39 |
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* such damages. |
40 |
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*/ |
41 |
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|
42 |
+ |
#include <stack> |
43 |
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#include "selection/SelectionEvaluator.hpp" |
44 |
+ |
#include "primitives/Atom.hpp" |
45 |
+ |
#include "primitives/DirectionalAtom.hpp" |
46 |
+ |
#include "primitives/RigidBody.hpp" |
47 |
+ |
#include "primitives/Molecule.hpp" |
48 |
+ |
|
49 |
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namespace oopse { |
50 |
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|
51 |
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|
52 |
+ |
SelectionEvaluator::SelectionEvaluator(SimInfo* si) : info(si), finder(info), isLoaded_(false){ |
53 |
+ |
|
54 |
+ |
} |
55 |
+ |
|
56 |
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bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) { |
57 |
+ |
clearDefinitionsAndLoadPredefined(); |
58 |
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this->filename = filename; |
59 |
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this->script = script; |
60 |
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if (! compiler.compile(filename, script)) { |
61 |
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error = true; |
62 |
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errorMessage = compiler.getErrorMessage(); |
63 |
+ |
std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl; |
64 |
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return false; |
65 |
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} |
66 |
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|
68 |
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aatoken = compiler.getAatokenCompiled(); |
69 |
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linenumbers = compiler.getLineNumbers(); |
70 |
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lineIndices = compiler.getLineIndices(); |
71 |
+ |
|
72 |
+ |
std::vector<std::vector<Token> >::const_iterator i; |
73 |
+ |
|
74 |
+ |
isDynamic_ = false; |
75 |
+ |
for (i = aatoken.begin(); i != aatoken.end(); ++i) { |
76 |
+ |
if (containDynamicToken(*i)) { |
77 |
+ |
isDynamic_ = true; |
78 |
+ |
break; |
79 |
+ |
} |
80 |
+ |
} |
81 |
+ |
|
82 |
+ |
isLoaded_ = true; |
83 |
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return true; |
84 |
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} |
85 |
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|
86 |
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void SelectionEvaluator::clearState() { |
87 |
< |
for (int i = scriptLevelMax; --i >= 0; ) |
88 |
< |
stack[i] = null; |
89 |
< |
scriptLevel = 0; |
87 |
> |
//for (int i = scriptLevelMax; --i >= 0; ) |
88 |
> |
// stack[i].clear(); |
89 |
> |
//scriptLevel = 0; |
90 |
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error = false; |
91 |
< |
errorMessage = null; |
91 |
> |
errorMessage = ""; |
92 |
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} |
93 |
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|
94 |
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bool SelectionEvaluator::loadScriptString(const std::string& script) { |
95 |
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clearState(); |
96 |
< |
return loadScript(null, script); |
96 |
> |
return loadScript("", script); |
