diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 46cedceae031f8b4d02da6a8ee8e0f9cce3c8171..4517ed943dbfa741a95702d886bec8dd0354b2ef 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -815,16 +815,14 @@ namespace {
}
ost::io::StarWriterLoopPtr Setup_atom_type_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_atom_type");
+ ost::io::StarWriterLoopDesc desc("_atom_type");
desc.Add("symbol");
ost::io::StarWriterLoopPtr sl(new ost::io::StarWriterLoop(desc));
return sl;
}
ost::io::StarWriterLoopPtr Setup_atom_site_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_atom_site");
+ ost::io::StarWriterLoopDesc desc("_atom_site");
desc.Add("group_PDB");
desc.Add("type_symbol");
desc.Add("label_atom_id");
@@ -847,8 +845,7 @@ namespace {
}
ost::io::StarWriterLoopPtr Setup_pdbx_poly_seq_scheme_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_pdbx_poly_seq_scheme");
+ ost::io::StarWriterLoopDesc desc("_pdbx_poly_seq_scheme");
desc.Add("asym_id");
desc.Add("entity_id");
desc.Add("mon_id");
@@ -861,8 +858,7 @@ namespace {
}
ost::io::StarWriterLoopPtr Setup_entity_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_entity");
+ ost::io::StarWriterLoopDesc desc("_entity");
desc.Add("id");
desc.Add("type");
ost::io::StarWriterLoopPtr sl(new ost::io::StarWriterLoop(desc));
@@ -870,8 +866,7 @@ namespace {
}
ost::io::StarWriterLoopPtr Setup_struct_asym_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_struct_asym");
+ ost::io::StarWriterLoopDesc desc("_struct_asym");
desc.Add("id");
desc.Add("entity_id");
ost::io::StarWriterLoopPtr sl(new ost::io::StarWriterLoop(desc));
@@ -879,8 +874,7 @@ namespace {
}
ost::io::StarWriterLoopPtr Setup_entity_poly_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_entity_poly");
+ ost::io::StarWriterLoopDesc desc("_entity_poly");
desc.Add("entity_id");
desc.Add("type");
desc.Add("pdbx_seq_one_letter_code");
@@ -890,8 +884,7 @@ namespace {
}
ost::io::StarWriterLoopPtr Setup_entity_poly_seq_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_entity_poly_seq");
+ ost::io::StarWriterLoopDesc desc("_entity_poly_seq");
desc.Add("entity_id");
desc.Add("mon_id");
desc.Add("num");
@@ -900,8 +893,7 @@ namespace {
}
ost::io::StarWriterLoopPtr Setup_chem_comp_ptr() {
- ost::io::StarWriterLoopDesc desc;
- desc.SetCategory("_chem_comp");
+ ost::io::StarWriterLoopDesc desc("_chem_comp");
desc.Add("id");
desc.Add("type");
ost::io::StarWriterLoopPtr sl(new ost::io::StarWriterLoop(desc));
@@ -916,14 +908,14 @@ namespace {
int desc_size = atom_site_ptr->GetDesc().GetSize();
int type_symbol_idx = atom_site_ptr->GetDesc().GetIndex("type_symbol");
int N = atom_site_ptr->GetN();
- const std::vector<ost::io::StarWriterLoopDataItem>& data = atom_site_ptr->GetData();
+ const std::vector<ost::io::StarWriterValue>& data = atom_site_ptr->GetData();
for(int i = 0; i < N; ++i) {
symbols.insert(data[i*desc_size + type_symbol_idx].GetValue());
}
- std::vector<ost::io::StarWriterLoopDataItem> atom_type_data;
- atom_type_data.push_back(ost::io::StarWriterLoopDataItem(""));
+ std::vector<ost::io::StarWriterValue> atom_type_data;
+ atom_type_data.push_back(ost::io::StarWriterValue::FromString(""));
for(auto symbol: symbols) {
- atom_type_data[0] = ost::io::StarWriterLoopDataItem(symbol);
+ atom_type_data[0] = ost::io::StarWriterValue::FromString(symbol);
atom_type_ptr->AddData(atom_type_data);
}
}
@@ -934,14 +926,14 @@ namespace {
ost::io::MMCifWriterEntity& entity_info,
const ost::mol::ResidueHandleList& res_list) {
- std::vector<ost::io::StarWriterLoopDataItem> data;
- data.push_back(ost::io::StarWriterLoopDataItem(label_asym_id));
- data.push_back(ost::io::StarWriterLoopDataItem(label_entity_id));
