Commit a7c7aee6 authored by Iakov Davydov's avatar Iakov Davydov
Browse files

fix multiple angular brackets and some comments formatting

parent 6db2cd70
......@@ -273,16 +273,11 @@ void BranchSiteModel::setLimits(size_t aNumTimes, size_t aNumVariables,
} else {
mLowerBound.reserve(aNumTimes + aNumVariables);
mUpperBound.reserve(aNumTimes + aNumVariables);
// Set lower constrains // Set
// upper
// constrains
// Set lower & upper constrains
mLowerBound.assign(aNumTimes, 0);
mUpperBound.assign(aNumTimes, 50.0); // T
}
// Set lower constrains // Set
// upper
// constrains
#ifdef USE_ORIGINAL_PROPORTIONS
mLowerBound.push_back(-99.0);
mUpperBound.push_back(99.0); // x0 -> p0
......
......@@ -17,27 +17,21 @@ class Ming2 {
public:
/// Constructor
///
/// @param[in] aModel The pointer to the hypothesis class that will
/// be
/// used
/// @param[in] aTrace Trace or not the optimizer
/// progress
/// @param[in] aVerbose The verbose level
/// @param[in] aLowerBound Lower limit of the variables to constrain
/// the
/// interval on which the optimum should be computed
/// @param[in] aUpperBound Upper limit of the variables to constrain
/// the
/// interval on which the optimum should be computed
/// @param[in] aDeltaForGradient Delta used to compute the gradient
/// @param[in] aRelativeError Relative error to stop computation
/// @param[in] aStopIfBigger If true stop computation as soon as value
/// is
/// over aThreshold
/// @param[in] aThreshold The threshold at which the maximization
/// should
/// be stopped
/// @param[in] aMaxIterations Maximum number of iterations for the
/// @param[in] aModel The pointer to the hypothesis class that will
/// be used
/// @param[in] aTrace Trace or not the optimizer progress
/// @param[in] aVerbose The verbose level
/// @param[in] aLowerBound Lower limit of the variables to
/// constrain the interval on which the optimum should be computed
/// @param[in] aUpperBound Upper limit of the variables to
/// constrain the interval on which the optimum should be computed
/// @param[in] aDeltaForGradient Delta used to compute the gradient
/// @param[in] aRelativeError Relative error to stop computation
/// @param[in] aStopIfBigger If true stop computation as soon as
/// value is over aThreshol
/// @param[in] aThreshold The threshold at which the maximization
/// should be stopped
/// @param[in] aMaxIterations Maximum number of iterations for the
/// maximization
///
Ming2(BranchSiteModel *aModel, bool aTrace, unsigned int aVerbose,
......
......@@ -22,7 +22,7 @@ CodonFrequencies *CodonFrequencies::getInstance(void) {
}
void CodonFrequencies::setCodonFrequencies(
const std::vector<std::vector<unsigned int>> &aCodons,
const std::vector<std::vector<unsigned int> > &aCodons,
CodonFrequencyModel aModel, bool aShowMessages) {
// Compute mCodonFrequencies based on the selected model
if (aModel == CODON_FREQ_MODEL_F3X4) {
......@@ -106,7 +106,7 @@ void CodonFrequencies::setCodonFrequencies(
}
void CodonFrequencies::updateCodonCount(
const std::vector<std::vector<unsigned int>> &aCodons,
const std::vector<std::vector<unsigned int> > &aCodons,
std::vector<double> &aCodonCount) const {
// Zero the count array
aCodonCount.assign(N, 0.);
......
......@@ -45,7 +45,7 @@ public:
/// @exception FastCodeMLFatal If invalid codon frequency model requested
///
void
setCodonFrequencies(const std::vector<std::vector<unsigned int>> &aCodons,
setCodonFrequencies(const std::vector<std::vector<unsigned int> > &aCodons,
CodonFrequencyModel aModel, bool aShowMessages);
/// Return a pointer to the codon frequencies array
......@@ -106,7 +106,7 @@ private:
/// @param[in] aCodons Codon positions and multiplicity.
/// @param[in,out] aCodonCount The count of each codon occurrences.
///
void updateCodonCount(const std::vector<std::vector<unsigned int>> &aCodons,
void updateCodonCount(const std::vector<std::vector<unsigned int> > &aCodons,
std::vector<double> &aCodonCount) const;
/// Convert the codon number in the 1 to 64 range to 1 to 61
......