97 |
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} |
98 |
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|
99 |
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bool SelectionEvaluator::loadScriptFile(const std::string& filename) { |
101 |
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return loadScriptFileInternal(filename); |
102 |
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} |
103 |
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|
104 |
+ |
bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) { |
105 |
+ |
ifstream ifs(filename.c_str()); |
106 |
+ |
if (!ifs.is_open()) { |
107 |
+ |
return false; |
108 |
+ |
} |
109 |
|
|
110 |
< |
void SelectionEvaluator::instructionDispatchLoop(){ |
110 |
> |
const int bufferSize = 65535; |
111 |
> |
char buffer[bufferSize]; |
112 |
> |
std::string script; |
113 |
> |
while(ifs.getline(buffer, bufferSize)) { |
114 |
> |
script += buffer; |
115 |
> |
} |
116 |
> |
return loadScript(filename, script); |
117 |
> |
} |
118 |
|
|
119 |
< |
while ( pc < aatoken.length) { |
119 |
> |
void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){ |
120 |
> |
|
121 |
> |
while ( pc < aatoken.size()) { |
122 |
|
statement = aatoken[pc++]; |
123 |
< |
statementLength = statement.length; |
123 |
> |
statementLength = statement.size(); |
124 |
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Token token = statement[0]; |
125 |
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switch (token.tok) { |
126 |
< |
case Token.define: |
126 |
> |
case Token::define: |
127 |
|
define(); |
128 |
|
break; |
129 |
< |
case Token.select: |
130 |
< |
select(); |
129 |
> |
case Token::select: |
130 |
> |
select(bs); |
131 |
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break; |
132 |
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default: |
133 |
|
unrecognizedCommand(token); |
134 |
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return; |
135 |
|
} |
136 |
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} |
137 |
+ |
|
138 |
|
} |
139 |
|
|
140 |
< |
void SelectionEvaluator::predefine(String script) { |
102 |
< |
if (compiler.compile("#predefine", script)) { |
103 |
< |
Token [][] aatoken = compiler.getAatokenCompiled(); |
104 |
< |
if (aatoken.length != 1) { |
105 |
< |
viewer.scriptStatus("predefinition does not have exactly 1 command:" |
106 |
< |
+ script); |
107 |
< |
return; |
108 |
< |
} |
109 |
< |
Token[] statement = aatoken[0]; |
110 |
< |
if (statement.length > 2) { |
111 |
< |
int tok = statement[1].tok; |
112 |
< |
if (tok == Token.identifier || |
113 |
< |
(tok & Token.predefinedset) == Token.predefinedset) { |
114 |
< |
String variable = (String)statement[1].value; |
115 |
< |
variables.put(variable, statement); |
116 |
< |
} else { |
117 |
< |
viewer.scriptStatus("invalid variable name:" + script); |
118 |
< |
} |
119 |
< |
} else { |
120 |
< |
viewer.scriptStatus("bad predefinition length:" + script); |
121 |
< |
} |
122 |
< |
} else { |
123 |
< |
viewer.scriptStatus("predefined set compile error:" + script + |
124 |
< |
"\ncompile error:" + compiler.getErrorMessage()); |
125 |
< |
} |
126 |
< |
} |
127 |
< |
|
128 |
< |
|
129 |
< |
|
130 |
< |
BitSet SelectionEvaluator::expression(Token[] code, int pcStart) throws ScriptException { |
131 |
< |
int numberOfAtoms = viewer.getAtomCount(); |
140 |
> |
BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) { |
141 |
|