- data.push_back(ost::io::StarWriterLoopDataItem(""));
- data.push_back(ost::io::StarWriterLoopDataItem(0));
- data.push_back(ost::io::StarWriterLoopDataItem(""));
- data.push_back(ost::io::StarWriterLoopDataItem(0));
- data.push_back(ost::io::StarWriterLoopDataItem(""));
+ std::vector<ost::io::StarWriterValue> data;
+ data.push_back(ost::io::StarWriterValue::FromString(label_asym_id));
+ data.push_back(ost::io::StarWriterValue::FromInt(label_entity_id));
+ data.push_back(ost::io::StarWriterValue::FromString(""));
+ data.push_back(ost::io::StarWriterValue::FromInt(0));
+ data.push_back(ost::io::StarWriterValue::FromString(""));
+ data.push_back(ost::io::StarWriterValue::FromInt(0));
+ data.push_back(ost::io::StarWriterValue::FromString(""));
int asym_idx = entity_info.GetAsymIdx(label_asym_id);
const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
@@ -957,35 +949,34 @@ namespace {
throw "ksajdhfgjkaljshdfsfgd";
}
- data[2] = ost::io::StarWriterLoopDataItem(res_name);
- data[3] = ost::io::StarWriterLoopDataItem(label_seq_id + 1);
+ data[2] = ost::io::StarWriterValue::FromString(res_name);
+ data[3] = ost::io::StarWriterValue::FromInt(label_seq_id + 1);
// the remaining data items honor String properties if set:
// pdb_auth_chain_name, pdb_auth_resnum and pdb_auth_ins_code
if(res.GetChain().HasProp("pdb_auth_chain_name")) {
data[4] =
- ost::io::StarWriterLoopDataItem(res.GetChain().GetStringProp("pdb_auth_chain_name"));
+ ost::io::StarWriterValue::FromString(res.GetChain().GetStringProp("pdb_auth_chain_name"));
} else {
- data[4] = ost::io::StarWriterLoopDataItem(res.GetChain().GetName());
+ data[4] = ost::io::StarWriterValue::FromString(res.GetChain().GetName());
}
if(res.HasProp("pdb_auth_resnum")) {
- data[5] = ost::io::StarWriterLoopDataItem(res.GetStringProp("pdb_auth_resnum"));
+ // this feels so wrong that this is stored as a string property...
+ data[5] = ost::io::StarWriterValue::FromString(res.GetStringProp("pdb_auth_resnum"));
} else {
- data[5] = ost::io::StarWriterLoopDataItem(res.GetNumber().GetNum());
+ data[5] = ost::io::StarWriterValue::FromInt(res.GetNumber().GetNum());
}
if(res.HasProp("pdb_auth_ins_code")) {
- data[6] = ost::io::StarWriterLoopDataItem(res.GetStringProp("pdb_auth_ins_code"));
+ data[6] = ost::io::StarWriterValue::FromString(res.GetStringProp("pdb_auth_ins_code"));
} else {
char ins_code = res.GetNumber().GetInsCode();
if(ins_code == '\0') {
- data[6] = ost::io::StarWriterLoopDataItem("");
+ data[6] = ost::io::StarWriterValue::FromString("");
} else {
- String tmp = " ";
- tmp[0] = ins_code;
- data[6] = ost::io::StarWriterLoopDataItem(tmp);
+ data[6] = ost::io::StarWriterValue::FromString(String(1, ' '));
}
}
pdbx_poly_seq_scheme_ptr->AddData(data);
@@ -1030,52 +1021,51 @@ namespace {
}
for(auto at: at_list) {
- std::vector<ost::io::StarWriterLoopDataItem> at_data;
+ std::vector<ost::io::StarWriterValue> at_data;
// group_PDB
if(at.IsHetAtom()) {
- at_data.push_back(ost::io::StarWriterLoopDataItem("HETATM"));
+ at_data.push_back(ost::io::StarWriterValue::FromString("HETATM"));
} else {
- at_data.push_back(ost::io::StarWriterLoopDataItem("ATOM"));
+ at_data.push_back(ost::io::StarWriterValue::FromString("ATOM"));
}
// type_symbol
- at_data.push_back(ost::io::StarWriterLoopDataItem(at.GetElement()));
+ at_data.push_back(ost::io::StarWriterValue::FromString(at.GetElement()));
// label_atom_id
- at_data.push_back(ost::io::StarWriterLoopDataItem(at.GetName()));
+ at_data.push_back(ost::io::StarWriterValue::FromString(at.GetName()));
// label_comp_id
- at_data.push_back(ost::io::StarWriterLoopDataItem(comp_id));
+ at_data.push_back(ost::io::StarWriterValue::FromString(comp_id));
// label_asym_id
