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namespace oopse { |
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|
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|
46 |
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bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) { |
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this->filename = filename; |
48 |
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this->script = script; |
49 |
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if (! compiler.compile(filename, script)) { |
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error = true; |
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errorMessage = compiler.getErrorMessage(); |
52 |
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return false; |
53 |
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} |
54 |
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|
55 |
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pc = 0; |
56 |
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aatoken = compiler.getAatokenCompiled(); |
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linenumbers = compiler.getLineNumbers(); |
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lineIndices = compiler.getLineIndices(); |
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return true; |
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} |
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|
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void SelectionEvaluator::clearState() { |
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for (int i = scriptLevelMax; --i >= 0; ) |
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stack[i] = null; |
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scriptLevel = 0; |
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error = false; |
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errorMessage = null; |
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} |
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|
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bool SelectionEvaluator::loadScriptString(const std::string& script) { |
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clearState(); |
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return loadScript(null, script); |
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} |
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|
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bool SelectionEvaluator::loadScriptFile(const std::string& filename) { |
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clearState(); |
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return loadScriptFileInternal(filename); |
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} |
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|
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|
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void SelectionEvaluator::instructionDispatchLoop(){ |
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|
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while ( pc < aatoken.length) { |
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statement = aatoken[pc++]; |
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statementLength = statement.length; |
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Token token = statement[0]; |
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switch (token.tok) { |
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case Token.define: |
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define(); |
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break; |
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case Token.select: |
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select(); |
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break; |
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default: |
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unrecognizedCommand(token); |
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return; |
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} |
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} |
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} |
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|
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void SelectionEvaluator::predefine(String script) { |
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if (compiler.compile("#predefine", script)) { |
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Token [][] aatoken = compiler.getAatokenCompiled(); |
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if (aatoken.length != 1) { |
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viewer.scriptStatus("predefinition does not have exactly 1 command:" |
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+ script); |
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return; |
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} |
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Token[] statement = aatoken[0]; |
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if (statement.length > 2) { |
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int tok = statement[1].tok; |
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if (tok == Token.identifier || |
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(tok & Token.predefinedset) == Token.predefinedset) { |
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String variable = (String)statement[1].value; |
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variables.put(variable, statement); |
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} else { |
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viewer.scriptStatus("invalid variable name:" + script); |
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} |
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} else { |
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viewer.scriptStatus("bad predefinition length:" + script); |
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} |
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} else { |
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viewer.scriptStatus("predefined set compile error:" + script + |
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"\ncompile error:" + compiler.getErrorMessage()); |
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} |
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} |
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|
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|
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|
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BitSet SelectionEvaluator::expression(Token[] code, int pcStart) throws ScriptException { |
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int numberOfAtoms = viewer.getAtomCount(); |
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BitSet bs; |
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BitSet[] stack = new BitSet[10]; |
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int sp = 0; |
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|
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for (int pc = pcStart; ; ++pc) { |
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Token instruction = code[pc]; |
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if (logMessages) |
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viewer.scriptStatus("instruction=" + instruction); |
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switch (instruction.tok) { |
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case Token.expressionBegin: |
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break; |
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case Token.expressionEnd: |
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break expression_loop; |
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case Token.all: |
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bs = stack[sp++] = new BitSet(numberOfAtoms); |
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for (int i = numberOfAtoms; --i >= 0; ) |
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bs.set(i); |
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break; |
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case Token.none: |
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stack[sp++] = new BitSet(); |
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break; |
153 |
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case Token.opOr: |
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bs = stack[--sp]; |
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stack[sp-1].or(bs); |
156 |
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break; |
157 |
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case Token.opAnd: |
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bs = stack[--sp]; |
159 |
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stack[sp-1].and(bs); |
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break; |
161 |
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case Token.opNot: |
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bs = stack[sp - 1]; |
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notSet(bs); |
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break; |
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case Token.within: |
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bs = stack[sp - 1]; |
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stack[sp - 1] = new BitSet(); |
168 |
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withinInstruction(instruction, bs, stack[sp - 1]); |
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break; |
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case Token.selected: |
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stack[sp++] = copyBitSet(viewer.getSelectionSet()); |
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break; |
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case Token.y: |
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case Token.amino: |
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case Token.backbone: |
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case Token.solvent: |
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case Token.identifier: |
