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run clang-tidy with readability-braces-around-statements (#2899)

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* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke

* fix problem on windows
This commit is contained in:
Greg Landrum
2020-01-25 14:19:32 +01:00
committed by GitHub
parent fb3cad523e
commit d41752d558
261 changed files with 7449 additions and 3545 deletions
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121
Code/DataStructs/BitOps.cpp
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@@ -110,12 +110,18 @@ bool AllProbeBitsMatch(const char* probe, const char* ref) {
while (nProbeOn) {
while (currRefBit < currProbeBit && nRefOn > 0) {
if (refFormat == 2) currRefBit++;
if (refFormat == 2) {
currRefBit++;
}
currRefBit = getBitId(ref, refFormat, refSize, currRefBit);
nRefOn--;
}
if (currRefBit != currProbeBit) return false;
if (probeFormat == 2) currProbeBit++;
if (currRefBit != currProbeBit) {
return false;
}
if (probeFormat == 2) {
currProbeBit++;
}
currProbeBit = getBitId(probe, probeFormat, probeSize, currProbeBit);
nProbeOn--;
}
@@ -154,11 +160,15 @@ bool AllProbeBitsMatch(const T1& probe, const std::string& pkl) {
// if(probe.getBit(i)){
for (std::vector<int>::const_iterator i = obl.begin(); i != obl.end(); i++) {
while (currBit < *i && nOn > 0) {
if (format == 2) currBit++;
if (format == 2) {
currBit++;
}
currBit = getBitId(text, format, size, currBit);
nOn--;
}
if (currBit != *i) return false;
if (currBit != *i) {
return false;
}
//}
}
return true;
@@ -208,15 +218,19 @@ const bool canUseBitmapHack =
bool EBVToBitmap(const ExplicitBitVect& bv, const unsigned char*& fp,
unsigned int& nBytes) {
if (!canUseBitmapHack) return false;
const bitset_impl* p1 = (const bitset_impl*)(const void*)bv.dp_bits;
if (!canUseBitmapHack) {
return false;
}
const auto* p1 = (const bitset_impl*)(const void*)bv.dp_bits;
// Run-time sanity check (just in case)
if (p1->m_num_bits != bv.dp_bits->size()) {
return false;
}
fp = (const unsigned char*)p1->m_bits.data();
nBytes = (unsigned int)p1->m_num_bits / 8;
if (p1->m_num_bits % 8) ++nBytes;
if (p1->m_num_bits % 8) {
++nBytes;
}
return true;
}
} // end of local namespace
@@ -254,10 +268,13 @@ int NumOnBitsInCommon(const ExplicitBitVect& bv1, const ExplicitBitVect& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
double TanimotoSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
unsigned int total = bv1.getNumOnBits() + bv2.getNumOnBits();
if (total == 0) return 1.0;
if (total == 0) {
return 1.0;
}
unsigned int common = NumOnBitsInCommon(bv1, bv2);
return (double)common / (double)(total - common);
}
@@ -266,22 +283,25 @@ template <typename T1, typename T2>
double TverskySimilarity(const T1& bv1, const T2& bv2, double a, double b) {
RANGE_CHECK(0, a, 1);
RANGE_CHECK(0, b, 1);
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
double denom = a * y + b * z + (1 - a - b) * x;
if (denom == 0.0)
if (denom == 0.0) {
return 1.0;
else
} else {
return x / denom;
}
}
template <typename T1, typename T2>
double CosineSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
@@ -295,8 +315,9 @@ double CosineSimilarity(const T1& bv1, const T2& bv2) {
template <typename T1, typename T2>
double KulczynskiSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
@@ -310,8 +331,9 @@ double KulczynskiSimilarity(const T1& bv1, const T2& bv2) {
template <typename T1, typename T2>
double DiceSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
@@ -325,8 +347,9 @@ double DiceSimilarity(const T1& bv1, const T2& bv2) {
template <typename T1, typename T2>
double SokalSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
@@ -336,8 +359,9 @@ double SokalSimilarity(const T1& bv1, const T2& bv2) {
template <typename T1, typename T2>
double McConnaugheySimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
@@ -351,20 +375,25 @@ double McConnaugheySimilarity(const T1& bv1, const T2& bv2) {
template <typename T>
inline T tmin(T v1, T v2) {
if (v1 < v2) return v1;
if (v1 < v2) {
return v1;
}
return v2;
}
template <typename T>
inline T tmax(T v1, T v2) {
if (v1 > v2) return v1;
if (v1 > v2) {
return v1;
}
return v2;
}
template <typename T1, typename T2>
double AsymmetricSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
@@ -378,8 +407,9 @@ double AsymmetricSimilarity(const T1& bv1, const T2& bv2) {
template <typename T1, typename T2>
double BraunBlanquetSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
@@ -393,25 +423,28 @@ double BraunBlanquetSimilarity(const T1& bv1, const T2& bv2) {
template <typename T1, typename T2>
double RusselSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
return x / bv1.getNumBits();
}
template <typename T1, typename T2>
double RogotGoldbergSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double x = NumOnBitsInCommon(bv1, bv2);
double y = bv1.getNumOnBits();
double z = bv2.getNumOnBits();
double l = bv1.getNumBits();
double d = l - y - z + x;
if ((x == l) || (d == l))
if ((x == l) || (d == l)) {
return 1.0;
else
} else {
return (x / (y + z) + (d) / (2 * l - y - z));
}
}
// """ -------------------------------------------------------
@@ -428,8 +461,9 @@ double RogotGoldbergSimilarity(const T1& bv1, const T2& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
double OnBitSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
double num = NumOnBitsInCommon(bv1, bv2);
double denom = (bv1 | bv2).getNumOnBits();
@@ -456,8 +490,9 @@ double OnBitSimilarity(const T1& bv1, const T2& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
int NumBitsInCommon(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
return bv1.getNumBits() - (bv1 ^ bv2).getNumOnBits();
}
@@ -483,8 +518,9 @@ int NumBitsInCommon(const ExplicitBitVect& bv1, const ExplicitBitVect& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
double AllBitSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
return double(NumBitsInCommon(bv1, bv2)) / bv1.getNumBits();
}
@@ -505,8 +541,9 @@ double AllBitSimilarity(const T1& bv1, const T2& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
IntVect OnBitsInCommon(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
IntVect res;
(bv1 & bv2).getOnBits(res);
return res;
@@ -528,8 +565,9 @@ IntVect OnBitsInCommon(const T1& bv1, const T2& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
IntVect OffBitsInCommon(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
IntVect res;
(~(bv1 | bv2)).getOnBits(res);
return res;
@@ -562,8 +600,9 @@ IntVect OffBitsInCommon(const T1& bv1, const T2& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
DoubleVect OnBitProjSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
DoubleVect res(2, 0.0);
double num = NumOnBitsInCommon(bv1, bv2);
if (num) {
@@ -600,8 +639,9 @@ DoubleVect OnBitProjSimilarity(const T1& bv1, const T2& bv2) {
// """ -------------------------------------------------------
template <typename T1, typename T2>
DoubleVect OffBitProjSimilarity(const T1& bv1, const T2& bv2) {
if (bv1.getNumBits() != bv2.getNumBits())
if (bv1.getNumBits() != bv2.getNumBits()) {
throw ValueErrorException("BitVects must be same length");
}
DoubleVect res(2, 0.0);
double num = (bv1 | bv2).getNumOffBits();
if (num) {
@@ -613,8 +653,9 @@ DoubleVect OffBitProjSimilarity(const T1& bv1, const T2& bv2) {
template <typename T1>
T1* FoldFingerprint(const T1& bv1, unsigned int factor) {
if (factor <= 0 || factor >= bv1.getNumBits())
if (factor <= 0 || factor >= bv1.getNumBits()) {
throw ValueErrorException("invalid fold factor");
}
int initSize = bv1.getNumBits();
int resSize = initSize / factor;
@@ -633,7 +674,9 @@ template <typename T1>
std::string BitVectToText(const T1& bv1) {
std::string res(bv1.getNumBits(), '0');
for (unsigned int i = 0; i < bv1.getNumBits(); i++) {
if (bv1.getBit(i)) res[i] = '1';
if (bv1.getBit(i)) {
res[i] = '1';
}
}
return res;
}
@@ -706,7 +749,9 @@ void UpdateBitVectFromFPSText(T1& bv1, const std::string& fps) {
}
for (unsigned int bit = 0; bit < 8 && bitIdx < bv1.getNumBits();
++bit, ++bitIdx) {
if (c & (1 << bit)) bv1.setBit(bitIdx);
if (c & (1 << bit)) {
bv1.setBit(bitIdx);
}
}
}
}
@@ -719,7 +764,9 @@ void UpdateBitVectFromBinaryText(T1& bv1, const std::string& fps) {
unsigned short c = fps[i];
for (unsigned int bit = 0; bit < 8 && bitIdx < bv1.getNumBits();
++bit, ++bitIdx) {
if (c & (1 << bit)) bv1.setBit(bitIdx);
if (c & (1 << bit)) {
bv1.setBit(bitIdx);
}
}
}
}