BitSet bs; |
142 |
< |
BitSet[] stack = new BitSet[10]; |
143 |
< |
int sp = 0; |
144 |
< |
|
136 |
< |
for (int pc = pcStart; ; ++pc) { |
142 |
> |
std::stack<BitSet> stack; |
143 |
> |
|
144 |
> |
for (int pc = pcStart; pc < code.size(); ++pc) { |
145 |
|
Token instruction = code[pc]; |
146 |
< |
if (logMessages) |
139 |
< |
viewer.scriptStatus("instruction=" + instruction); |
146 |
> |
|
147 |
|
switch (instruction.tok) { |
148 |
< |
case Token.expressionBegin: |
148 |
> |
case Token::expressionBegin: |
149 |
|
break; |
150 |
< |
case Token.expressionEnd: |
144 |
< |
break expression_loop; |
145 |
< |
case Token.all: |
146 |
< |
bs = stack[sp++] = new BitSet(numberOfAtoms); |
147 |
< |
for (int i = numberOfAtoms; --i >= 0; ) |
148 |
< |
bs.set(i); |
150 |
> |
case Token::expressionEnd: |
151 |
|
break; |
152 |
< |
case Token.none: |
153 |
< |
stack[sp++] = new BitSet(); |
152 |
> |
case Token::all: |
153 |
> |
bs = BitSet(nStuntDouble); |
154 |
> |
bs.setAll(); |
155 |
> |
stack.push(bs); |
156 |
|
break; |
157 |
< |
case Token.opOr: |
158 |
< |
bs = stack[--sp]; |
159 |
< |
stack[sp-1].or(bs); |
157 |
> |
case Token::none: |
158 |
> |
bs = BitSet(nStuntDouble); |
159 |
> |
stack.push(bs); |
160 |
|
break; |
161 |
< |
case Token.opAnd: |
162 |
< |
bs = stack[--sp]; |
163 |
< |
stack[sp-1].and(bs); |
161 |
> |
case Token::opOr: |
162 |
> |
bs = stack.top(); |
163 |
> |
stack.pop(); |
164 |
> |
stack.top() |= bs; |
165 |
|
break; |
166 |
< |
case Token.opNot: |
167 |
< |
bs = stack[sp - 1]; |
168 |
< |
notSet(bs); |
166 |
> |
case Token::opAnd: |
167 |
> |
bs = stack.top(); |
168 |
> |
stack.pop(); |
169 |
> |
stack.top() &= bs; |
170 |
|
break; |
171 |
< |
case Token.within: |
172 |
< |
bs = stack[sp - 1]; |
167 |
< |
stack[sp - 1] = new BitSet(); |
168 |
< |
withinInstruction(instruction, bs, stack[sp - 1]); |
171 |
> |
case Token::opNot: |
172 |
> |
stack.top().flip(); |
173 |
|
break; |
174 |
< |
case Token.selected: |
175 |
< |
stack[sp++] = copyBitSet(viewer.getSelectionSet()); |
174 |
> |
case Token::within: |
175 |
> |
|
176 |
> |
withinInstruction(instruction, stack.top()); |
177 |
|
break; |
178 |
< |
case Token.y: |
179 |
< |
case Token.amino: |
180 |
< |
case Token.backbone: |
181 |
< |
case Token.solvent: |
182 |
< |
case Token.identifier: |
178 |
< |
case Token.sidechain: |
179 |
< |
case Token.surface: |
180 |
< |
stack[sp++] = lookupIdentifierValue((String)instruction.value); |
178 |
> |
//case Token::selected: |
179 |
> |
// stack.push(getSelectionSet()); |
180 |
> |
// break; |
181 |
> |
case Token::name: |
182 |
> |
stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value))); |
183 |
|
break; |
182 |
– |
case Token.opLT: |
183 |
– |
case Token.opLE: |
184 |
– |
case Token.opGE: |
185 |
– |
case Token.opGT: |
186 |
– |
case Token.opEQ: |
187 |
– |
case Token.opNE: |
188 |
– |
bs = stack[sp++] = new BitSet(); |
189 |
– |
comparatorInstruction(instruction, bs); |
184 |
|
break; |
185 |
+ |
case Token::identifier: |
186 |
+ |
stack.push(lookupValue(boost::any_cast<std::string>(instruction.value))); |
187 |
+ |
break; |
188 |
+ |
case Token::opLT: |
189 |
+ |
case Token::opLE: |
190 |
+ |
case Token::opGE: |
191 |
+ |
case Token::opGT: |
192 |
+ |
case Token::opEQ: |
193 |
+ |
case Token::opNE: |
194 |
+ |
stack.push(comparatorInstruction(instruction)); |
195 |
+ |
break; |
196 |
|
default: |
197 |
|
unrecognizedExpression(); |
198 |
|
} |
199 |
|
} |
200 |
< |
if (sp != 1) |
