--- trunk/src/selection/SelectionEvaluator.cpp	2005/02/03 14:04:59	282
+++ trunk/src/selection/SelectionEvaluator.cpp	2006/05/17 21:51:42	963
@@ -39,75 +39,108 @@
  * such damages.
  */
 
+#include <stack>
 #include "selection/SelectionEvaluator.hpp"
+#include "primitives/Atom.hpp"
+#include "primitives/DirectionalAtom.hpp"
+#include "primitives/RigidBody.hpp"
+#include "primitives/Molecule.hpp"
+
 namespace oopse {
 
 
-bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
+  SelectionEvaluator::SelectionEvaluator(SimInfo* si) 
+    : info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
+    
+      nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
+    }            
+
+  bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
+    clearDefinitionsAndLoadPredefined();
     this->filename = filename;
     this->script = script;
     if (! compiler.compile(filename, script)) {
-        error = true;
-        errorMessage = compiler.getErrorMessage();
-        return false;
+      error = true;
+      errorMessage = compiler.getErrorMessage();
+      std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
+      return false;
     }
 
     pc = 0;
     aatoken = compiler.getAatokenCompiled();
     linenumbers = compiler.getLineNumbers();
     lineIndices = compiler.getLineIndices();
+
+    std::vector<std::vector<Token> >::const_iterator i;   
+
+    isDynamic_ = false;
+    for (i = aatoken.begin(); i != aatoken.end(); ++i) {
+      if (containDynamicToken(*i)) {
+	isDynamic_ = true;
+	break;
+      }
+    }
+
+    isLoaded_ = true;
     return true;
-}
+  }
 
-void SelectionEvaluator::clearState() {
-    for (int i = scriptLevelMax; --i >= 0; )
-        stack[i].clear();
-    scriptLevel = 0;
+  void SelectionEvaluator::clearState() {
     error = false;
     errorMessage = "";
-}
+  }
 
-bool SelectionEvaluator::loadScriptString(const std::string& script) {
+  bool SelectionEvaluator::loadScriptString(const std::string& script) {
     clearState();
     return loadScript("", script);
-}
+  }
 
-bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
+  bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
     clearState();
     return loadScriptFileInternal(filename);
-}
+  }
 
-bool SelectionEvaluator::loadScriptFileInternal(const  string & filename) {
+  bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
+    std::ifstream ifs(filename.c_str());
+    if (!ifs.is_open()) {
+      return false;
+    }
 
-}
+    const int bufferSize = 65535;
+    char buffer[bufferSize];
+    std::string script;
+    while(ifs.getline(buffer, bufferSize)) {
+      script += buffer;
+    }
+    return loadScript(filename, script);
+  }
 
-void SelectionEvaluator::instructionDispatchLoop(){
-
+  void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){
+    
     while ( pc < aatoken.size()) {
-        statement = aatoken[pc++];
-        statementLength = statement.size();
-        Token token = statement[0];
-        switch (token.tok) {
-            case Token::define:
-                define();
-            break;
-            case Token::select:
-                select();
-            break;
-            default:
-                unrecognizedCommand(token);
-            return;
-        }
+      statement = aatoken[pc++];
+      statementLength = statement.size();
+      Token token = statement[0];
+      switch (token.tok) {
+      case Token::define:
+	define();
+	break;
+      case Token::select:
+	select(bs);
+	break;
+      default:
+	unrecognizedCommand(token);
+	return;
+      }
     }
-}
 
-  BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
-    int numberOfAtoms = viewer.getAtomCount();
-    BitSet bs;
-    BitSet[] stack = new BitSet[10];
-    int sp = 0;
+  }
 
