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root/OpenMD/branches/development/src/selection/NameFinder.cpp
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Comparing trunk/src/selection/NameFinder.cpp (file contents):
Revision 284 by tim, Fri Feb 4 04:57:04 2005 UTC vs.
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC

# Line 40 | Line 40
40   */
41   #include "selection/NameFinder.hpp"
42   #include "utils/wildcards.hpp"
43 + #include "utils/StringTokenizer.hpp"
44 + #include "primitives/Molecule.hpp"
45 + #include "utils/StringUtils.hpp"
46   namespace oopse {
47  
48 < TreeNode::~TreeNode(){
48 >  TreeNode::~TreeNode(){
49      std::map<std::string, TreeNode*>::iterator i;
50      for ( i = children.begin(); i != children.end(); ++i) {
51 <        i->second->~TreeNode();
51 >      i->second->~TreeNode();
52      }
53      children.clear();
54 < }
54 >  }
55  
56  
57 < NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58 <    nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies()
57 >  NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58 >    nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
59      loadNames();
60 < }
60 >  }
61  
62  
63 < NameFinder::~NameFinder(){
63 >  NameFinder::~NameFinder(){
64      delete root_;
65 < }
65 >  }
66  
67 < void NameFinder::loadNames() {
67 >  void NameFinder::loadNames() {
68  
69      std::map<std::string, TreeNode*>::iterator foundIter;
70      SimInfo::MoleculeIterator mi;
# Line 72 | Line 75 | void NameFinder::loadNames() {
75      RigidBody* rb;
76  
77      root_ = new TreeNode;
78 <    root_->bs.resize(nStuntDobule_);
78 >    root_->bs.resize(nStuntDouble_);
79      root_->bs.setAll(); //
80      
81      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
82 <        TreeNode* currentMolNode;            
83 <        std::string molName = mol->getMoleculeName();
84 <
82 <        foundIter = root_->children.find(molName);
83 <        if ( foundIter  == root_->children.end()) {
84 <            currentMolNode = new TreeNode;
85 <            currentMolNode->name = molName;
86 <            currentMolNode->bs.resize(nStuntDouble_);
87 <        }else {
88 <            currentMolNode = i->second;
89 <        }
82 >          
83 >      std::string molName = mol->getMoleculeName();
84 >      TreeNode* currentMolNode = createNode(root_, molName);
85          
86 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
87 <            std::string atomName = atom->getType();
88 <            TreeNode* currentAtomNode;
89 <            foundIter = currentMolNode->children.find(molName);
90 <            if (foundIter == currentMolNode->children.end()) {
91 <                currentAtomNode = new TreeNode;
92 <                currentAtomNode->name = atomName;
98 <                currentAtomNode->bs.resize(nStuntDouble_);
99 <            } else {
100 <                currentAtomNode = foundIter->second;
101 <            }
102 <            currentMolNode->bs.setBitOn(atom->getGlobalIndex());
103 <            currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
104 <        }
86 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
87 >        std::string atomName = atom->getType();
88 >        TreeNode* currentAtomNode = createNode(currentMolNode, atomName);
89 >            
90 >        currentMolNode->bs.setBitOn(atom->getGlobalIndex());
91 >        currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
92 >      }
93  
94 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
95 <            std::string rbName = atom->getType();
96 <            TreeNode* currentRbNode;
109 <            foundIter = currentMolNode->children.find(molName);
110 <            if (foundIter == currentMolNode->children.end()) {
111 <                currentRbNode = new TreeNode;
112 <                currentRbNode->name = rbName;
113 <                currentRbNode->bs.resize(nStuntDouble_);
114 <            } else {
115 <                currentRbNode = foundIter->second;
116 <            }
94 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
95 >        std::string rbName = rb->getType();
96 >        TreeNode* currentRbNode = createNode(currentMolNode, rbName);
97              
98 <            currentMolNode->bs.setBitOn(rb->getGlobalIndex());
99 <            currentRbNode->bs.setBitOn(rb->getGlobalIndex());
98 >        currentMolNode->bs.setBitOn(rb->getGlobalIndex());
99 >        currentRbNode->bs.setBitOn(rb->getGlobalIndex());
100  
101 <            //create nodes for atoms belong to this rigidbody