200 |
> |
if (stack.size() != 1) |
201 |
|
evalError("atom expression compiler error - stack over/underflow"); |
202 |
< |
return stack[0]; |
202 |
> |
|
203 |
> |
return stack.top(); |
204 |
|
} |
205 |
|
|
206 |
|
|
207 |
|
|
208 |
< |
void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) { |
208 |
> |
BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
209 |
|
int comparator = instruction.tok; |
210 |
|
int property = instruction.intValue; |
211 |
< |
float propertyValue = 0; // just for temperature |
212 |
< |
int comparisonValue = ((Integer)instruction.value).intValue(); |
213 |
< |
int numberOfAtoms = viewer.getAtomCount(); |
214 |
< |
Frame frame = viewer.getFrame(); |
215 |
< |
for (int i = 0; i < numberOfAtoms; ++i) { |
216 |
< |
Atom atom = frame.getAtomAt(i); |
217 |
< |
switch (property) { |
218 |
< |
case Token.atomno: |
219 |
< |
propertyValue = atom.getAtomNumber(); |
220 |
< |
break; |
221 |
< |
case Token.elemno: |
222 |
< |
propertyValue = atom.getElementNumber(); |
223 |
< |
break; |
224 |
< |
case Token.temperature: |
225 |
< |
propertyValue = atom.getBfactor100(); |
226 |
< |
if (propertyValue < 0) |
227 |
< |
continue; |
228 |
< |
propertyValue /= 100; |
229 |
< |
break; |
230 |
< |
case Token._atomID: |
231 |
< |
propertyValue = atom.getSpecialAtomID(); |
226 |
< |
if (propertyValue < 0) |
227 |
< |
continue; |
228 |
< |
break; |
229 |
< |
case Token._structure: |
230 |
< |
propertyValue = getProteinStructureType(atom); |
231 |
< |
if (propertyValue == -1) |
232 |
< |
continue; |
233 |
< |
break; |
234 |
< |
case Token.radius: |
235 |
< |
propertyValue = atom.getRasMolRadius(); |
236 |
< |
break; |
237 |
< |
case Token._bondedcount: |
238 |
< |
propertyValue = atom.getCovalentBondCount(); |
239 |
< |
break; |
240 |
< |
case Token.model: |
241 |
< |
propertyValue = atom.getModelTagNumber(); |
242 |
< |
break; |
243 |
< |
default: |
244 |
< |
unrecognizedAtomProperty(property); |
245 |
< |
} |
246 |
< |
boolean match = false; |
247 |
< |
switch (comparator) { |
248 |
< |
case Token.opLT: |
249 |
< |
match = propertyValue < comparisonValue; |
250 |
< |
break; |
251 |
< |
case Token.opLE: |
252 |
< |
match = propertyValue <= comparisonValue; |
253 |
< |
break; |
254 |
< |
case Token.opGE: |
255 |
< |
match = propertyValue >= comparisonValue; |
256 |
< |
break; |
257 |
< |
case Token.opGT: |
258 |
< |
match = propertyValue > comparisonValue; |
259 |
< |
break; |
260 |
< |
case Token.opEQ: |
261 |
< |
match = propertyValue == comparisonValue; |
262 |
< |
break; |
263 |
< |
case Token.opNE: |
264 |
< |
match = propertyValue != comparisonValue; |
265 |
< |
break; |
266 |
< |
} |
267 |
< |
if (match) |
268 |
< |
bs.set(i); |
211 |
> |
float comparisonValue = boost::any_cast<float>(instruction.value); |
212 |
> |
float propertyValue; |
213 |
> |
BitSet bs(nStuntDouble); |
214 |
> |
|
215 |
> |
SimInfo::MoleculeIterator mi; |
216 |
> |
Molecule* mol; |
217 |
> |
Molecule::AtomIterator ai; |
218 |
> |
Atom* atom; |
219 |
> |
Molecule::RigidBodyIterator rbIter; |
220 |
> |
RigidBody* rb; |
221 |
> |
|
222 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
223 |
> |
|
224 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
225 |
> |
compareProperty(atom, bs, property, comparator, comparisonValue); |
226 |
> |
} |
227 |
> |
|
228 |
> |
//change the positions of atoms which belong to the rigidbodies |
229 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
