mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
first pass, using google style
This commit is contained in:
Greg Landrum
@@ -17,251 +17,255 @@
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#include <boost/cstdint.hpp>
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namespace RDKit {
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const int ci_DISCRETEVALUEVECTPICKLE_VERSION=0x1;
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const int ci_DISCRETEVALUEVECTPICKLE_VERSION = 0x1;
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DiscreteValueVect::DiscreteValueVect(const DiscreteValueVect &other) {
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d_type = other.getValueType();
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d_bitsPerVal = other.getNumBitsPerVal();
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d_numInts = other.getNumInts();
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d_length = other.getLength();
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d_valsPerInt = other.d_valsPerInt;
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d_mask = other.d_mask;
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const boost::uint32_t *odata = other.getData();
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boost::uint32_t *data = new boost::uint32_t[d_numInts];
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memcpy(static_cast<void *>(data), static_cast<const void *>(odata),
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d_numInts*sizeof(boost::uint32_t));
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d_data.reset(data);
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DiscreteValueVect::DiscreteValueVect(const DiscreteValueVect &other) {
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d_type = other.getValueType();
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d_bitsPerVal = other.getNumBitsPerVal();
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d_numInts = other.getNumInts();
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d_length = other.getLength();
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d_valsPerInt = other.d_valsPerInt;
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d_mask = other.d_mask;
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const boost::uint32_t *odata = other.getData();
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boost::uint32_t *data = new boost::uint32_t[d_numInts];
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memcpy(static_cast<void *>(data), static_cast<const void *>(odata),
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d_numInts * sizeof(boost::uint32_t));
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d_data.reset(data);
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}
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unsigned int DiscreteValueVect::getVal(unsigned int i) const {
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if (i >= d_length) {
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throw IndexErrorException(i);
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}
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unsigned int shift = d_bitsPerVal * (i % d_valsPerInt);
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unsigned int intId = i / d_valsPerInt;
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return ((d_data[intId] >> shift) & d_mask);
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}
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void DiscreteValueVect::setVal(unsigned int i, unsigned int val) {
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if (i >= d_length) {
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throw IndexErrorException(i);
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}
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if ((val & d_mask) != val) {
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throw ValueErrorException("Value out of range");
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}
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unsigned int shift = d_bitsPerVal * (i % d_valsPerInt);
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unsigned int intId = i / d_valsPerInt;
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unsigned int mask = ((1 << d_bitsPerVal) - 1) << shift;
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mask = ~mask;
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d_data[intId] = (d_data[intId] & mask) | (val << shift);
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}
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unsigned int DiscreteValueVect::getTotalVal() const {
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unsigned int i, j, res = 0;
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for (i = 0; i < d_numInts; ++i) {
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for (j = 0; j < d_valsPerInt; ++j) {
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res += ((d_data[i] >> (j * d_bitsPerVal)) & d_mask);
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}
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}
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return res;
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}
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unsigned int DiscreteValueVect::getLength() const { return d_length; }
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const boost::uint32_t *DiscreteValueVect::getData() const {
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return d_data.get();
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}
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unsigned int computeL1Norm(const DiscreteValueVect &v1,
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const DiscreteValueVect &v2) {
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if (v1.getLength() != v2.getLength()) {
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throw ValueErrorException("Comparing vectors of different lengths");
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}
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unsigned int DiscreteValueVect::getVal(unsigned int i) const {
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if(i >= d_length){
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throw IndexErrorException(i);
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}
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unsigned int shift = d_bitsPerVal*(i%d_valsPerInt);
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unsigned int intId = i/d_valsPerInt;
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return ( (d_data[intId] >> shift) & d_mask);