-    for (int pc = pcStart; ; ++pc) {
+  OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
+    OOPSEBitSet bs;
+    std::stack<OOPSEBitSet> stack;
+    
+    for (int pc = pcStart; pc < code.size(); ++pc) {
       Token instruction = code[pc];
 
       switch (instruction.tok) {
@@ -116,46 +149,42 @@ void SelectionEvaluator::instructionDispatchLoop(){
       case Token::expressionEnd:
         break;
       case Token::all:
-        bs = stack[sp++] = new BitSet(numberOfAtoms);
-        for (int i = numberOfAtoms; --i >= 0; )
-          bs.set(i);
+        bs = OOPSEBitSet(nStuntDouble);
+        bs.setAll();
+        stack.push(bs);            
         break;
       case Token::none:
-        stack[sp++] = new BitSet();
+        bs = OOPSEBitSet(nStuntDouble);
+        stack.push(bs);            
         break;
       case Token::opOr:
-        bs = stack[--sp];
-        stack[sp-1].or(bs);
+        bs = stack.top();
+        stack.pop();
+        stack.top() |= bs;
         break;
       case Token::opAnd:
-        bs = stack[--sp];
-        stack[sp-1].and(bs);
+        bs = stack.top();
+        stack.pop();
+        stack.top() &= bs;
         break;
       case Token::opNot:
-        bs = stack[sp - 1];
-        notSet(bs);
+        stack.top().flip();
         break;
       case Token::within:
-        bs = stack[sp - 1];
-        stack[sp - 1] = new BitSet();
-        withinInstruction(instruction, bs, stack[sp - 1]);
+
+        withinInstruction(instruction, stack.top());
         break;
-      case Token::selected:
-        stack[sp++] = copyBitSet(viewer.getSelectionSet());
-        break;
+	//case Token::selected:
+	//  stack.push(getSelectionSet());
+	//  break;
       case Token::name:
-
+        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
         break;
-      case  Token::index:
-        
+      case Token::index:
+        stack.push(indexInstruction(instruction.value));
         break;
-      case Token::molname:  
-
-        break;
-      case Token::molindex:
-        break;
       case Token::identifier:
-        stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
+        stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
         break;
       case Token::opLT:
       case Token::opLE:
@@ -163,151 +192,258 @@ void SelectionEvaluator::instructionDispatchLoop(){
       case Token::opGT:
       case Token::opEQ:
       case Token::opNE:
-        bs = stack[sp++] = new BitSet();
-        comparatorInstruction(instruction, bs);
+        stack.push(comparatorInstruction(instruction));
         break;
       default:
         unrecognizedExpression();
       }
     }
-    if (sp != 1)
+    if (stack.size() != 1)
       evalError("atom expression compiler error - stack over/underflow");
-    return stack[0];
+          
+    return stack.top();
   }
 
 
 
-  void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
+  OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
     int comparator = instruction.tok;
     int property = instruction.intValue;
-    float propertyValue = 0; // just for temperature
-    int comparisonValue = ((Integer)instruction.value).intValue();
-    int numberOfAtoms = viewer.getAtomCount();
-    Frame frame = viewer.getFrame();
-    for (int i = 0; i < numberOfAtoms; ++i) {
-      Atom atom = frame.getAtomAt(i);
-      switch (property) {
-      case Token::mass:
-        //propertyValue = atom.getAtomNumber();
-        break;
-      case Token::charge:
+    float comparisonValue = boost::any_cast<float>(instruction.value);
+    float propertyValue;
+    OOPSEBitSet bs(nStuntDouble);
+    bs.clearAll();
+    
+    SimInfo::MoleculeIterator mi;
+    Molecule* mol;
+    Molecule::AtomIterator ai;
+    Atom* atom;
+    Molecule::RigidBodyIterator rbIter;
+    RigidBody* rb;
+    
+    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
 
-        break;
-      case Token::dipole:
-
-        break; 
-      default:
-        unrecognizedAtomProperty(property);
+      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
+	compareProperty(atom, bs, property, comparator, comparisonValue);
       }
-      bool match = false;
-      switch (comparator) {
-      case Token::opLT:
-        match = propertyValue < comparisonValue;
-        break;
-      case Token::opLE:
-        match = propertyValue <= comparisonValue;
-        break;
-      case Token::opGE:
-        match = propertyValue >= comparisonValue;
-        break;
-      case Token::opGT:
-        match = propertyValue > comparisonValue;
-        break;
-      case Token::opEQ:
-        match = propertyValue == comparisonValue;
-        break;
-      case Token::opNE:
-        match = propertyValue != comparisonValue;
-        break;
-      }
-      if (match)
-        bs.set(i);
+        
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+	compareProperty(rb, bs, property, comparator, comparisonValue);
+      }        
     }
+
+    return bs;
   }
 