102 <            for(atom = rb->beginAtom(ai); rb != NULL; atom = rb->nextAtom(ai)) {
103 <                std::string rbAtomName = atom->getType();
104 <                TreeNode* currentRbAtomNode;
125 <                foundIter = currentRbNode->children.find(molName);
126 <                if (foundIter == currentRbNode->children.end()) {
127 <                    currentRbAtomNode = new TreeNode;
128 <                    currentRbAtomNode->name = rbAtomName;
129 <                    currentRbAtomNode->bs.resize(nStuntDouble_);
130 <                } else {
131 <                    currentRbAtomNode = foundIter->second;
132 <                }
133 <                currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
134 <            }
101 >        //create nodes for atoms belong to this rigidbody
102 >        for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
103 >          std::string rbAtomName = atom->getType();
104 >          TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);;
105  
106 <        }
106 >          currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
107 >        }
108 >
109 >      }
110          
111      }    
112  
113 <    std::map<std::string, TreeNode*>::iterator i;
114 <    for( i = root_->children.begin(); i != ; ++i){
115 <        i->bs =
113 >  }
114 >
115 >  TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
116 >    TreeNode* node;    
117 >    std::map<std::string, TreeNode*>::iterator foundIter;
118 >    foundIter = parent->children.find(name);
119 >    if ( foundIter  == parent->children.end()) {
120 >      node = new TreeNode;
121 >      node->name = name;
122 >      node->bs.resize(nStuntDouble_);
123 >      parent->children.insert(std::make_pair(name, node));
124 >    }else {
125 >      node = foundIter->second;
126      }
127 < }
127 >    return node;
128 >  }
129  
130 < bool NameFinder::match(const std::string& name, BitSet& bs){
131 <
132 <    bool error = true;
130 >  OOPSEBitSet NameFinder::match(const std::string& name){
131 >    OOPSEBitSet bs(nStuntDouble_);
132 >  
133      StringTokenizer tokenizer(name, ".");
134  
135      std::vector<std::string> names;
136      while(tokenizer.hasMoreTokens()) {
137 <        names.push_back(tokenizer.nextToken());
137 >      names.push_back(tokenizer.nextToken());
138      }
139  
140      int size = names.size();
141      switch(size) {
142 <        case 1 :
143 <            //could be molecule name, atom name and rigidbody name
144 <            if (names[0] == "*"){
145 <                //if all molecules are selected, we don't need to do the matching, just set all of the bits
162 <                bs.setAll();
163 <            } else{
164 <                matchMolecule(name[0]);
165 <                matchStuntDouble("*", names[0]);
166 <            }
142 >    case 1 :
143 >      //could be molecule name, atom name and rigidbody name
144 >      matchMolecule(names[0], bs);
145 >      matchStuntDouble("*", names[0], bs);
146              
147 <            break;
148 <        case 2:
149 <            //could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
150 <            matchRigidAtoms("*", names[0], names[1], bs);
151 <            matchStuntDouble(names[0], names[1]);
147 >      break;
148 >    case 2:
149 >      //could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody)
150 >
151 >      if (!isInteger(names[1])){
152 >        matchRigidAtoms("*", names[0], names[1], bs);
153 >        matchStuntDouble(names[0], names[1], bs);
154 >      } else {
155 >        int internalIndex = lexi_cast<int>(names[1]);
156 >        if (internalIndex < 0) {
157 >          std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl;          
158 >        } else {
159 >          matchInternalIndex(names[0], internalIndex, bs);
160 >        }
161 >      }
162              
163 <            break;
164 <        case 3:
165 <            //must be molecule.rigidbody.*
166 <            matchRigidAtoms(names[0], names[1], names[2], bs)
167 <            break;
168 <        default:            
169 <            break;          
163 >      break;
164 >    case 3:
165 >      //must be molecule.rigidbody.*
166 >      matchRigidAtoms(names[0], names[1], names[2], bs);
167 >      break;
168 >    default:      
169 >      std::cerr << "invalid name: " << name << std::endl;
170 >      break;          
171      }
172  
173 <    return matched;
174 < }
173 >    return bs;
174 >  }
175  
176 < void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) {