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DiscreteValueVect::DiscreteValueType valType = v1.getValueType();
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if (valType != v2.getValueType()) {
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throw ValueErrorException("Comparing vector of different value types");
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}
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void DiscreteValueVect::setVal(unsigned int i, unsigned int val) {
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if(i >= d_length){
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throw IndexErrorException(i);
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}
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if ((val & d_mask) != val) {
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throw ValueErrorException("Value out of range");
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}
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unsigned int shift = d_bitsPerVal*(i%d_valsPerInt);
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unsigned int intId = i/d_valsPerInt;
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unsigned int mask = ((1<<d_bitsPerVal) -1) << shift;
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mask = ~mask;
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d_data[intId] = (d_data[intId]&mask)|(val << shift);
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}
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const boost::uint32_t *data1 = v1.getData();
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const boost::uint32_t *data2 = v2.getData();
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unsigned int DiscreteValueVect::getTotalVal() const {
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unsigned int i, j, res = 0;
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for (i = 0; i < d_numInts; ++i) {
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for (j = 0; j < d_valsPerInt; ++j) {
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res += ((d_data[i] >> (j*d_bitsPerVal)) & d_mask);
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}
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}
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return res;
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}
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unsigned int res = 0;
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if (valType <= DiscreteValueVect::EIGHTBITVALUE) {
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DiscreteDistMat *dmat = getDiscreteDistMat();
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unsigned int DiscreteValueVect::getLength() const {
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return d_length;
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}
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const boost::uint32_t *DiscreteValueVect::getData() const {
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return d_data.get();
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}
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unsigned int computeL1Norm(const DiscreteValueVect &v1, const DiscreteValueVect &v2) {
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if (v1.getLength() != v2.getLength()) {
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throw ValueErrorException("Comparing vectors of different lengths");
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}
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DiscreteValueVect::DiscreteValueType valType = v1.getValueType();
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if (valType != v2.getValueType()) {
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throw ValueErrorException("Comparing vector of different value types");
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}
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const boost::uint32_t* data1 = v1.getData();
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const boost::uint32_t* data2 = v2.getData();
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unsigned int res = 0;
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if (valType <= DiscreteValueVect::EIGHTBITVALUE) {
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DiscreteDistMat *dmat = getDiscreteDistMat();
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unsigned char *cd1 = (unsigned char *)(data1);
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unsigned char *cd2 = (unsigned char *)(data2);
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const unsigned char *cend = cd1 + (v1.getNumInts()*4);
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while (cd1 != cend) {
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if (*cd1 == *cd2) {
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cd1++;
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cd2++;
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continue;
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}
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res += dmat->getDist(*cd1, *cd2, valType);
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unsigned char *cd1 = (unsigned char *)(data1);
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unsigned char *cd2 = (unsigned char *)(data2);
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const unsigned char *cend = cd1 + (v1.getNumInts() * 4);
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while (cd1 != cend) {
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if (*cd1 == *cd2) {
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cd1++;
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cd2++;
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continue;
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}
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} else {
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// we have a sixteen bits per value type
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// REVIEW: we are making an assumption here that a short
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// is 16 bit - may fail on a different compiler
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const unsigned short int *sd1 = (unsigned short int *)(data1);
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const unsigned short int *sd2 = (unsigned short int *)(data2);
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const unsigned short int *send = sd1 + (v1.getNumInts()*2);
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while (sd1 != send) {
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if (*sd1 == *sd2) {
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sd1++;
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sd2++;