230 |
> |
compareProperty(rb, bs, property, comparator, comparisonValue); |
231 |
> |
} |
232 |
|
} |
270 |
– |
} |
233 |
|
|
234 |
< |
void SelectionEvaluator::withinInstruction(Token instruction, BitSet bs, BitSet bsResult) |
234 |
> |
return bs; |
235 |
> |
} |
236 |
|
|
237 |
< |
Object withinSpec = instruction.value; |
238 |
< |
if (withinSpec instanceof Float) { |
239 |
< |
withinDistance(((Float)withinSpec).floatValue(), bs, bsResult); |
237 |
> |
void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) { |
238 |
> |
double propertyValue; |
239 |
> |
switch (property) { |
240 |
> |
case Token::mass: |
241 |
> |
propertyValue = sd->getMass(); |
242 |
> |
break; |
243 |
> |
case Token::charge: |
244 |
> |
return; |
245 |
> |
//break; |
246 |
> |
case Token::dipole: |
247 |
> |
return; |
248 |
> |
//break; |
249 |
> |
default: |
250 |
> |
unrecognizedAtomProperty(property); |
251 |
> |
} |
252 |
> |
|
253 |
> |
bool match = false; |
254 |
> |
switch (comparator) { |
255 |
> |
case Token::opLT: |
256 |
> |
match = propertyValue < comparisonValue; |
257 |
> |
break; |
258 |
> |
case Token::opLE: |
259 |
> |
match = propertyValue <= comparisonValue; |
260 |
> |
break; |
261 |
> |
case Token::opGE: |
262 |
> |
match = propertyValue >= comparisonValue; |
263 |
> |
break; |
264 |
> |
case Token::opGT: |
265 |
> |
match = propertyValue > comparisonValue; |
266 |
> |
break; |
267 |
> |
case Token::opEQ: |
268 |
> |
match = propertyValue == comparisonValue; |
269 |
> |
break; |
270 |
> |
case Token::opNE: |
271 |
> |
match = propertyValue != comparisonValue; |
272 |
> |
break; |
273 |
> |
} |
274 |
> |
if (match) |
275 |
> |
bs.setBitOn(sd->getGlobalIndex()); |
276 |
> |
|
277 |
> |
} |
278 |
> |
|
279 |
> |
void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){ |
280 |
> |
|
281 |
> |
boost::any withinSpec = instruction.value; |
282 |
> |
if (withinSpec.type() == typeid(float)){ |
283 |
> |
// |
284 |
|
return; |
285 |
|
} |
286 |
< |
evalError("Unrecognized within parameter:" + withinSpec); |
286 |
> |
|
287 |
> |
evalError("Unrecognized within parameter"); |
288 |
|
} |
289 |
|
|
290 |
< |
void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) { |
291 |
< |
Frame frame = viewer.getFrame(); |
292 |
< |
for (int i = frame.getAtomCount(); --i >= 0; ) { |
293 |
< |
if (bs.get(i)) { |
294 |
< |
Atom atom = frame.getAtomAt(i); |
295 |
< |
AtomIterator iterWithin = |
296 |
< |
frame.getWithinIterator(atom, distance); |
297 |
< |
while (iterWithin.hasNext()) |
298 |
< |
bsResult.set(iterWithin.next().getAtomIndex()); |
299 |
< |
} |
290 |
> |
void SelectionEvaluator::define() { |
291 |
> |
assert(statement.size() >= 3); |
292 |
> |
|
293 |
> |
std::string variable = boost::any_cast<std::string>(statement[1].value); |
294 |
> |
|
295 |
> |
variables.insert(std::make_pair(variable, expression(statement, 2))); |
296 |
> |
} |
297 |
> |
|
298 |
> |
|
299 |
> |
/** @todo */ |
300 |
> |
void SelectionEvaluator::predefine(const std::string& script) { |
301 |
> |
|
302 |
> |
if (compiler.compile("#predefine", script)) { |
303 |
> |
std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled(); |
304 |
> |
if (aatoken.size() != 1) { |
305 |
> |
evalError("predefinition does not have exactly 1 command:" |
306 |
> |
+ script); |
307 |
> |
return; |
308 |
> |
} |
309 |
> |
std::vector<Token> statement = aatoken[0]; |
310 |
> |
if (statement.size() > 2) { |
311 |
> |
int tok = statement[1].tok; |
