONOP_SILENT)
- { }
- bool check_bond_feasibility;
- bool assign_torsions;
- bool connect;
- ConopAction unk_atom_treatment;
- ConopAction unk_res_treatment;
- ConopAction zero_occ_treatment;
-};
-
+class Processor;
+typedef boost::shared_ptr<Processor> ProcessorPtr;
// the base class for all options
class DLLEXPORT_OST_CONOP Processor {
public:
DiagnosticsPtr Process(mol::EntityHandle ent) const;
-
-
- virtual void PushFlags() = 0;
- virtual void PopFlags() = 0;
+ virtual ProcessorPtr Copy() const = 0;
protected:
virtual void DoProcess(DiagnosticsPtr diags,
mol::EntityHandle ent) const = 0;
@@ -62,85 +48,70 @@ protected:
mol::EntityHandle ent) const { return true; }
virtual bool EndProcessing(DiagnosticsPtr diags,
mol::EntityHandle ent) const { return true; }
-};
-
-// Provides accessor methods for the basic Processor options. All
-// processors should derive from this class
-template <typename O>
-class ProcessorBase : public Processor {
public:
- typedef O option_type;
- ProcessorBase(): option_stack_(1, O())
- {}
-
+ Processor(): strict_hydrogens_(false), check_bond_feasibility_(false),
+ assign_torsions_(false), connect_(true), unk_atom_treatment_(CONOP_WARN),
+ unk_res_treatment_(CONOP_WARN), zero_occ_treatment_(CONOP_SILENT) {}
void SetConnect(bool connect) {
- this->GetOptions().connect = connect;
+ connect_ = connect;
}
bool GetConnect() const {
- return this->GetOptions().connect;
+ return connect_;
}
void SetAssignTorsions(bool flag) {
- this->GetOptions().assign_torsions = flag;
+ assign_torsions_ = flag;
}
bool GetAssignTorsions() const {
- return this->GetOptions().assign_torsions;
+ return assign_torsions_;
}
ConopAction GetUnkResidueTreatment() const {
- return this->GetOptions().unk_res_treatment;
+ return unk_res_treatment_;
}
ConopAction GetUnkAtomTreatment() const {
- return this->GetOptions().unk_atom_treatment;
+ return unk_atom_treatment_;
}
bool GetCheckBondFeasibility() const {
- return this->GetOptions().check_bond_feasibility;
+ return check_bond_feasibility_;
}
bool GetStrictHydrogens() const {
- return this->GetOptions().strict_hydrogens;
+ return strict_hydrogens_;
}
void SetStrictHydrogens(bool flag) {
- this->GetOptions().strict_hydrogens = flag;
+ strict_hydrogens_ = flag;
}
void SetCheckBondFeasibility(bool flag) {
- this->GetOptions().check_bond_feasibility = flag;
+ check_bond_feasibility_ = flag;
}
void SetUnkResidueTreatment(ConopAction action) {
- this->GetOptions().unk_res_treatment = action;
+ unk_res_treatment_ = action;
}
void SetUnkAtomTreatment(ConopAction action) {
- this->GetOptions().unk_atom_treatment = action;
+ unk_atom_treatment_ = action;
}
ConopAction GetZeroOccTreatment() const {
- return this->GetOptions().zero_occ_treatment;
+ return zero_occ_treatment_;
}
void SetZeroOccTreatment(ConopAction action) {
- this->GetOptions().zero_occ_treatment = action;
- }
-
- virtual void PushFlags() {
- option_stack_.push_back(option_stack_.back());
+ zero_occ_treatment_ = action;
}
-
- virtual void PopFlags() {
- if (option_stack_.size() == 1) {
- throw std::runtime_error("Can't pop from stack with one item left");
- }
- option_stack_.pop_back();
- }
-protected:
- const option_type& GetOptions() const { return option_stack_.back(); }
- option_type& GetOptions() { return option_stack_.back(); }
private:
- std::vector<option_type> option_stack_;
+ bool strict_hydrogens_;
+ bool check_bond_feasibility_;
+ bool assign_torsions_;
+ bool connect_;
+ ConopAction unk_atom_treatment_;
+ ConopAction unk_res_treatment_;
+ ConopAction zero_occ_treatment_;
};