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continue;
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}
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res += abs((*sd1) - (*sd2));
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res += dmat->getDist(*cd1, *cd2, valType);
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cd1++;
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cd2++;
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}
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} else {
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// we have a sixteen bits per value type
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// REVIEW: we are making an assumption here that a short
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// is 16 bit - may fail on a different compiler
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const unsigned short int *sd1 = (unsigned short int *)(data1);
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const unsigned short int *sd2 = (unsigned short int *)(data2);
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const unsigned short int *send = sd1 + (v1.getNumInts() * 2);
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while (sd1 != send) {
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if (*sd1 == *sd2) {
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sd1++;
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sd2++;
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continue;
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}
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res += abs((*sd1) - (*sd2));
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sd1++;
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sd2++;
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}
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return res;
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}
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return res;
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}
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std::string DiscreteValueVect::toString() const {
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std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
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std::string DiscreteValueVect::toString() const {
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std::stringstream ss(std::ios_base::binary | std::ios_base::out |
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std::ios_base::in);
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boost::int32_t tVers=ci_DISCRETEVALUEVECTPICKLE_VERSION*-1;
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streamWrite(ss,tVers);
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boost::uint32_t tInt;
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tInt=d_type;
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streamWrite(ss,tInt);
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tInt=d_bitsPerVal;
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streamWrite(ss,tInt);
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tInt=d_mask;
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streamWrite(ss,tInt);
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tInt=d_length;
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streamWrite(ss,tInt);
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tInt=d_numInts;
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streamWrite(ss,tInt);
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boost::int32_t tVers = ci_DISCRETEVALUEVECTPICKLE_VERSION * -1;
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streamWrite(ss, tVers);
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boost::uint32_t tInt;
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tInt = d_type;
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streamWrite(ss, tInt);
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tInt = d_bitsPerVal;
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streamWrite(ss, tInt);
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tInt = d_mask;
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streamWrite(ss, tInt);
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tInt = d_length;
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streamWrite(ss, tInt);
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tInt = d_numInts;
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streamWrite(ss, tInt);
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#if defined(BOOST_BIG_ENDIAN)
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boost::uint32_t *td = new boost::uint32_t[d_numInts];
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for(unsigned int i=0;i<d_numInts;++i) td[i]=EndianSwapBytes<HOST_ENDIAN_ORDER,LITTLE_ENDIAN_ORDER>(d_data.get()[i]);
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ss.write((const char *)td,d_numInts*sizeof(tInt));
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delete [] td;
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#else
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ss.write((const char *)d_data.get(),d_numInts*sizeof(tInt));
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#endif
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std::string res(ss.str());
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return res;
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};
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boost::uint32_t *td = new boost::uint32_t[d_numInts];
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for (unsigned int i = 0; i < d_numInts; ++i)
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td[i] = EndianSwapBytes<HOST_ENDIAN_ORDER, LITTLE_ENDIAN_ORDER>(
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d_data.get()[i]);
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ss.write((const char *)td, d_numInts * sizeof(tInt));
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delete[] td;
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#else
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ss.write((const char *)d_data.get(), d_numInts * sizeof(tInt));
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#endif
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std::string res(ss.str());
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return res;
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};
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void DiscreteValueVect::initFromText(const char *pkl,const unsigned int len){
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std::stringstream ss(std::ios_base::binary|std::ios_base::in|std::ios_base::out);