......@@ -62,7 +62,7 @@ void DAGScheduler::dumpDAG(std::ostream &aOut) const {
aOut << '#' << std::endl;
// Then output all edges
std::vector<std::pair<const void *, const void *>>::const_iterator ied =
std::vector<std::pair<const void *, const void *> >::const_iterator ied =
mEdges.begin();
for (; ied != mEdges.end(); ++ied) {
aOut << ied->first << ' ' << ied->second << std::endl;
......
......@@ -67,7 +67,8 @@ public:
private:
std::set<const void *> mNodes; ///< Load the distinct node addresses
std::vector<std::pair<const void *, const void *>> mEdges; ///< Load the edges
std::vector<std::pair<const void *, const void *> >
mEdges; ///< Load the edges
std::map<const void *, int> mRefCounter; ///< Reference counter
std::map<const void *, int>
mRefCounterSave; ///< Save the reference counter map
......
......@@ -14,12 +14,12 @@
#endif
void FatVectorTransform::setBranchDependencies(
const std::vector<std::vector<ForestNode *>> &aNodesByLevel) {
const std::vector<std::vector<ForestNode *> > &aNodesByLevel) {
// Push only the branch id's (and compute num branches). The root is not
// pushed!
mNumBranches = 0;
mBranchByLevel.clear();
std::vector<std::vector<ForestNode *>>::const_reverse_iterator inbl;
std::vector<std::vector<ForestNode *> >::const_reverse_iterator inbl;
for (inbl = aNodesByLevel.rbegin(); inbl != aNodesByLevel.rend(); ++inbl) {
std::vector<unsigned int> v;
std::vector<ForestNode *>::const_iterator ifn = inbl->begin();
......@@ -96,9 +96,9 @@ void FatVectorTransform::printBranchVisitSequence(void) const {
std::cout << std::endl
<< "Branch at level" << std::endl;
unsigned int level = 1;
std::vector<std::vector<unsigned int>>::const_iterator inbl =
std::vector<std::vector<unsigned int> >::const_iterator inbl =
mBranchByLevel.begin();
const std::vector<std::vector<unsigned int>>::const_iterator end =
const std::vector<std::vector<unsigned int> >::const_iterator end =
mBranchByLevel.end();
for (; inbl != end; ++inbl, ++level) {
std::cout << level << ": ";
......
......@@ -37,7 +37,7 @@ public:
/// level
///
void setBranchDependencies(
const std::vector<std::vector<ForestNode *>> &aNodesByLevel);
const std::vector<std::vector<ForestNode *> > &aNodesByLevel);
/// Initialize the class instance
///
......@@ -212,7 +212,7 @@ private:
/// position, to position)
typedef std::vector<VectorOfRangesNoCnt>
VectorOfVectorOfRangesNoCnt; ///< Vector of vectors of single item copies
typedef std::vector<std::pair<size_t, size_t>>
typedef std::vector<std::pair<size_t, size_t> >
VectorOfPairs; ///< Vector of pairs of values
VectorOfPairs mLimits; ///< Lower index and total count for each branch
......@@ -225,7 +225,7 @@ private:
/// is the first entry for its level
bool mNoTransformations; ///< If set no transformation will take place
///(corresponds to no tree prune case)
std::vector<std::vector<unsigned int>> mBranchByLevel; ///< Each level
std::vector<std::vector<unsigned int> > mBranchByLevel; ///< Each level
/// contains a list of
/// branch numbers at
/// this level. List
......
......@@ -44,7 +44,7 @@ void Forest::loadTreeAndGenes(
const std::vector<unsigned int> &mult = aGenes.getSiteMultiplicity();
// Initialize the codon info list
std::vector<std::vector<unsigned int>> codons_info;
std::vector<std::vector<unsigned int> > codons_info;
codons_info.reserve(mNumSites * aGenes.getNumSpecies());
// Initialize the array of all probability vectors to be all zeros
......@@ -208,9 +208,9 @@ void Forest::postLoad(void) {
unsigned int max_level = 0;
unsigned int max_leaf = 0;
unsigned int level = 0;
std::vector<std::vector<ForestNode *>>::iterator inbl(
std::vector<std::vector<ForestNode *> >::iterator inbl(
mNodesByLevel.begin());
const std::vector<std::vector<ForestNode *>>::iterator end(
const std::vector<std::vector<ForestNode *> >::iterator end(
mNodesByLevel.end());
for (level = 0; inbl != end; ++inbl, ++level) {
unsigned int num_leaves = 0;
......@@ -532,7 +532,7 @@ void Forest::computeLikelihoods(const ProbabilityMatrixSet &aSet,
// For each level of the tree (except the root)
unsigned int level = 0;
std::vector<std::vector<ForestNode *>>::reverse_iterator inbl;
std::vector<std::vector<ForestNode *> >::reverse_iterator inbl;
for (inbl = mNodesByLevel.rbegin(); inbl != mNodesByLevel.rend();
++inbl, ++level) {
const int num_sites = static_cast<int>(inbl->size());
......
