--- trunk/src/selection/NameFinder.cpp	2005/02/04 05:42:49	287
+++ trunk/src/selection/NameFinder.cpp	2005/04/05 23:09:48	452
@@ -42,6 +42,7 @@
 #include "utils/wildcards.hpp"
 #include "utils/StringTokenizer.hpp"
 #include "primitives/Molecule.hpp"
+#include "utils/StringUtils.hpp"
 namespace oopse {
 
 TreeNode::~TreeNode(){
@@ -78,60 +79,30 @@ void NameFinder::loadNames() {
     root_->bs.setAll(); //
     
     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
-        TreeNode* currentMolNode;            
+           
         std::string molName = mol->getMoleculeName();
-
-        foundIter = root_->children.find(molName);
-        if ( foundIter  == root_->children.end()) {
-            currentMolNode = new TreeNode;
-            currentMolNode->name = molName;
-            currentMolNode->bs.resize(nStuntDouble_);
-        }else {
-            currentMolNode = foundIter->second;
-        }
+         TreeNode* currentMolNode = createNode(root_, molName);
         
         for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
             std::string atomName = atom->getType();
-            TreeNode* currentAtomNode;
-            foundIter = currentMolNode->children.find(molName);
-            if (foundIter == currentMolNode->children.end()) {
-                currentAtomNode = new TreeNode;
-                currentAtomNode->name = atomName;
-                currentAtomNode->bs.resize(nStuntDouble_);
-            } else {
-                currentAtomNode = foundIter->second;
-            }
+            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 = atom->getType();
-            TreeNode* currentRbNode;
-            foundIter = currentMolNode->children.find(molName);
-            if (foundIter == currentMolNode->children.end()) {
-                currentRbNode = new TreeNode;
-                currentRbNode->name = rbName;
-                currentRbNode->bs.resize(nStuntDouble_);
-            } else {
-                currentRbNode = foundIter->second;
-            }
+            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); rb != NULL; atom = rb->nextAtom(ai)) {
+            for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
                 std::string rbAtomName = atom->getType();
-                TreeNode* currentRbAtomNode;
-                foundIter = currentRbNode->children.find(molName);
-                if (foundIter == currentRbNode->children.end()) {
-                    currentRbAtomNode = new TreeNode;
-                    currentRbAtomNode->name = rbAtomName;
-                    currentRbAtomNode->bs.resize(nStuntDouble_);
-                } else {
-                    currentRbAtomNode = foundIter->second;
-                }
+                TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
+
                 currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
             }
 
@@ -141,9 +112,24 @@ void NameFinder::loadNames() {
 
 }
 
-bool NameFinder::match(const std::string& name, BitSet& bs){
+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;
+}
 
-    bool hasError = false;
+BitSet NameFinder::match(const std::string& name){
+    BitSet bs(nStuntDouble_);
+  
     StringTokenizer tokenizer(name, ".");
 
     std::vector<std::string> names;
@@ -155,19 +141,24 @@ bool NameFinder::match(const std::string& name, BitSet
     switch(size) {
         case 1 :
             //could be molecule name, atom name and rigidbody name
-            if (names[0] == "*"){
-                //if all molecules are selected, we don't need to do the matching, just set all of the bits
-                bs.setAll();
-            } else{
-                matchMolecule(names[0], bs);
-                matchStuntDouble("*", names[0], bs);
-            } 
+            matchMolecule(names[0], bs);
+            matchStuntDouble("*", names[0], bs);
             
             break;
         case 2:
             //could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
-            matchRigidAtoms("*", names[0], names[1], bs);
-            matchStuntDouble(names[0], names[1], bs);
+
+            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:
@@ -175,11 +166,11 @@ bool NameFinder::match(const std::string& name, BitSet
             matchRigidAtoms(names[0], names[1], names[2], bs);
             break;
         default:      
-            hasError = true;	    
+            std::cerr << "invalid name: " << name << std::endl;
             break;           
     }
 
-    return hasError; 
+    return bs; 
 }
 
 void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) {
@@ -237,4 +228,40 @@ bool NameFinder::isMatched(const std::string& str, con
     return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
 }
 
+
+void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& 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;
+ }
+
+}