--- trunk/src/selection/NameFinder.cpp	2005/02/03 23:14:05	283
+++ trunk/src/selection/NameFinder.cpp	2005/12/02 15:38:03	770
@@ -39,72 +39,229 @@
  * such damages.
  */
 #include "selection/NameFinder.hpp"
+#include "utils/wildcards.hpp"
+#include "utils/StringTokenizer.hpp"
+#include "primitives/Molecule.hpp"
+#include "utils/StringUtils.hpp"
 namespace oopse {
 
-NameFinder::NameFinder(SimInfo* info) {
-    loadNames();
-}
+  TreeNode::~TreeNode(){
+    std::map<std::string, TreeNode*>::iterator i;
+    for ( i = children.begin(); i != children.end(); ++i) {
+      i->second->~TreeNode();
+    }
+    children.clear();
+  }
 
 
+  NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
+    nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
+    loadNames();
+  }
 
-void NameFinder::loadNames() {
 
-    root_ = new NameNode;
-    root_.type = rootNode;
+  NameFinder::~NameFinder(){
+    delete root_;
+  }
 
-    NameNode* newNode;            
+  void NameFinder::loadNames() {
+
+    std::map<std::string, TreeNode*>::iterator foundIter;
     SimInfo::MoleculeIterator mi;
     Molecule* mol;
     Molecule::AtomIterator ai;
     Atom* atom;
     Molecule::RigidBodyIterator rbIter;
     RigidBody* rb;
+
+    root_ = new TreeNode;
+    root_->bs.resize(nStuntDouble_);
+    root_->bs.setAll(); //
+    
     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
-        newNode = new NameNode;
-        newNode.type = molNode;
-        newNode.name = mol->getMoleculeName();
+           
+      std::string molName = mol->getMoleculeName();
+      TreeNode* currentMolNode = createNode(root_, molName);
         
-        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
-            atomNames_.insert(atom->getType());
-        }
+      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
+	std::string atomName = atom->getType();
+	TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
+            
+	currentMolNode->bs.setBitOn(atom->getGlobalIndex());
+	currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
+      }
+
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+	std::string rbName = rb->getType();
+	TreeNode* currentRbNode = createNode(currentMolNode, rbName);
+            
+	currentMolNode->bs.setBitOn(rb->getGlobalIndex());
+	currentRbNode->bs.setBitOn(rb->getGlobalIndex());
+
+	//create nodes for atoms belong to this rigidbody
+	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
+	  std::string rbAtomName = atom->getType();
+	  TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
+
+	  currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
+	}
+
+      }
         
-        //change the positions of atoms which belong to the rigidbodies
-        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
-            rbNames_.insert(rb->getType());
-        }        
     }    
-}
 
-bool NameFinder::match(const std::string& name, BitSet& bs){
+  }
 
-    bool error = true;
+  TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
+    TreeNode* node;    
+    std::map<std::string, TreeNode*>::iterator foundIter;
+    foundIter = parent->children.find(name);
+    if ( foundIter  == parent->children.end()) {
+      node = new TreeNode;
+      node->name = name;
+      node->bs.resize(nStuntDouble_);
+      parent->children.insert(std::make_pair(name, node));
+    }else {
+      node = foundIter->second;
+    }
+    return node;
+  }
+
+  OOPSEBitSet NameFinder::match(const std::string& name){
+    OOPSEBitSet bs(nStuntDouble_);
+  
     StringTokenizer tokenizer(name, ".");
 
     std::vector<std::string> names;
     while(tokenizer.hasMoreTokens()) {
-        names.push_back(tokenizer.nextToken());
+      names.push_back(tokenizer.nextToken());
     }
 
     int size = names.size();
     switch(size) {
-        case 1 :
-            //could be molecule name, atom name, rigidbody name
-            isMolName();
-            isAtomName();
-            isRigidBodyName();
-            break;
-        case 2:
-            //could be molecule.*(include atoms and rigidbodies) or rigidbody.*
-            break;
-        case 3:
-            //must be molecule.rigidbody.*
+    case 1 :
+      //could be molecule name, atom name and rigidbody name
+      matchMolecule(names[0], bs);
+      matchStuntDouble("*", names[0], bs);
             
-            break;
-        default:            
-            break;           
+      break;
+    case 2:
+      //could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
+
+      if (!isInteger(names[1])){
+	matchRigidAtoms("*", names[0], names[1], bs);
+	matchStuntDouble(names[0], names[1], bs);
+      } else {
+	int internalIndex = lexi_cast<int>(names[1]);
+	if (internalIndex < 0) {
+	  std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;           
+	} else {
+	  matchInternalIndex(names[0], internalIndex, bs);
+	}
+      }
+            
+      break;
+    case 3:
+      //must be molecule.rigidbody.*
+      matchRigidAtoms(names[0], names[1], names[2], bs);
+      break;
+    default:      
+      std::cerr << "invalid name: " << name << std::endl;
+      break;           
     }
 
-    return matched;
-}
+    return bs; 
+  }
 
+  void NameFinder::matchMolecule(const std::string& molName, OOPSEBitSet& bs) {
+    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
+    std::vector<TreeNode*>::iterator i;
+    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
+      bs |= (*i)->bs;
+    }    
+  }
+
+  void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OOPSEBitSet& bs){
+    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
+    std::vector<TreeNode*>::iterator i;
+    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
+      std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);   
+      std::vector<TreeNode*>::iterator j;
+      for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
+	bs |= (*j)->bs;
+      }
+    }
+
+  }
+
+  void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OOPSEBitSet& bs){
+    std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
+    std::vector<TreeNode*>::iterator i;
+    for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
+      std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);   
+      std::vector<TreeNode*>::iterator j;
+      for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
+	std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
+	std::vector<TreeNode*>::iterator k;
+	for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
+	  bs |= (*k)->bs;
+	}
+      }
+    }
+
+  }
+
+
+  std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
+    std::vector<TreeNode*> matchedNodes;
+    std::map<std::string, TreeNode*>::iterator i;
+    for (i = node->children.begin(); i != node->children.end(); ++i) {
+      if (isMatched( i->first, name)) {
+	matchedNodes.push_back(i->second);
+      }
+    }
+
+    return matchedNodes;
+  }
+
+  bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
+    return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
+  }
+
+
+  void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OOPSEBitSet& bs){
+
+    std::map<std::string, TreeNode*>::iterator foundIter;
+    SimInfo::MoleculeIterator mi;
+    Molecule* mol;
+
+    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+           
+      if (isMatched(mol->getMoleculeName(), name) ) {
+	int natoms = mol->getNAtoms();
+	int nrigidbodies = mol->getNRigidBodies();
+	if (internalIndex >= natoms + nrigidbodies) {
+	  continue;
+	} else if (internalIndex < natoms) {
+	  bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
+	  continue;
+	} else if ( internalIndex < natoms + nrigidbodies) {
+	  bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
+	}
+      }
+        
+    }    
+    
+  }
+
+  bool NameFinder::isInteger(const std::string str) {
+    for(int i =0; i < str.size(); ++i){
+      if (!std::isdigit(str[i])) {
+	return false;
+      }
+    }
+
+    return true;
+  }
+
 }