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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){ |
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RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){ |
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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validateSelection1(seleMan1_); |
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} |
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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validateSelection2(seleMan2_); |
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} |
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if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
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if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
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//if all selections are static, we can precompute the number of real pairs |
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common_ = seleMan1_ & seleMan2_; |
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sele1_minus_common_ = seleMan1_ - common_; |
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sele2_minus_common_ = seleMan2_ - common_; |
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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|
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BitSet bs = seleMan1_.getSelectionSet(); |
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bs &= seleMan2_.getSelectionSet(); |
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int nIntersect = bs.countBits(); |
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|
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nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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int nIntersect = common_.getSelectionCount(); |
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|
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nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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} |
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} |
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void RadialDistrFunc::process() { |
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void RadialDistrFunc::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames / step_ + 1; |
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nProcessed_ = nFrames / step_; |
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for (int i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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if (evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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if (evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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if (evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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validateSelection1(seleMan1_); |
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} |
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if (evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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validateSelection2(seleMan2_); |
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} |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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initalizeHistogram(); |
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initalizeHistogram(); |
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StuntDouble* sd1; |
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int j; |
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for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) { |
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StuntDouble* sd2; |
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int k; |
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for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) { |
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if (sd1 != sd2) { |
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collectHistogram(sd1, sd2); |
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} |
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} |
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} |
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|
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//selections may overlap. |
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// |
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// |s1 -c | c | |
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// | c |s2 - c| |
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// |
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// s1 : number of selected stuntdoubles in selection1 |
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// s2 : number of selected stuntdoubles in selection2 |
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// c : number of intersect stuntdouble between selection1 and selection2 |
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//when loop over the pairs, we can divide the looping into 3 stages |
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//stage 1 : [s1-c] [s2] |
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//stage 2 : [c] [s2 - c] |
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//stage 3 : [c] [c] |
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//stage 1 and stage 2 are completly non-overlapping |
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//stage 3 are completely overlapping |
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processHistogram(); |
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if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
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|
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common_ = seleMan1_ & seleMan2_; |
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sele1_minus_common_ = seleMan1_ - common_; |
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sele2_minus_common_ = seleMan2_ - common_; |
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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int nIntersect = common_.getSelectionCount(); |
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|
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nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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|
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processNonOverlapping(sele1_minus_common_, seleMan2_); |
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processNonOverlapping(common_, sele2_minus_common_); |
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processOverlapping(common_); |
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processHistogram(); |
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} |
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postProcess(); |
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writeRdf(); |
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} |
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} |
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int RadialDistrFunc::getNRealPairs() { |
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if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
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//if one of the selection is static, need to recompute it |
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void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) { |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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int i; |
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int j; |
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|
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for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) { |
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) { |
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collectHistogram(sd1, sd2); |
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} |
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} |
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BitSet bs = seleMan1_.getSelectionSet(); |
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bs &= seleMan2_.getSelectionSet(); |
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int nIntersect = bs.countBits(); |
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} |
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nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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void RadialDistrFunc::processOverlapping( SelectionManager& sman) { |
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StuntDouble* sd1; |
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StuntDouble* sd2; |
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int i; |
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int j; |
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|
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//basically, it is the same as below loop |
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//for (int i = 0; i < n; ++i ) |
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// for (int j = i + 1; j < n; ++j) {} |
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|
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for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) { |
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for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) { |
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collectHistogram(sd1, sd2); |
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} |
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} |
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return nRealPairs_; |
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} |
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} |
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} |