- at_data.push_back(ost::io::StarWriterLoopDataItem(label_asym_id));
+ at_data.push_back(ost::io::StarWriterValue::FromString(label_asym_id));
// label_entity_id
- at_data.push_back(ost::io::StarWriterLoopDataItem(label_entity_id));
+ at_data.push_back(ost::io::StarWriterValue::FromInt(label_entity_id));
// label_seq_id
if(entity_info.is_poly) {
- at_data.push_back(ost::io::StarWriterLoopDataItem(label_seq_id+1));
+ at_data.push_back(ost::io::StarWriterValue::FromInt(label_seq_id+1));
} else {
- at_data.push_back(ost::io::StarWriterLoopDataItem("."));
+ at_data.push_back(ost::io::StarWriterValue::FromString("."));
}
// label_alt_id
- at_data.push_back(ost::io::StarWriterLoopDataItem("."));
+ at_data.push_back(ost::io::StarWriterValue::FromString("."));
// Cartn_x
- at_data.push_back(ost::io::StarWriterLoopDataItem(at.GetPos().GetX(), 3));
+ at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetPos().GetX(), 3));
// Cartn_y
- at_data.push_back(ost::io::StarWriterLoopDataItem(at.GetPos().GetY(), 3));
+ at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetPos().GetY(), 3));
// Cartn_z
- at_data.push_back(ost::io::StarWriterLoopDataItem(at.GetPos().GetZ(), 3));
+ at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetPos().GetZ(), 3));
// occupancy
- at_data.push_back(ost::io::StarWriterLoopDataItem(at.GetOccupancy(), 2));
+ at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetOccupancy(), 2));
// B_iso_or_equiv
- at_data.push_back(ost::io::StarWriterLoopDataItem(at.GetBFactor(), 2));
+ at_data.push_back(ost::io::StarWriterValue::FromFloat(at.GetBFactor(), 2));
// auth_seq_id
- at_data.push_back(ost::io::StarWriterLoopDataItem(auth_seq_id));
+ at_data.push_back(ost::io::StarWriterValue::FromString(auth_seq_id));
// auth_asym_id
- at_data.push_back(ost::io::StarWriterLoopDataItem(auth_asym_id));
+ at_data.push_back(ost::io::StarWriterValue::FromString(auth_asym_id));
// id
- at_data.push_back(ost::io::StarWriterLoopDataItem(atom_site_ptr->GetN()));
+ at_data.push_back(ost::io::StarWriterValue::FromInt(atom_site_ptr->GetN()));
// pdbx_PDB_ins_code
- at_data.push_back(ost::io::StarWriterLoopDataItem(ins_code));
+ at_data.push_back(ost::io::StarWriterValue::FromString(ins_code));
atom_site_ptr->AddData(at_data);
}
-
++label_seq_id;
}
}
@@ -1083,9 +1073,9 @@ namespace {
void Feed_entity(ost::io::StarWriterLoopPtr entity_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
- std::vector<ost::io::StarWriterLoopDataItem> ent_data;
- ent_data.push_back(ost::io::StarWriterLoopDataItem(entity_idx));
- ent_data.push_back(ost::io::StarWriterLoopDataItem(entity_info[entity_idx].type));
+ std::vector<ost::io::StarWriterValue> ent_data;
+ ent_data.push_back(ost::io::StarWriterValue::FromInt(entity_idx));
+ ent_data.push_back(ost::io::StarWriterValue::FromString(entity_info[entity_idx].type));
entity_ptr->AddData(ent_data);
}
}
@@ -1094,9 +1084,9 @@ namespace {
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
for(auto asym_id : entity_info[entity_idx].asym_ids) {
- std::vector<ost::io::StarWriterLoopDataItem> asym_data;
- asym_data.push_back(ost::io::StarWriterLoopDataItem(asym_id));
- asym_data.push_back(ost::io::StarWriterLoopDataItem(entity_idx));
+ std::vector<ost::io::StarWriterValue> asym_data;
+ asym_data.push_back(ost::io::StarWriterValue::FromString(asym_id));
+ asym_data.push_back(ost::io::StarWriterValue::FromInt(entity_idx));
struct_asym_ptr->AddData(asym_data);
}
}
@@ -1105,18 +1095,18 @@ namespace {
void Feed_entity_poly_seq(ost::io::StarWriterLoopPtr entity_poly_seq_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
// reuse data vector for efficiency
- std::vector<ost::io::StarWriterLoopDataItem> entity_poly_seq_data;