-void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
+  void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue) {
+    RealType propertyValue = 0.0;
+    switch (property) {
+    case Token::mass:
+      propertyValue = sd->getMass();
+      break;
+    case Token::charge:
+      if (sd->isAtom()){
+	Atom* atom = static_cast<Atom*>(sd);
+	propertyValue = getCharge(atom);
+      } else if (sd->isRigidBody()) {
+	RigidBody* rb = static_cast<RigidBody*>(sd);
+	RigidBody::AtomIterator ai;
+	Atom* atom;
+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
+	  propertyValue+=  getCharge(atom);
+	}
+      }
+      break;
+    default:
+      unrecognizedAtomProperty(property);
+    }
+        
+    bool match = false;
+    switch (comparator) {
+    case Token::opLT:
+      match = propertyValue < comparisonValue;
+      break;
+    case Token::opLE:
+      match = propertyValue <= comparisonValue;
+      break;
+    case Token::opGE:
+      match = propertyValue >= comparisonValue;
+      break;
+    case Token::opGT:
+      match = propertyValue > comparisonValue;
+      break;
+    case Token::opEQ:
+      match = propertyValue == comparisonValue;
+      break;
+    case Token::opNE:
+      match = propertyValue != comparisonValue;
+      break;
+    }
+    if (match)
+      bs.setBitOn(sd->getGlobalIndex());
 
+  }
+
+  void SelectionEvaluator::withinInstruction(const Token& instruction, OOPSEBitSet& bs){
+    
     boost::any withinSpec = instruction.value;
+    float distance;
     if (withinSpec.type() == typeid(float)){
-        withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
-        return;
+      distance = boost::any_cast<float>(withinSpec);
+    } else if (withinSpec.type() == typeid(int)) {
+      distance = boost::any_cast<int>(withinSpec);    
+    } else {
+      evalError("casting error in withinInstruction");
+      bs.clearAll();
     }
     
-    evalError("Unrecognized within parameter:" + withinSpec);
-}
-
-  void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
-    Frame frame = viewer.getFrame();
-    for (int i = frame.getAtomCount(); --i >= 0; ) {
-      if (bs.get(i)) {
-        Atom atom = frame.getAtomAt(i);
-        AtomIterator iterWithin =
-          frame.getWithinIterator(atom, distance);
-        while (iterWithin.hasNext())
-          bsResult.set(iterWithin.next().getAtomIndex());
-      }
-    }
+    bs = distanceFinder.find(bs, distance);            
   }
 
   void SelectionEvaluator::define() {
     assert(statement.size() >= 3);
 
     std::string variable = boost::any_cast<std::string>(statement[1].value);
-    
-    variables.insert(std::make_pair(variable, expression(statement, 2)));
+
+    variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
   }
-}
 
-/** @todo */
-void SelectionEvaluator::predefine(const std::string& script) {
 
+  /** @todo */
+  void SelectionEvaluator::predefine(const std::string& script) {
+
     if (compiler.compile("#predefine", script)) {
-        std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
-        if (aatoken.size() != 1) {
-            evalError("predefinition does not have exactly 1 command:"
-                + script);
-            return;
-        }
-        std::vector<Token> statement = aatoken[0];
-        if (statement.size() > 2) {
-            int tok = statement[1].tok;
-            if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
-                std::string variable = (std::string)statement[1].value;
-                variables.insert(std::make_pair(variable, statement));
+      std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
+      if (aatoken.size() != 1) {
+	evalError("predefinition does not have exactly 1 command:"
+		  + script);
+	return;
+      }
+      std::vector<Token> statement = aatoken[0];
+      if (statement.size() > 2) {
+	int tok = statement[1].tok;
+	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
+	  std::string variable = boost::any_cast<std::string>(statement[1].value);
+	  variables.insert(VariablesType::value_type(variable, statement));
 
