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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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TreeNode::~TreeNode(){ |
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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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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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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()) { |
| 96 |
< |
currentAtomNode = new TreeNode; |
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< |
currentAtomNode->name = atomName; |
| 98 |
< |
currentAtomNode->bs.resize(nStuntDouble_); |
| 99 |
< |
} else { |
| 100 |
< |
currentAtomNode = foundIter->second; |
| 101 |
< |
} |
| 87 |
> |
TreeNode* currentAtomNode = createNode(currentMolNode, atomName); |
| 88 |
> |
|
| 89 |
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currentMolNode->bs.setBitOn(atom->getGlobalIndex()); |
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currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
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} |
| 92 |
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| 93 |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 94 |
< |
std::string rbName = atom->getType(); |
| 95 |
< |
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(); |
| 95 |
> |
TreeNode* currentRbNode = createNode(currentMolNode, rbName); |
| 96 |
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|
| 97 |
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currentMolNode->bs.setBitOn(rb->getGlobalIndex()); |
| 98 |
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currentRbNode->bs.setBitOn(rb->getGlobalIndex()); |
| 99 |
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|
| 100 |
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//create nodes for atoms belong to this rigidbody |
| 101 |
< |
for(atom = rb->beginAtom(ai); rb != NULL; atom = rb->nextAtom(ai)) { |
| 101 |
> |
for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
| 102 |
|
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 |
|
currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 106 |
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} |
| 107 |
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| 109 |
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| 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 |
|
} |
| 126 |
+ |
return node; |
| 127 |
|
} |
| 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 |
|
|
| 134 |
|
std::vector<std::string> names; |
| 144 |
|
//if all molecules are selected, we don't need to do the matching, just set all of the bits |
| 145 |
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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); |
| 149 |
|
} |
| 150 |
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|
| 151 |
|
break; |
| 152 |
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case 2: |
| 153 |
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//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody) |
| 154 |
|
matchRigidAtoms("*", names[0], names[1], bs); |
| 155 |
< |
matchStuntDouble(names[0], names[1]); |
| 155 |
> |
matchStuntDouble(names[0], names[1], bs); |
| 156 |
|
|
| 157 |
|
break; |
| 158 |
|
case 3: |
| 159 |
|
//must be molecule.rigidbody.* |
| 160 |
< |
matchRigidAtoms(names[0], names[1], names[2], bs) |
| 160 |
> |
matchRigidAtoms(names[0], names[1], names[2], bs); |
| 161 |
|
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 |
|
} |