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case Token.sidechain: |
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case Token.surface: |
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stack[sp++] = lookupIdentifierValue((String)instruction.value); |
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break; |
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case Token.opLT: |
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case Token.opLE: |
184 |
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case Token.opGE: |
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case Token.opGT: |
186 |
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case Token.opEQ: |
187 |
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case Token.opNE: |
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bs = stack[sp++] = new BitSet(); |
189 |
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comparatorInstruction(instruction, bs); |
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break; |
191 |
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default: |
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unrecognizedExpression(); |
193 |
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} |
194 |
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} |
195 |
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if (sp != 1) |
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evalError("atom expression compiler error - stack over/underflow"); |
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return stack[0]; |
198 |
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} |
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|
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|
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|
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void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) { |
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int comparator = instruction.tok; |
204 |
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int property = instruction.intValue; |
205 |
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float propertyValue = 0; // just for temperature |
206 |
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int comparisonValue = ((Integer)instruction.value).intValue(); |
207 |
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int numberOfAtoms = viewer.getAtomCount(); |
208 |
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Frame frame = viewer.getFrame(); |
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for (int i = 0; i < numberOfAtoms; ++i) { |
210 |
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Atom atom = frame.getAtomAt(i); |
211 |
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switch (property) { |
212 |
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case Token.atomno: |
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propertyValue = atom.getAtomNumber(); |
214 |
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break; |
215 |
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case Token.elemno: |
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propertyValue = atom.getElementNumber(); |
217 |
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break; |
218 |
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case Token.temperature: |
219 |
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propertyValue = atom.getBfactor100(); |
220 |
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if (propertyValue < 0) |
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continue; |
222 |
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propertyValue /= 100; |
223 |
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break; |
224 |
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case Token._atomID: |
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propertyValue = atom.getSpecialAtomID(); |
226 |
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if (propertyValue < 0) |
227 |
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continue; |
228 |
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break; |
229 |
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case Token._structure: |
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propertyValue = getProteinStructureType(atom); |
231 |
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if (propertyValue == -1) |
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continue; |
233 |
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break; |
234 |
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case Token.radius: |
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propertyValue = atom.getRasMolRadius(); |
236 |
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break; |
237 |
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case Token._bondedcount: |
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propertyValue = atom.getCovalentBondCount(); |
239 |
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break; |
240 |
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case Token.model: |
241 |
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propertyValue = atom.getModelTagNumber(); |
242 |
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break; |
243 |
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default: |
244 |
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unrecognizedAtomProperty(property); |
245 |
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} |
246 |
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boolean match = false; |
247 |
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switch (comparator) { |
248 |
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case Token.opLT: |
249 |
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match = propertyValue < comparisonValue; |
250 |
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break; |
251 |
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case Token.opLE: |
252 |
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match = propertyValue <= comparisonValue; |
253 |
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break; |
254 |
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case Token.opGE: |
255 |
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match = propertyValue >= comparisonValue; |
256 |
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break; |
257 |
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case Token.opGT: |
258 |
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match = propertyValue > comparisonValue; |
259 |
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break; |
260 |
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case Token.opEQ: |
261 |
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match = propertyValue == comparisonValue; |
262 |
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break; |
263 |
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case Token.opNE: |
264 |
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match = propertyValue != comparisonValue; |
265 |
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break; |
266 |
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} |
267 |
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if (match) |
268 |
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bs.set(i); |
269 |
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} |
270 |
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} |
271 |
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|
272 |
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void SelectionEvaluator::withinInstruction(Token instruction, BitSet bs, BitSet bsResult) |
273 |
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|
274 |
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Object withinSpec = instruction.value; |
275 |
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if (withinSpec instanceof Float) { |
276 |
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withinDistance(((Float)withinSpec).floatValue(), bs, bsResult); |
277 |
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return; |
278 |
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} |
279 |
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evalError("Unrecognized within parameter:" + withinSpec); |
280 |
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} |
281 |
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|
282 |
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void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) { |
283 |
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Frame frame = viewer.getFrame(); |
284 |
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for (int i = frame.getAtomCount(); --i >= 0; ) { |
285 |
+ |
if (bs.get(i)) { |
286 |
+ |
Atom atom = frame.getAtomAt(i); |
287 |
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AtomIterator iterWithin = |
288 |
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frame.getWithinIterator(atom, distance); |
289 |
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while (iterWithin.hasNext()) |
290 |
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bsResult.set(iterWithin.next().getAtomIndex()); |
291 |
+ |
} |
292 |
+ |
} |
293 |
+ |
} |
294 |
+ |
|
295 |
+ |
void SelectionEvaluator::define() throws ScriptException { |
296 |
+ |
String variable = (String)statement[1].value; |
297 |
+ |
variables.put(variable, (expression(statement, 2))); |
298 |
+ |
} |
299 |
+ |
} |
300 |
+ |
|
301 |
+ |
void SelectionEvaluator::predefine(Token[] statement) { |
302 |
+ |
String variable = (String)statement[1].value; |
303 |
+ |
variables.put(variable, statement); |
304 |
+ |
} |
305 |
+ |
|
306 |
+ |
void SelectionEvaluator::select(){ |
307 |
+ |
// NOTE this is called by restrict() |
308 |
+ |
if (statementLength == 1) { |
309 |
+ |
viewer.selectAll(); |
310 |
+ |
if (!viewer.getRasmolHydrogenSetting()) |
311 |
+ |
viewer.excludeSelectionSet(getHydrogenSet()); |
312 |
+ |
if (!viewer.getRasmolHeteroSetting()) |
313 |
+ |
viewer.excludeSelectionSet(getHeteroSet()); |
314 |
+ |
} else { |
315 |
+ |
viewer.setSelectionSet(expression(statement, 1)); |
316 |
+ |
} |
317 |
+ |
viewer.scriptStatus("" + viewer.getSelectionCount() + " atoms selected"); |
318 |
+ |
} |
319 |
+ |
|
320 |
+ |
} |