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*/ |
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#include "selection/NameFinder.hpp" |
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#include "utils/wildcards.hpp" |
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#include "utils/StringTokenizer.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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|
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TreeNode::~TreeNode(){ |
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|
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|
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NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
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nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies() |
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nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
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loadNames(); |
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} |
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RigidBody* rb; |
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|
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root_ = new TreeNode; |
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root_->bs.resize(nStuntDobule_); |
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root_->bs.resize(nStuntDouble_); |
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root_->bs.setAll(); // |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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TreeNode* currentMolNode; |
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|
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std::string molName = mol->getMoleculeName(); |
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|
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foundIter = root_->children.find(molName); |
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if ( foundIter == root_->children.end()) { |
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currentMolNode = new TreeNode; |
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currentMolNode->name = molName; |
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currentMolNode->bs.resize(nStuntDouble_); |
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}else { |
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currentMolNode = i->second; |
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} |
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> |
TreeNode* currentMolNode = createNode(root_, molName); |
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|
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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std::string atomName = atom->getType(); |
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< |
TreeNode* currentAtomNode; |
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< |
foundIter = currentMolNode->children.find(molName); |
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< |
if (foundIter == currentMolNode->children.end()) { |
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< |
currentAtomNode = new TreeNode; |
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< |
currentAtomNode->name = atomName; |
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< |
currentAtomNode->bs.resize(nStuntDouble_); |
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< |
} else { |
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currentAtomNode = foundIter->second; |
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} |
87 |
> |
TreeNode* currentAtomNode = createNode(currentMolNode, atomName); |
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> |
|
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currentMolNode->bs.setBitOn(atom->getGlobalIndex()); |
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currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
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} |
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|
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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< |
std::string rbName = atom->getType(); |
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< |
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 |
> |
std::string rbName = rb->getType(); |
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> |
TreeNode* currentRbNode = createNode(currentMolNode, rbName); |
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|
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currentMolNode->bs.setBitOn(rb->getGlobalIndex()); |
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currentRbNode->bs.setBitOn(rb->getGlobalIndex()); |
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|
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//create nodes for atoms belong to this rigidbody |
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< |
for(atom = rb->beginAtom(ai); rb != NULL; atom = rb->nextAtom(ai)) { |
101 |
> |
for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
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std::string rbAtomName = atom->getType(); |
103 |
< |
TreeNode* currentRbAtomNode; |
104 |
< |
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 |
< |
} |
103 |
> |
TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);; |
104 |
> |
|
105 |
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currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
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} |
107 |
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|
109 |
|
|
110 |
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} |
111 |
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|
112 |
< |
std::map<std::string, TreeNode*>::iterator i; |
113 |
< |
for( i = root_->children.begin(); i != ; ++i){ |
114 |
< |
i->bs = |
112 |
> |
} |
113 |
> |
|
114 |
> |
TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) { |
115 |
> |
TreeNode* node; |
116 |
> |
std::map<std::string, TreeNode*>::iterator foundIter; |
117 |
> |
foundIter = parent->children.find(name); |
118 |
> |
if ( foundIter == parent->children.end()) { |
119 |
> |
node = new TreeNode; |
120 |
> |
node->name = name; |
121 |
> |
node->bs.resize(nStuntDouble_); |
122 |
> |
parent->children.insert(std::make_pair(name, node)); |
123 |
> |
}else { |
124 |
> |
node = foundIter->second; |
125 |
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} |
126 |
+ |
return node; |
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} |
128 |
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|
129 |
< |
bool NameFinder::match(const std::string& name, BitSet& bs){ |
130 |
< |
|
131 |
< |
bool error = true; |
129 |
> |
BitSet NameFinder::match(const std::string& name){ |
130 |
> |
BitSet bs(nStuntDouble_); |
131 |
> |
|
132 |
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StringTokenizer tokenizer(name, "."); |
133 |
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|
134 |
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std::vector<std::string> names; |
144 |
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//if all molecules are selected, we don't need to do the matching, just set all of the bits |
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bs.setAll(); |
146 |
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} else{ |
147 |
< |
matchMolecule(name[0]); |
148 |
< |
matchStuntDouble("*", names[0]); |
147 |
> |
matchMolecule(names[0], bs); |
148 |
> |
matchStuntDouble("*", names[0], bs); |
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} |
150 |
|
|
151 |
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break; |
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case 2: |
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//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody) |
154 |
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matchRigidAtoms("*", names[0], names[1], bs); |
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< |
matchStuntDouble(names[0], names[1]); |
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> |
matchStuntDouble(names[0], names[1], bs); |
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|
157 |
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break; |
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case 3: |
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//must be molecule.rigidbody.* |
160 |
< |
matchRigidAtoms(names[0], names[1], names[2], bs) |
160 |
> |
matchRigidAtoms(names[0], names[1], names[2], bs); |
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|
break; |
162 |
< |
default: |
162 |
> |
default: |
163 |
> |
std::cerr << "invalid name: " << name << std::endl; |
164 |
|
break; |
165 |
|
} |
166 |
|
|
167 |
< |
return matched; |
167 |
> |
return bs; |
168 |
|
} |
169 |
|
|
170 |
|
void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) { |
171 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
172 |
|
std::vector<TreeNode*>::iterator i; |
173 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
174 |
< |
bs |= i->bs; |
174 |
> |
bs |= (*i)->bs; |
175 |
|
} |
176 |
|
} |
177 |
|
|
182 |
|
std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName); |
183 |
|
std::vector<TreeNode*>::iterator j; |
184 |
|
for (j = sdNodes.begin(); j != sdNodes.end(); ++j) { |
185 |
< |
bs |= j->bs; |
185 |
> |
bs |= (*j)->bs; |
186 |
|
} |
187 |
|
} |
188 |
|
|
198 |
|
std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName); |
199 |
|
std::vector<TreeNode*>::iterator k; |
200 |
|
for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){ |
201 |
< |
bs |= k->bs; |
201 |
> |
bs |= (*k)->bs; |
202 |
|
} |
203 |
|
} |
204 |
|
} |