......@@ -286,7 +286,7 @@ public:
///
/// @return List of lists of dependencies
///
const std::vector<std::vector<unsigned int>> &
const std::vector<std::vector<unsigned int> > &
getTreeDependencies(void) const {
return mTreeDependencies;
}
......@@ -296,7 +296,7 @@ public:
///
/// @return List of lists of reverse dependencies
///
const std::vector<std::vector<unsigned int>> &
const std::vector<std::vector<unsigned int> > &
getTreeRevDependencies(void) const {
return mTreeRevDependencies;
}
......@@ -415,7 +415,8 @@ private:
/// classes
CacheAlignedDoubleVector
mProbsOut; ///< mProbs after multiplication by exp(Qt)
std::vector<std::vector<ForestNode *>> mNodesByLevel; ///< Each level contains
std::vector<std::vector<ForestNode *> >
mNodesByLevel; ///< Each level contains
/// a list of pointers to
/// nodes at this level.
/// List start from the
......@@ -426,23 +427,23 @@ private:
#else
/// Unified array for each branch probability vector
CacheAlignedDoubleVector mProbs; ///< The concatenation of all the probability
/// vectors for all the nodes and all the
/// classes
/// vectors for all the nodes and all the
/// classes
#endif
std::vector<std::vector<unsigned int>>
std::vector<std::vector<unsigned int> >
mTreeDependencies; ///< mTreeDependencies[tj] = [t1 t2 t3] means: tj can
/// be done after: t1 t2 t3
std::vector<std::vector<unsigned int>>
std::vector<std::vector<unsigned int> >
mTreeRevDependencies; ///< mTreeRevDependencies[tj] = [t1 t2 t3] means: tj
/// should be ready before: t1 t2 t3
#ifdef NON_RECURSIVE_VISIT
std::vector<std::vector<ForestNode *>> mVisitTree; ///< List of pointers to
std::vector<std::vector<ForestNode *> > mVisitTree; ///< List of pointers to
/// tree nodes (a list per
/// site) in the
/// non-recursive visit
/// order
std::vector<std::vector<ForestNode *>> mVisitTreeParents; ///< List of parent
std::vector<std::vector<ForestNode *> > mVisitTreeParents; ///< List of parent
/// pointers for the
/// corresponding
/// nodes in the
......
......@@ -10,8 +10,8 @@
#include "Forest.h"
void ForestExport::exportForest(const char *aFilename, size_t aCounter) const {
std::vector<std::pair<int, int>> node_from;
std::vector<std::pair<int, int>> node_to;
std::vector<std::pair<int, int> > node_from;
std::vector<std::pair<int, int> > node_to;
std::vector<double> branch_length;
// Get all forest connections
......@@ -22,8 +22,8 @@ void ForestExport::exportForest(const char *aFilename, size_t aCounter) const {
}
// Remove duplicated nodes
std::set<std::pair<int, int>> vertices;
std::vector<std::pair<int, int>>::const_iterator ip = node_from.begin();
std::set<std::pair<int, int> > vertices;
std::vector<std::pair<int, int> >::const_iterator ip = node_from.begin();
for (; ip != node_from.end(); ++ip)
vertices.insert(*ip);
for (ip = node_to.begin(); ip != node_to.end(); ++ip)
......@@ -32,7 +32,7 @@ void ForestExport::exportForest(const char *aFilename, size_t aCounter) const {
// Convert to node indices
std::map<std::pair<int, int>, int> map;
int idx;
std::set<std::pair<int, int>>::const_iterator iv = vertices.begin();
std::set<std::pair<int, int> >::const_iterator iv = vertices.begin();
for (idx = 1; iv != vertices.end(); ++iv, ++idx) {
std::pair<int, int> p(iv->first, iv->second);
map[p] = idx;
......@@ -106,8 +106,8 @@ void ForestExport::exportForest(const char *aFilename, size_t aCounter) const {
void ForestExport::exportForestWalker(
const ForestNode *aNode, const std::vector<double> &aBranchLengths,
std::vector<std::pair<int, int>> &aNodeFrom,
std::vector<std::pair<int, int>> &aNodeTo,
std::vector<std::pair<int, int> > &aNodeFrom,
std::vector<std::pair<int, int> > &aNodeTo,
std::vector<double> &aLength) const {
int my_node_id = aNode->mBranchId + 1;
int my_tree_id = aNode->mOwnTree;
......