-            } else {
-                evalError("invalid variable name:" + script);
-            }
-        }else {
-            evalError("bad predefinition length:" + script);
-        }
+	} else {
+	  evalError("invalid variable name:" + script);
+	}
+      }else {
+	evalError("bad predefinition length:" + script);
+      }
 
         
     } else {
-        evalError("predefined set compile error:" + script +
-          "\ncompile error:" + compiler.getErrorMessage());
+      evalError("predefined set compile error:" + script +
+		"\ncompile error:" + compiler.getErrorMessage());
     }
 
-}
+  }
 
-void SelectionEvaluator::select(){
-    viewer.setSelectionSet(expression(statement, 1));
-}
+  void SelectionEvaluator::select(OOPSEBitSet& bs){
+    bs = expression(statement, 1);
+  }
 
-BitSet SelectionEvaluator::lookupValue(const std::string& variable){
+  OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){
 
+    OOPSEBitSet bs(nStuntDouble);
     std::map<std::string, boost::any>::iterator i = variables.find(variable);
-
+    
     if (i != variables.end()) {
-        if (i->second.type() == typeid(BitSet)) {
-            return boost::any_cast<BitSet>(i->second);
-        } else if (i->second.type() ==  typeid(std::vector<Token>)){
-            BitSet bs = expression(boost::any_cast(i->second), 2);
-            i->second =  bs; /**@todo fixme */
-            return bs;
-        }
+      if (i->second.type() == typeid(OOPSEBitSet)) {
+	return boost::any_cast<OOPSEBitSet>(i->second);
+      } else if (i->second.type() ==  typeid(std::vector<Token>)){
+	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
+	i->second =  bs; /**@todo fixme */
+	return bs;
+      }
+    } else {
+      unrecognizedIdentifier(variable);
     }
 
-}
+    return bs;
+  }
 
+  OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){
+    
+    return nameFinder.match(name);
+
+  }    
+
+  bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
+    std::vector<Token>::const_iterator i;
+    for (i = tokens.begin(); i != tokens.end(); ++i) {
+      if (i->tok & Token::dynamic) {
+	return true;
+      }
+    }
+
+    return false;
+  }    
+
+  void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
+    variables.clear();
+    //load predefine
+    //predefine();
+  }
+
+  OOPSEBitSet SelectionEvaluator::evaluate() {
+    OOPSEBitSet bs(nStuntDouble);
+    if (isLoaded_) {
+      pc = 0;
+      instructionDispatchLoop(bs);
+    }
+
+    return bs;
+  }
+
+  OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
+    OOPSEBitSet bs(nStuntDouble);
+
+    if (value.type() == typeid(int)) {
+      int index = boost::any_cast<int>(value);
+      if (index < 0 || index >= bs.size()) {
+	invalidIndex(index);
+      } else {
+	bs = indexFinder.find(index);
+      }
+    } else if (value.type() == typeid(std::pair<int, int>)) {
+      std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
+      assert(indexRange.first <= indexRange.second);
+      if (indexRange.first < 0 || indexRange.second >= bs.size()) {
+	invalidIndexRange(indexRange);
+      }else {
+	bs = indexFinder.find(indexRange.first, indexRange.second);
+      }
+    }
+
+    return bs;
+  }
+
+
+  RealType SelectionEvaluator::getCharge(Atom* atom) {
+    RealType charge =0.0;
+    AtomType* atomType = atom->getAtomType();
+    if (atomType->isCharge()) {
+      GenericData* data = atomType->getPropertyByName("Charge");
+      if (data != NULL) {
+	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
+
+	if (doubleData != NULL) {
+	  charge = doubleData->getData();
+
+	} else {
+	  sprintf( painCave.errMsg,
+		   "Can not cast GenericData to DoubleGenericData\n");
+	  painCave.severity = OOPSE_ERROR;
+	  painCave.isFatal = 1;
+	  simError();          
+	}
+      } 
+    }
+
+    return charge;
+  }
+
 }