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(){ |
55 |
|
|
56 |
|
|
57 |
|
NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
58 |
< |
nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies() |
58 |
> |
nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
59 |
|
loadNames(); |
60 |
|
} |
61 |
|
|
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; |
82 |
> |
|
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 |
< |
} |
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); |
95 |
< |
if (foundIter == currentMolNode->children.end()) { |
96 |
< |
currentAtomNode = new TreeNode; |
97 |
< |
currentAtomNode->name = atomName; |
98 |
< |
currentAtomNode->bs.resize(nStuntDouble_); |
99 |
< |
} else { |
100 |
< |
currentAtomNode = foundIter->second; |
101 |
< |
} |
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 |
< |
} |
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()); |
100 |
|
|
101 |
|
//create nodes for atoms belong to this rigidbody |
102 |
< |
for(atom = rb->beginAtom(ai); rb != NULL; atom = rb->nextAtom(ai)) { |
102 |
> |
for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
103 |
|
std::string rbAtomName = atom->getType(); |
104 |
< |
TreeNode* currentRbAtomNode; |
105 |
< |
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 |
< |
} |
104 |
> |
TreeNode* currentRbAtomNode = createNode(currentRbNode, rbName);; |
105 |
> |
|
106 |
|
currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
107 |
|
} |
108 |
|
|
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 |
+ |
return node; |
128 |
|
} |
129 |
|
|
130 |
< |
bool NameFinder::match(const std::string& name, BitSet& bs){ |
131 |
< |
|
132 |
< |
bool error = true; |
130 |
> |
BitSet NameFinder::match(const std::string& name){ |
131 |
> |
BitSet bs(nStuntDouble_); |
132 |
> |
|
133 |
|
StringTokenizer tokenizer(name, "."); |
134 |
|
|
135 |
|
std::vector<std::string> names; |
145 |
|
//if all molecules are selected, we don't need to do the matching, just set all of the bits |
146 |
|
bs.setAll(); |
147 |
|
} else{ |
148 |
< |
matchMolecule(name[0]); |
149 |
< |
matchStuntDouble("*", names[0]); |
148 |
> |
matchMolecule(names[0], bs); |
149 |
> |
matchStuntDouble("*", names[0], bs); |
150 |
|
} |
151 |
|
|
152 |
|
break; |
153 |
|
case 2: |
154 |
|
//could be molecule.*(include atoms and rigidbodies) or rigidbody.*(atoms belong to rigidbody) |
155 |
< |
matchRigidAtoms("*", names[0], names[1], bs); |
156 |
< |
matchStuntDouble(names[0], names[1]); |
155 |
> |
|
156 |
> |
if (!isInteger(names[1])){ |
157 |
> |
matchRigidAtoms("*", names[0], names[1], bs); |
158 |
> |
matchStuntDouble(names[0], names[1], bs); |
159 |
> |
} else { |
160 |
> |
int internalIndex = lexi_cast<int>(names[1]); |
161 |
> |
if (internalIndex < 0) { |
162 |
> |
std::cerr << names[0] << ". " << names[1] << " is an invalid name" << std::endl; |
163 |
> |
} else { |
164 |
> |
matchInternalIndex(names[0], internalIndex, bs); |
165 |
> |
} |
166 |
> |
} |
167 |
|
|
168 |
|
break; |
169 |
|
case 3: |
170 |
|
//must be molecule.rigidbody.* |
171 |
< |
matchRigidAtoms(names[0], names[1], names[2], bs) |
171 |
> |
matchRigidAtoms(names[0], names[1], names[2], bs); |
172 |
|
break; |
173 |
< |
default: |
173 |
> |
default: |
174 |
> |
std::cerr << "invalid name: " << name << std::endl; |
175 |
|
break; |
176 |
|
} |
177 |
|
|
178 |
< |
return matched; |
178 |
> |
return bs; |
179 |
|
} |
180 |
|
|
181 |
|
void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) { |
182 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
183 |
|
std::vector<TreeNode*>::iterator i; |
184 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
185 |
< |
bs |= i->bs; |
185 |
> |
bs |= (*i)->bs; |
186 |
|
} |
187 |
|
} |
188 |
|
|
193 |
|
std::vector<TreeNode*> sdNodes = getMatchedChildren(*i, sdName); |
194 |
|
std::vector<TreeNode*>::iterator j; |
195 |
|
for (j = sdNodes.begin(); j != sdNodes.end(); ++j) { |
196 |
< |
bs |= j->bs; |
196 |
> |
bs |= (*j)->bs; |
197 |
|
} |
198 |
|
} |
199 |
|
|
209 |
|
std::vector<TreeNode*> rbAtomNodes = getMatchedChildren(*j, rbAtomName); |
210 |
|
std::vector<TreeNode*>::iterator k; |
211 |
|
for(k = rbAtomNodes.begin(); k != rbAtomNodes.end(); ++k){ |
212 |
< |
bs |= k->bs; |
212 |
> |
bs |= (*k)->bs; |
213 |
|
} |
214 |
|
} |
215 |
|
} |
233 |
|
return Wildcard::wildcardfit (wildcard.c_str(), str.c_str()); |
234 |
|
} |
235 |
|
|
236 |
+ |
|
237 |
+ |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& bs){ |
238 |
+ |
|
239 |
+ |
std::map<std::string, TreeNode*>::iterator foundIter; |
240 |
+ |
SimInfo::MoleculeIterator mi; |
241 |
+ |
Molecule* mol; |
242 |
+ |
|
243 |
+ |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
244 |
+ |
|
245 |
+ |
if (isMatched(mol->getMoleculeName(), name) ) { |
246 |
+ |
int natoms = mol->getNAtoms(); |
247 |
+ |
int nrigidbodies = mol->getNRigidBodies(); |
248 |
+ |
if (internalIndex >= natoms + nrigidbodies) { |
249 |
+ |
continue; |
250 |
+ |
} else if (internalIndex < natoms) { |
251 |
+ |
bs.setBitOn(mol->getAtomAt(internalIndex)->getGlobalIndex()); |
252 |
+ |
continue; |
253 |
+ |
} else if ( internalIndex < natoms + nrigidbodies) { |
254 |
+ |
bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex()); |
255 |
+ |
} |
256 |
+ |
} |
257 |
+ |
|
258 |
+ |
} |
259 |
+ |
|
260 |
|
} |
261 |
+ |
|
262 |
+ |
bool NameFinder::isInteger(const std::string str) { |
263 |
+ |
for(int i =0; i < str.size(); ++i){ |
264 |
+ |
if (!std::isdigit(str[i])) { |
265 |
+ |
return false; |
266 |
+ |
} |
267 |
+ |
} |
268 |
+ |
|
269 |
+ |
return true; |
270 |
+ |
} |
271 |
+ |
|
272 |
+ |
} |