......@@ -42,8 +42,8 @@ private:
///
void exportForestWalker(const ForestNode *aNode,
const std::vector<double> &aBranchLengths,
std::vector<std::pair<int, int>> &aNodeFrom,
std::vector<std::pair<int, int>> &aNodeTo,
std::vector<std::pair<int, int> > &aNodeFrom,
std::vector<std::pair<int, int> > &aNodeTo,
std::vector<double> &aLength) const;
/// Disabled assignment operator to avoid warnings on Windows.
......
......@@ -91,7 +91,7 @@ void Genes::setLeaveProb(double *aLeaveProbVect) const {
}
}
void Genes::saveCodonsForCount(std::vector<std::vector<unsigned int>> &aCodons,
void Genes::saveCodonsForCount(std::vector<std::vector<unsigned int> > &aCodons,
unsigned int aSiteMultiplicity) const {
// Check if valid translation of the codon
size_t cnt = mCurrentPositions.size();
......@@ -436,7 +436,7 @@ void Genes::initFullCodonMap(void) {
// This is a valid, possibly ambiguous codon
if (valid) {
mMapCodonToPosition.insert(std::pair<std::string, std::vector<int>>(
mMapCodonToPosition.insert(std::pair<std::string, std::vector<int> >(
std::string(codona), pos));
}
}
......@@ -468,7 +468,7 @@ const std::vector<int> &Genes::getPositions(const char *aCodon) const {
codon[3] = '\0';
// Check if it is in the list of valid codons
std::map<std::string, std::vector<int>>::const_iterator im(
std::map<std::string, std::vector<int> >::const_iterator im(
mMapCodonToPosition.find(std::string(codon)));
// If no, return an empty list, else return the list of corresponding
......
......@@ -84,7 +84,7 @@ public:
///
/// @exception FastCodeMLFatal If saved codon is invalid.
///
void saveCodonsForCount(std::vector<std::vector<unsigned int>> &aCodons,
void saveCodonsForCount(std::vector<std::vector<unsigned int> > &aCodons,
unsigned int aSiteMultiplicity) const;
/// Check coherence between tree and genes.
......@@ -181,26 +181,17 @@ private:
std::vector<std::string> mDnaSpecies; ///< The list of species labels
std::vector<std::string> mDnaGene; ///< The gene DNA basis strings
std::vector<unsigned int> mSiteMultiplicity; ///< Site multiplicity (sites
/// with multiplicity of zero has
/// been removed from the site
/// list)
/// with multiplicity of zero has been removed from the site list)
std::vector<unsigned int>
mMapSiteToDnaGene; ///< Map the site number to the position in mDnaGene
std::map<std::string, unsigned int> mMapSpecieToDnaGene; ///< Map specie name
/// to position in the
/// gene list mDnaGene
/// to position in the gene list mDnaGene
std::multimap<size_t, size_t> mSitesMappingToOriginal; ///< Map reduced site
/// num. to list of
/// corresponding
/// original sites
/// num. to list of corresponding original sites
size_t mOriginalNumSites; ///< Original number of sites (before cleaning)
std::map<std::string, std::vector<int>> mMapCodonToPosition; ///< Map codons
///(including
/// ambiguous
/// ones) to
/// positions on
/// the CPV
std::map<std::string, std::vector<int> > mMapCodonToPosition; ///< Map codons
///(including ambiguous ones) to positions on the CPV
std::vector<int>
mEmptyVector; ///< Empty vector to be returned if no position available
mutable std::vector<int>
......
......@@ -99,9 +99,8 @@ struct HighLevelCoordinator::WorkTable {
///
/// @param[out] aJob The job request: [0] is set to the kind of job (JOB_H0,
/// JOB_H1, JOB_BEB, JOB_SHUTDOWN);
/// [1] to the fg branch number (or zero
///for
/// JOB_SHUTDOWN);
/// [1] to the fg branch number (or zero
/// for JOB_SHUTDOWN);
/// [2] zero or the number of variables for
/// a JOB_BEB or JOB_H0 requests
/// @param[in] aRank The current worker rank
......