- entity_poly_seq_data.push_back(ost::io::StarWriterLoopDataItem(0));
- entity_poly_seq_data.push_back(ost::io::StarWriterLoopDataItem("ALA"));
- entity_poly_seq_data.push_back(ost::io::StarWriterLoopDataItem(1));
+ std::vector<ost::io::StarWriterValue> entity_poly_seq_data;
+ entity_poly_seq_data.push_back(ost::io::StarWriterValue::FromInt(0));
+ entity_poly_seq_data.push_back(ost::io::StarWriterValue::FromString("ALA"));
+ entity_poly_seq_data.push_back(ost::io::StarWriterValue::FromInt(1));
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
if(entity_info[entity_idx].is_poly) {
const std::vector<String>& mon_ids = entity_info[entity_idx].mon_ids;
for(size_t mon_idx = 0; mon_idx < mon_ids.size(); ++mon_idx) {
- entity_poly_seq_data[0] = ost::io::StarWriterLoopDataItem(entity_idx);
- entity_poly_seq_data[1] = ost::io::StarWriterLoopDataItem(mon_ids[mon_idx]);
- entity_poly_seq_data[2] = ost::io::StarWriterLoopDataItem(mon_idx+1);
+ entity_poly_seq_data[0] = ost::io::StarWriterValue::FromInt(entity_idx);
+ entity_poly_seq_data[1] = ost::io::StarWriterValue::FromString(mon_ids[mon_idx]);
+ entity_poly_seq_data[2] = ost::io::StarWriterValue::FromInt(mon_idx+1);
entity_poly_seq_ptr->AddData(entity_poly_seq_data);
}
}
@@ -1126,15 +1116,15 @@ namespace {
void Feed_entity_poly(ost::io::StarWriterLoopPtr entity_poly_ptr,
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
// reuse data vector for efficiency
- std::vector<ost::io::StarWriterLoopDataItem> entity_poly_data;
- entity_poly_data.push_back(ost::io::StarWriterLoopDataItem(0));
- entity_poly_data.push_back(ost::io::StarWriterLoopDataItem("other"));
- entity_poly_data.push_back(ost::io::StarWriterLoopDataItem("A"));
- entity_poly_data.push_back(ost::io::StarWriterLoopDataItem("A"));
+ std::vector<ost::io::StarWriterValue> entity_poly_data;
+ entity_poly_data.push_back(ost::io::StarWriterValue::FromInt(0));
+ entity_poly_data.push_back(ost::io::StarWriterValue::FromString("other"));
+ entity_poly_data.push_back(ost::io::StarWriterValue::FromString("A"));
+ entity_poly_data.push_back(ost::io::StarWriterValue::FromString("A"));
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
if(entity_info[entity_idx].is_poly) {
- entity_poly_data[0] = ost::io::StarWriterLoopDataItem(entity_idx);
- entity_poly_data[1] = ost::io::StarWriterLoopDataItem(entity_info[entity_idx].poly_type);
+ entity_poly_data[0] = ost::io::StarWriterValue::FromInt(entity_idx);
+ entity_poly_data[1] = ost::io::StarWriterValue::FromString(entity_info[entity_idx].poly_type);
std::stringstream seq;
std::stringstream seq_can;
for(size_t idx = 0; idx < entity_info[entity_idx].mon_ids.size(); ++idx) {
@@ -1151,8 +1141,8 @@ namespace {
seq_can << entity_info[entity_idx].seq_can_olcs[idx];
}
}
- entity_poly_data[2] = seq.str();
- entity_poly_data[3] = seq_can.str();
+ entity_poly_data[2] = ost::io::StarWriterValue::FromString(seq.str());
+ entity_poly_data[3] = ost::io::StarWriterValue::FromString(seq_can.str());
entity_poly_ptr->AddData(entity_poly_data);
}
}
@@ -1160,12 +1150,12 @@ namespace {
void Feed_chem_comp(ost::io::StarWriterLoopPtr chem_comp_ptr,
const std::map<String, CompInfo>& comp_infos) {
- std::vector<ost::io::StarWriterLoopDataItem> comp_data;
- comp_data.push_back(ost::io::StarWriterLoopDataItem("ALA"));
- comp_data.push_back(ost::io::StarWriterLoopDataItem("L-PEPTIDE LINKING"));
+ std::vector<ost::io::StarWriterValue> comp_data;
+ comp_data.push_back(ost::io::StarWriterValue::FromString("ALA"));
+ comp_data.push_back(ost::io::StarWriterValue::FromString("L-PEPTIDE LINKING"));
for(auto it = comp_infos.begin(); it != comp_infos.end(); ++it) {
- comp_data[0] = it->first;
- comp_data[1] = it->second.type;