176 >  void NameFinder::matchMolecule(const std::string& molName, OOPSEBitSet& bs) {
177      std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
178      std::vector<TreeNode*>::iterator i;
179      for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
180 <        bs |= i->bs;
180 >      bs |= (*i)->bs;
181      }    
182 < }
182 >  }
183  
184 < void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){
184 >  void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OOPSEBitSet& bs){
185      std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
186      std::vector<TreeNode*>::iterator i;
187      for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
188 <        std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);  
189 <        std::vector<TreeNode*>::iterator j;
190 <        for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
191 <            bs |= j->bs;
192 <        }
188 >      std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName);  
189 >      std::vector<TreeNode*>::iterator j;
190 >      for (j = sdNodes.begin(); j != sdNodes.end(); ++j) {
191 >        bs |= (*j)->bs;
192 >      }
193      }
194  
195 < }
195 >  }
196  
197 < void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){
197 >  void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OOPSEBitSet& bs){
198      std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
199      std::vector<TreeNode*>::iterator i;
200      for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
201 <        std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);  
202 <        std::vector<TreeNode*>::iterator j;
203 <        for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
204 <            std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
205 <            std::vector<TreeNode*>::iterator k;
206 <            for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
207 <                bs |= k->bs;
208 <            }
209 <        }
201 >      std::vector<TreeNode*> rbNodes = getMatchedChildren(*i, rbName);  
202 >      std::vector<TreeNode*>::iterator j;
203 >      for (j = rbNodes.begin(); j != rbNodes.end(); ++j) {
204 >        std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName);
205 >        std::vector<TreeNode*>::iterator k;
206 >        for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){
207 >          bs |= (*k)->bs;
208 >        }
209 >      }
210      }
211  
212 < }
212 >  }
213  
214  
215 < std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
215 >  std::vector<TreeNode*> NameFinder::getMatchedChildren(TreeNode* node, const std::string& name) {
216      std::vector<TreeNode*> matchedNodes;
217      std::map<std::string, TreeNode*>::iterator i;
218      for (i = node->children.begin(); i != node->children.end(); ++i) {
219 <        if (isMatched( i->first, name)) {
220 <            matchedNodes.push_back(i->second);
221 <        }
219 >      if (isMatched( i->first, name)) {
220 >        matchedNodes.push_back(i->second);
221 >      }
222      }
223  
224      return matchedNodes;
225 < }
225 >  }
226  
227 < bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
227 >  bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
228      return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
229 < }
229 >  }
230  
231 +
232 +  void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OOPSEBitSet& bs){
233 +
234 +    std::map<std::string, TreeNode*>::iterator foundIter;
235 +    SimInfo::MoleculeIterator mi;
236 +    Molecule* mol;
237 +
238 +    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
239 +          
240 +      if (isMatched(mol->getMoleculeName(), name) ) {
241 +        int natoms = mol->getNAtoms();
242 +        int nrigidbodies = mol->getNRigidBodies();
243 +        if (internalIndex >= natoms + nrigidbodies) {
244 +          continue;
245 +        } else if (internalIndex < natoms) {
246 +          bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex());
247 +          continue;
248 +        } else if ( internalIndex < natoms + nrigidbodies) {
249 +          bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
250 +        }
251 +      }
252 +        
253 +    }    
254 +    
255 +  }
256 +
257 +  bool NameFinder::isInteger(const std::string str) {
258 +    for(int i =0; i < str.size(); ++i){
259 +      if (!std::isdigit(str[i])) {
260 +        return false;
261 +      }
262 +    }
263 +
264 +    return true;
265 +  }
266 +
267   }

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