......@@ -45,16 +45,16 @@ struct NewickGrammar : public grammar<NewickGrammar> {
marker = leaf_node_d[+alnum_p];
}
rule<ScannerT, parser_context<>, parser_tag<treeID>> tree;
rule<ScannerT, parser_context<>, parser_tag<nodelistID>> nodelist;
rule<ScannerT, parser_context<>, parser_tag<subtreeID>> subtree;
rule<ScannerT, parser_context<>, parser_tag<fulllabelID>> full_label;
rule<ScannerT, parser_context<>, parser_tag<branchlenID>> branch_length;
rule<ScannerT, parser_context<>, parser_tag<cblenID>> colon_plus_len;
rule<ScannerT, parser_context<>, parser_tag<labelID>> label;
rule<ScannerT, parser_context<>, parser_tag<markerID>> marker;
rule<ScannerT, parser_context<>, parser_tag<treeID>> const &start() const {
rule<ScannerT, parser_context<>, parser_tag<treeID> > tree;
rule<ScannerT, parser_context<>, parser_tag<nodelistID> > nodelist;
rule<ScannerT, parser_context<>, parser_tag<subtreeID> > subtree;
rule<ScannerT, parser_context<>, parser_tag<fulllabelID> > full_label;
rule<ScannerT, parser_context<>, parser_tag<branchlenID> > branch_length;
rule<ScannerT, parser_context<>, parser_tag<cblenID> > colon_plus_len;
rule<ScannerT, parser_context<>, parser_tag<labelID> > label;
rule<ScannerT, parser_context<>, parser_tag<markerID> > marker;
rule<ScannerT, parser_context<>, parser_tag<treeID> > const &start() const {
return tree;
}
};
......
......@@ -33,11 +33,11 @@ void TreeAndSetsDependencies::computeDependencies(unsigned int aNumSets,
// Take values from forest
size_t num_sites = mForest.getNumSites();
std::vector<std::vector<unsigned int>> tree_dependencies =
std::vector<std::vector<unsigned int> > tree_dependencies =
mForest.getTreeDependencies();
// Collect the class dependencies
std::vector<std::vector<unsigned int>> tree_groups_dependencies;
std::vector<std::vector<unsigned int> > tree_groups_dependencies;
// If no dependencies
if (aNoParallel) {
......@@ -219,7 +219,7 @@ bool TreeAndSetsDependencies::balanceDependenciesClassesAndTrees(bool aGreedy) {
if (mNoParallel)
return false;
const std::vector<std::vector<unsigned int>> &tree_rev_dependencies =
const std::vector<std::vector<unsigned int> > &tree_rev_dependencies =
mForest.getTreeRevDependencies();
// At each level collect the 'jolly' threads (trees that are not preconditions
......
......@@ -4,7 +4,7 @@
/// List (each list depends on the previous) of list (sites to be executed in
/// parallel) of pairs (site, site class) stored as site*4+site_class
typedef std::vector<std::vector<unsigned int>> ListDependencies;
typedef std::vector<std::vector<unsigned int> > ListDependencies;
#include "Forest.h"
......
......@@ -8,12 +8,12 @@
/// Array of doubles aligned on a cache line
///
typedef std::vector<double, AlignedAllocator<double, CACHE_LINE_ALIGN>>
typedef std::vector<double, AlignedAllocator<double, CACHE_LINE_ALIGN> >
CacheAlignedDoubleVector;
/// Array of doubles to be used by SSE instructions
///
typedef std::vector<double, AlignedAllocator<double, 16>>
typedef std::vector<double, AlignedAllocator<double, 16> >
SSEAlignedDoubleVector;
#endif
......@@ -84,7 +84,7 @@ void WriteResults::outputResults(void) {
// they start from 1 and not zero)
for (size_t branch = min_branch; branch <= max_branch; ++branch) {
std::map<size_t, std::pair<std::vector<unsigned int>,
std::vector<double>>>::const_iterator ipss;
std::vector<double> > >::const_iterator ipss;
ipss = mPositiveSelSites.find(branch);
if (ipss != mPositiveSelSites.end()) {
const std::vector<unsigned int> &site = ipss->second.first;
......
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