+ comp_data[0] = ost::io::StarWriterValue::FromString(it->first);
+ comp_data[1] = ost::io::StarWriterValue::FromString(it->second.type);
chem_comp_ptr->AddData(comp_data);
}
}
diff --git a/modules/io/src/mol/star_writer.hh b/modules/io/src/mol/star_writer.hh
index 41e6fbfa875a01717db79066148f7564a218e7c2..61e0f2602c2aee46346d345425900801fec1d8a6 100644
--- a/modules/io/src/mol/star_writer.hh
+++ b/modules/io/src/mol/star_writer.hh
@@ -68,112 +68,93 @@ namespace{
namespace ost { namespace io {
class StarWriterObject;
+class StarWriterValue;
class StarWriterDataItem;
-class StarWriterDataCategory;
class StarWriterLoopDesc;
-class StarWriterLoopDataItem;
class StarWriterLoop;
typedef boost::shared_ptr<StarWriterObject> StarWriterObjectPtr;
+typedef boost::shared_ptr<StarWriterValue> StarWriterValuePtr;
typedef boost::shared_ptr<StarWriterDataItem> StarWriterDataItemPtr;
-typedef boost::shared_ptr<StarWriterDataCategory> StarWriterDataCategoryPtr;
typedef boost::shared_ptr<StarWriterLoopDesc> StarWriterLoopDescPtr;
-typedef boost::shared_ptr<StarWriterLoopDataItem> StarWriterLoopDataItemPtr;
typedef boost::shared_ptr<StarWriterLoop> StarWriterLoopPtr;
+
class DLLEXPORT_OST_IO StarWriterObject {
public:
virtual ~StarWriterObject() { }
virtual void ToStream(std::ostream& s) = 0;
};
-class DLLEXPORT_OST_IO StarWriterDataItem : public StarWriterObject {
+class DLLEXPORT_OST_IO StarWriterValue{
public:
- StarWriterDataItem(const String& category, const String& name,
- const String& value): category_(category), name_(name) {
+ static StarWriterValue FromInt(int int_value) {
+ StarWriterValue value;
+ value.value_ = std::to_string(int_value);
+ return value;
+ }
+ static StarWriterValue FromFloat(Real float_value, int decimals) {
+ StarWriterValue value;
+ fts(float_value, decimals, value.value_);
+ return value;
+ }
+ static StarWriterValue FromString(const String& string_value) {
+ StarWriterValue value;
// cases we still need to deal with:
// - special characters in strings (put in quotation marks)
// - long strings (semicolon based syntax)
// see https://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html
- if(value == "") {
- value_ = ".";
+ if(string_value == "") {
+ value.value_ = ".";
} else {
- value_ = value;
+ value.value_ = string_value;
}
+ return value;
}
-
- StarWriterDataItem(const String& category, const String& name,
- Real value, int decimals): category_(category),
- name_(name) {
- fts(value, decimals, value_);
- }
-
- StarWriterDataItem(const String& category, const String& name,
- int value): category_(category), name_(name) {
- value_ = std::to_string(value);
- }
-
- virtual void ToStream(std::ostream& s) {
- s << category_ << '.' << name_ << ' ' << value_ << std::endl;
- }
-
- const String& GetCategory() const { return category_; }
- const String& GetName() const { return name_; }
const String& GetValue() const { return value_; }
private:
- String category_;
- String name_;
- String value_;
+// force construction through static members
+StarWriterValue() { }
+String value_;
};
-class DLLEXPORT_OST_IO StarWriterDataCategory : public StarWriterObject {
-public:
- StarWriterDataCategory(const String& category): category_(category) { }
-
- void Add(const StarWriterDataItem& data_item) {
- if(data_item.GetCategory() != category_) {
- throw ost::io::IOException("category mismatch");
- }
- data_items_.push_back(data_item);
- }
+class DLLEXPORT_OST_IO StarWriterDataItem : public StarWriterObject {
+public:
+ StarWriterDataItem(const String& category, const String& attribute,
+ const StarWriterValue& value): category_(category),
+ attribute_(attribute),
+ value_(value) { }
virtual void ToStream(std::ostream& s) {