312 |
> |
if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) { |
313 |
> |
std::string variable = boost::any_cast<std::string>(statement[1].value); |
314 |
> |
variables.insert(std::make_pair(variable, statement)); |
315 |
> |
|
316 |
> |
} else { |
317 |
> |
evalError("invalid variable name:" + script); |
318 |
> |
} |
319 |
> |
}else { |
320 |
> |
evalError("bad predefinition length:" + script); |
321 |
> |
} |
322 |
> |
|
323 |
> |
|
324 |
> |
} else { |
325 |
> |
evalError("predefined set compile error:" + script + |
326 |
> |
"\ncompile error:" + compiler.getErrorMessage()); |
327 |
|
} |
293 |
– |
} |
328 |
|
|
295 |
– |
void SelectionEvaluator::define() throws ScriptException { |
296 |
– |
String variable = (String)statement[1].value; |
297 |
– |
variables.put(variable, (expression(statement, 2))); |
298 |
– |
} |
329 |
|
} |
330 |
|
|
331 |
< |
void SelectionEvaluator::predefine(Token[] statement) { |
332 |
< |
String variable = (String)statement[1].value; |
333 |
< |
variables.put(variable, statement); |
304 |
< |
} |
331 |
> |
void SelectionEvaluator::select(BitSet& bs){ |
332 |
> |
bs = expression(statement, 1); |
333 |
> |
} |
334 |
|
|
335 |
< |
void SelectionEvaluator::select(){ |
336 |
< |
// NOTE this is called by restrict() |
337 |
< |
if (statementLength == 1) { |
338 |
< |
viewer.selectAll(); |
339 |
< |
if (!viewer.getRasmolHydrogenSetting()) |
340 |
< |
viewer.excludeSelectionSet(getHydrogenSet()); |
341 |
< |
if (!viewer.getRasmolHeteroSetting()) |
342 |
< |
viewer.excludeSelectionSet(getHeteroSet()); |
335 |
> |
BitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
336 |
> |
|
337 |
> |
std::map<std::string, boost::any>::iterator i = variables.find(variable); |
338 |
> |
|
339 |
> |
if (i != variables.end()) { |
340 |
> |
if (i->second.type() == typeid(BitSet)) { |
341 |
> |
return boost::any_cast<BitSet>(i->second); |
342 |
> |
} else if (i->second.type() == typeid(std::vector<Token>)){ |
343 |
> |
BitSet bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2); |
344 |
> |
i->second = bs; /**@todo fixme */ |
345 |
> |
return bs; |
346 |
> |
} |
347 |
|
} else { |
348 |
< |
viewer.setSelectionSet(expression(statement, 1)); |
348 |
> |
unrecognizedIdentifier(variable); |
349 |
|
} |
350 |
< |
viewer.scriptStatus("" + viewer.getSelectionCount() + " atoms selected"); |
351 |
< |
} |
352 |
< |
|
353 |
< |
} |
350 |
> |
} |
351 |
> |
|
352 |
> |
BitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
353 |
> |
|
354 |
> |
return finder.match(name); |
355 |
> |
|
356 |
> |
} |
357 |
> |
|
358 |
> |
bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){ |
359 |
> |
std::vector<Token>::const_iterator i; |
360 |
> |
for (i = tokens.begin(); i != tokens.end(); ++i) { |
361 |
> |
if (i->tok & Token::dynamic) { |
362 |
> |
return true; |
363 |
> |
} |
364 |
> |
} |
365 |
> |
|
366 |
> |
return false; |
367 |
> |
} |
368 |
> |
|
369 |
> |
void SelectionEvaluator::clearDefinitionsAndLoadPredefined() { |
370 |
> |
variables.clear(); |
371 |
> |
//load predefine |
372 |
> |
//predefine(); |
373 |
> |
} |
374 |
> |
|
375 |
> |
BitSet SelectionEvaluator::evaluate() { |
376 |
> |
BitSet bs(nStuntDouble); |
377 |
> |
if (isLoaded_) { |
378 |
> |
instructionDispatchLoop(bs); |
379 |
> |
} |
380 |
> |
|
381 |
> |
return bs; |
382 |
> |
} |
383 |
> |
|
384 |
> |
//BitSet SelectionEvaluator::evaluate(int frameNo) { |
385 |
> |
// |
386 |
> |
//} |
387 |
> |
|
388 |
> |
} |