diff --git a/modules/conop/src/rule_based.cc b/modules/conop/src/rule_based.cc
index 3425fb076..224b11024 100644
--- a/modules/conop/src/rule_based.cc
+++ b/modules/conop/src/rule_based.cc
@@ -69,7 +69,7 @@ void RuleBasedProcessor::ProcessUnkAtoms(DiagnosticsPtr diags,
return;
}
- assert(unks.empty() && "empty unk list");
+ assert(!unks.empty() && "empty unk list");
mol::XCSEditor edi = unks.front().GetEntity().EditXCS();
for (mol::AtomHandleList::iterator
i = unks.begin(), e = unks.end(); i != e; ++i) {
diff --git a/modules/conop/src/rule_based.hh b/modules/conop/src/rule_based.hh
index 62b2417f3..4ea5246a6 100644
--- a/modules/conop/src/rule_based.hh
+++ b/modules/conop/src/rule_based.hh
@@ -26,39 +26,25 @@
namespace ost { namespace conop {
-struct RuleBasedProcessorOptions : ProcessorOptions {
- RuleBasedProcessorOptions(): ProcessorOptions(),
- strict_hydrogens(false), fix_element(true)
- {}
- bool strict_hydrogens;
- bool fix_element;
-};
-
/// \brief returns all atoms not listed in the specifictaion of compound
mol::AtomHandleList DLLEXPORT_OST_CONOP GetUnknownAtoms(mol::ResidueHandle res,
CompoundPtr compound);
-class DLLEXPORT_OST_CONOP RuleBasedProcessor :
- public ProcessorBase<RuleBasedProcessorOptions> {
+class DLLEXPORT_OST_CONOP RuleBasedProcessor : public Processor {
public:
RuleBasedProcessor(CompoundLibPtr compound_lib):
- ProcessorBase<RuleBasedProcessorOptions>(), lib_(compound_lib)
+ lib_(compound_lib)
{
}
- bool GetStrictHydrogens() const {
- return this->GetOptions().strict_hydrogens;
- }
-
- void SetStrictHydrogens(bool flag) {
- this->GetOptions().strict_hydrogens = flag;
- }
-
bool GetFixElement() const {
- return this->GetOptions().fix_element;
+ return fix_element_;
}
void SetFixElement(bool flag) {
- this->GetOptions().fix_element = flag;
+ fix_element_ = flag;
+ }
+ virtual ProcessorPtr Copy() const {
+ return ProcessorPtr(new RuleBasedProcessor(*this));
}
protected:
virtual void DoProcess(DiagnosticsPtr diags,
@@ -76,6 +62,7 @@ private:
bool IsBondFeasible(const mol::AtomHandle&, const mol::AtomHandle&) const;
mol::AtomHandle LocateAtom(const mol::AtomHandleList&, int ordinal) const;
CompoundLibPtr lib_;
+ bool fix_element_;
};
diff --git a/modules/conop/tests/test_rule_based_conop.cc b/modules/conop/tests/test_rule_based_conop.cc
index 7c0af2735..3d08c8061 100644
--- a/modules/conop/tests/test_rule_based_conop.cc
+++ b/modules/conop/tests/test_rule_based_conop.cc
@@ -61,32 +61,18 @@ BOOST_AUTO_TEST_CASE(rule_based_set_get_flags)
BOOST_CHECK_EQUAL(rbc.GetUnkAtomTreatment(), CONOP_WARN);
BOOST_CHECK_EQUAL(rbc.GetUnkResidueTreatment(), CONOP_WARN);
BOOST_CHECK_EQUAL(rbc.GetStrictHydrogens(), false);
- rbc.PushFlags();
rbc.SetConnect(false);
+ rbc.SetStrictHydrogens(true);
rbc.SetCheckBondFeasibility(true);
rbc.SetUnkResidueTreatment(CONOP_FATAL);
rbc.SetUnkAtomTreatment(CONOP_REMOVE);
BOOST_CHECK_EQUAL(rbc.GetConnect(), false);
+ BOOST_CHECK_EQUAL(rbc.GetStrictHydrogens(), true);
BOOST_CHECK_EQUAL(rbc.GetCheckBondFeasibility(),true);
BOOST_CHECK_EQUAL(rbc.GetUnkResidueTreatment(),CONOP_FATAL);
BOOST_CHECK_EQUAL(rbc.GetUnkAtomTreatment(),CONOP_REMOVE);
- rbc.PopFlags();
}
-BOOST_AUTO_TEST_CASE(rule_based_push_pop_flags)
-{
- CompoundLibPtr lib=load_lib();
- if (!lib) { return; }
- RuleBasedProcessor rbc(lib);
- BOOST_CHECK_THROW(rbc.PopFlags(), std::runtime_error);
- rbc.PushFlags();
- rbc.PopFlags();
- rbc.PushFlags();
- rbc.SetConnect(false);
- BOOST_CHECK(!rbc.GetConnect());
- rbc.PopFlags();
- BOOST_CHECK(rbc.GetConnect());
-}
BOOST_AUTO_TEST_CASE(rule_based_connect)
{
--
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