- for(auto it = data_items_.begin(); it != data_items_.end(); ++it) {
- it->ToStream(s);
- }
+ s << category_ << '.' << attribute_ << ' ' << value_.GetValue() << std::endl;
}
-
+ const String& GetCategory() const { return category_; }
+ const String& GetAttribute() const { return attribute_; }
+ const StarWriterValue& GetValue() const { return value_; }
private:
String category_;
- std::vector<StarWriterDataItem> data_items_;
+ String attribute_;
+ StarWriterValue value_;
};
+
class DLLEXPORT_OST_IO StarWriterLoopDesc : public StarWriterObject {
public:
- StarWriterLoopDesc(): category_("") { }
+ StarWriterLoopDesc(const String& category): category_(category) { }
- int GetIndex(const String& name) const {
- std::map<String, int>::const_iterator i=index_map_.find(name);
+ int GetIndex(const String& attribute) const {
+ std::map<String, int>::const_iterator i=index_map_.find(attribute);
return i==index_map_.end() ? -1 : i->second;
}
- void SetCategory(const String& category) {
- category_=category;
- }
-
- void Add(const String& name) {
- index_map_.insert(std::make_pair(name, index_map_.size()));
+ void Add(const String& attribute) {
+ index_map_.insert(std::make_pair(attribute, index_map_.size()));
}
size_t GetSize() const {
return index_map_.size();
}
- void Clear() {
- category_.clear();
- index_map_.clear();
- }
-
virtual void ToStream(std::ostream& s) {
std::vector<std::pair<int, String> > tmp;
for(auto it = index_map_.begin(); it != index_map_.end(); ++it) {
@@ -191,76 +172,22 @@ private:
std::map<String, int> index_map_;
};
-class DLLEXPORT_OST_IO StarWriterLoopDataItem{
-public:
-
- StarWriterLoopDataItem(const String& value) {
- // cases we still need to deal with:
- // - special characters in strings (put in quotation marks)
- // - long strings (semicolon based syntax)
- // see https://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html
-
-
- bool has_space = false;
- for(char c: value) {
- if(isspace(c)) {
- has_space = true;
- break;
- }
- }
- if(value == "") {
- value_ = ".";
- } else if(has_space) {
- value_ = "'" + value + "'";
- }
- else {
- value_ = value;
- }
- }
-
- StarWriterLoopDataItem(Real value, int decimals) {
- fts(value, decimals, value_);
- }
-
- StarWriterLoopDataItem(int value) {
- value_ = std::to_string(value);
- }
-
- const String& GetValue() const { return value_; }
-
- virtual void ToStream(std::ostream& s) {
- s << value_;
- }
-
-private:
- String value_;
-};
class DLLEXPORT_OST_IO StarWriterLoop: public StarWriterObject {
public:
- StarWriterLoop() { }
-
StarWriterLoop(const StarWriterLoopDesc& desc): desc_(desc) { }
- void SetDesc(const StarWriterLoopDesc& desc) {
- if(!data_.empty()) {
- throw ost::io::IOException("Can only set new StarLoop desc in "
- "in empty loop");
- }
- desc_ = desc;
- }
-
const StarWriterLoopDesc& GetDesc() { return desc_; }
- void AddData(const std::vector<StarWriterLoopDataItem>& data) {
+ void AddData(const std::vector<StarWriterValue>& data) {
if(data.size() != desc_.GetSize()) {
throw ost::io::IOException("Invalid data size when adding to StarLoop");
}
data_.insert(data_.end(), data.begin(), data.end());
}
- const std::vector<StarWriterLoopDataItem>& GetData() { return data_; }
+ const std::vector<StarWriterValue>& GetData() { return data_; }
int GetN() {
return data_.size() / desc_.GetSize();
@@ -271,7 +198,7 @@ public:
desc_.ToStream(s);
int desc_size = desc_.GetSize();
for(size_t i = 0; i < data_.size(); ++i) {
- data_[i].ToStream(s);
+ s << data_[i].GetValue();
if((i+1) % desc_size == 0) {
s << std::endl;
} else {
@@ -282,7 +209,7 @@ public:
private:
StarWriterLoopDesc desc_;
- std::vector<StarWriterLoopDataItem> data_;
+ std::vector<StarWriterValue> data_;
};