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ss.write(pkl,len);
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boost::int32_t tVers;
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streamRead(ss,tVers);
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tVers *= -1;
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if(tVers==0x1){
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void DiscreteValueVect::initFromText(const char *pkl, const unsigned int len) {
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std::stringstream ss(std::ios_base::binary | std::ios_base::in |
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std::ios_base::out);
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ss.write(pkl, len);
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boost::int32_t tVers;
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streamRead(ss, tVers);
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tVers *= -1;
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if (tVers == 0x1) {
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} else {
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throw ValueErrorException("bad version in DiscreteValueVect pickle");
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}
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boost::uint32_t tInt;
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streamRead(ss, tInt);
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d_type = static_cast<DiscreteValueType>(tInt);
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streamRead(ss, tInt);
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d_bitsPerVal = tInt;
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d_valsPerInt = BITS_PER_INT / d_bitsPerVal;
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streamRead(ss, tInt);
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d_mask = tInt;
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streamRead(ss, tInt);
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d_length = tInt;
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streamRead(ss, tInt);
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d_numInts = tInt;
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boost::uint32_t *data = new boost::uint32_t[d_numInts];
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ss.read((char *)data, d_numInts * sizeof(boost::uint32_t));
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#if defined(BOOST_BIG_ENDIAN)
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boost::uint32_t *td = new boost::uint32_t[d_numInts];
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for (unsigned int i = 0; i < d_numInts; ++i)
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td[i] = EndianSwapBytes<LITTLE_ENDIAN_ORDER, HOST_ENDIAN_ORDER>(data[i]);
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d_data.reset(td);
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delete[] data;
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#else
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d_data.reset(data);
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#endif
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};
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DiscreteValueVect DiscreteValueVect::operator&(
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const DiscreteValueVect &other) const {
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PRECONDITION(other.d_length == d_length, "length mismatch");
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DiscreteValueType typ = d_type;
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if (other.d_type < typ) {
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typ = other.d_type;
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}
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DiscreteValueVect ans(typ, d_length);
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for (unsigned int i = 0; i < d_length; ++i) {
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unsigned int v1 = getVal(i);
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unsigned int v2 = other.getVal(i);
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if (v1 < v2) {
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ans.setVal(i, v1);
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} else {
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throw ValueErrorException("bad version in DiscreteValueVect pickle");
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ans.setVal(i, v2);
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}
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boost::uint32_t tInt;
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streamRead(ss,tInt);
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d_type=static_cast<DiscreteValueType>(tInt);
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streamRead(ss,tInt);
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d_bitsPerVal=tInt;
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d_valsPerInt = BITS_PER_INT/d_bitsPerVal;
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streamRead(ss,tInt);
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d_mask=tInt;
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streamRead(ss,tInt);
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d_length=tInt;
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streamRead(ss,tInt);
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d_numInts=tInt;
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boost::uint32_t *data = new boost::uint32_t[d_numInts];
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ss.read((char *)data,d_numInts*sizeof(boost::uint32_t));
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#if defined(BOOST_BIG_ENDIAN)
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boost::uint32_t *td = new boost::uint32_t[d_numInts];
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for(unsigned int i=0;i<d_numInts;++i) td[i]=EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(data[i]);
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d_data.reset(td);
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delete [] data;
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#else
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d_data.reset(data);
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#endif
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};
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DiscreteValueVect DiscreteValueVect::operator& (const DiscreteValueVect &other) const {
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PRECONDITION(other.d_length==d_length,"length mismatch");
|
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DiscreteValueType typ=d_type;
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if(other.d_type<typ){
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typ=other.d_type;
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}
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DiscreteValueVect ans(typ,d_length);
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for(unsigned int i=0;i<d_length;++i){
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unsigned int v1=getVal(i);
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unsigned int v2=other.getVal(i);
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if(v1<v2){
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ans.setVal(i,v1);
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}else{
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ans.setVal(i,v2);
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}
|
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}
|
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return(ans);
|
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};
|
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|
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DiscreteValueVect DiscreteValueVect::operator|(const DiscreteValueVect &other) const {
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PRECONDITION(other.d_length==d_length,"length mismatch");
|
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DiscreteValueType typ=d_type;
|
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if(other.d_type>typ){
|
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typ=other.d_type;
|
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}
|
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DiscreteValueVect ans(typ,d_length);
|
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for(unsigned int i=0;i<d_length;++i){
|
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unsigned int v1=getVal(i);
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unsigned int v2=other.getVal(i);
|
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if(v1>v2){
|
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ans.setVal(i,v1);
|
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}else{
|
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ans.setVal(i,v2);
|
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}
|
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}
|
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return(ans);
|
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};
|
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|
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DiscreteValueVect& DiscreteValueVect::operator+=(const DiscreteValueVect &other) {
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PRECONDITION(other.d_length==d_length,"length mismatch");
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unsigned int maxVal = (1<<d_bitsPerVal) - 1;
|
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|
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for(unsigned int i=0;i<d_length;i++){
|
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unsigned int v=getVal(i)+other.getVal(i);
|
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if(v>maxVal){
|
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v=maxVal;
|
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}
|
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setVal(i,v);
|
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}
|
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return *this;
|
||||
}
|
||||
DiscreteValueVect& DiscreteValueVect::operator-=(const DiscreteValueVect &other) {
|
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PRECONDITION(other.d_length==d_length,"length mismatch");
|
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return (ans);
|
||||
};
|
||||
|
||||
for(unsigned int i=0;i<d_length;i++){
|
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unsigned int v1=getVal(i);
|
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unsigned int v2=other.getVal(i);
|
||||
if(v1>v2){
|
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setVal(i,v1-v2);
|
||||
}else{
|
||||
setVal(i,0);
|
||||
}
|
||||
}
|
||||
return *this;
|
||||
DiscreteValueVect DiscreteValueVect::operator|(
|
||||
const DiscreteValueVect &other) const {
|
||||
PRECONDITION(other.d_length == d_length, "length mismatch");
|
||||
DiscreteValueType typ = d_type;
|
||||
if (other.d_type > typ) {
|
||||
typ = other.d_type;
|
||||
}
|
||||
DiscreteValueVect ans(typ, d_length);
|
||||
for (unsigned int i = 0; i < d_length; ++i) {
|
||||
unsigned int v1 = getVal(i);
|
||||
unsigned int v2 = other.getVal(i);
|
||||
if (v1 > v2) {
|
||||
ans.setVal(i, v1);
|
||||
} else {
|
||||
ans.setVal(i, v2);
|
||||
}
|
||||
}
|
||||
return (ans);
|
||||
};
|
||||
|
||||
DiscreteValueVect &DiscreteValueVect::operator+=(
|
||||
const DiscreteValueVect &other) {
|
||||
PRECONDITION(other.d_length == d_length, "length mismatch");
|
||||
unsigned int maxVal = (1 << d_bitsPerVal) - 1;
|
||||
|
||||
for (unsigned int i = 0; i < d_length; i++) {
|
||||
unsigned int v = getVal(i) + other.getVal(i);
|
||||
if (v > maxVal) {
|
||||
v = maxVal;
|
||||
}
|
||||
setVal(i, v);
|
||||
}
|
||||
return *this;
|
||||
}
|
||||
DiscreteValueVect &DiscreteValueVect::operator-=(
|
||||
const DiscreteValueVect &other) {
|
||||
PRECONDITION(other.d_length == d_length, "length mismatch");
|
||||
|
||||
for (unsigned int i = 0; i < d_length; i++) {
|
||||
unsigned int v1 = getVal(i);
|
||||
unsigned int v2 = other.getVal(i);
|
||||
if (v1 > v2) {
|
||||
setVal(i, v1 - v2);
|
||||
} else {
|
||||
setVal(i, 0);
|
||||
}
|
||||
}
|
||||
return *this;
|
||||
}
|
||||
|
||||
#if 0
|
||||
DiscreteValueVect DiscreteValueVect::operator~() const {
|
||||
@@ -275,19 +279,17 @@ namespace RDKit {
|
||||
};
|
||||
#endif
|
||||
|
||||
DiscreteValueVect operator+ (const DiscreteValueVect& p1,
|
||||
const DiscreteValueVect& p2){
|
||||
DiscreteValueVect res(p1);
|
||||
res+=p2;
|
||||
return res;
|
||||
};
|
||||
DiscreteValueVect operator- (const DiscreteValueVect& p1,
|
||||
const DiscreteValueVect& p2){
|
||||
DiscreteValueVect res(p1);
|
||||
res-=p2;
|
||||
return res;
|
||||
};
|
||||
|
||||
|
||||
} // end of namespace RDKit
|
||||
DiscreteValueVect operator+(const DiscreteValueVect &p1,
|
||||
const DiscreteValueVect &p2) {
|
||||
DiscreteValueVect res(p1);
|
||||
res += p2;
|
||||
return res;
|
||||
};
|
||||
DiscreteValueVect operator-(const DiscreteValueVect &p1,
|
||||
const DiscreteValueVect &p2) {
|
||||
DiscreteValueVect res(p1);
|
||||
res -= p2;
|
||||
return res;
|
||||
};
|
||||
|
||||
} // end of namespace RDKit
|
||||
|
||||
Reference in New Issue
Block a user