Commit d1fba584 authored by akalantz's avatar akalantz
Browse files

Version display added

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7154 95c5a404-1f88-0410-a6b0-c3f062b6f34a
parent 870e382a
......@@ -15,7 +15,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-12-22 (initial version)
/// @version 1.0
/// @version 1.1
///
template <typename T, size_t A> class AlignedAllocator
{
......@@ -45,7 +45,7 @@ public:
// The following has been carefully written to be independent of
// the definition of size_t and to avoid signed/unsigned warnings.
return (static_cast<size_t>(0) - static_cast<size_t>(1)) / sizeof(T);
}
}
/// Internal definition for AlignedAllocator.
/// The following must be the same for all allocators.
......
......@@ -41,7 +41,7 @@ public:
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-12-22 (initial version)
/// @version 1.0
/// @version 1.1
///
class BayesTest
{
......@@ -74,7 +74,7 @@ public:
/// @param[in] aScales The two scales ([0] bg; [1] fg) to rescale the branch lengths. They are computed in H1.
///
void computeBEB(const std::vector<double>& aVars, size_t aFgBranch, const std::vector<double>& aScales);
/// Print the sites under positive selection.
///
/// @param[in] aFgBranch Identifier of the branch marked as foreground branch
......@@ -89,9 +89,9 @@ public:
void extractPositiveSelSites(std::vector<unsigned int>& aPositiveSelSites, std::vector<double>& aPositiveSelSitesProb) const;
private:
/// This sets up the grid (mPara[][]) according to the priors.
/// It calculates the probability of data at each site given w: f(f_h|w).
/// This is calculated using the branch model (NSsites = 0 model = 2), with
/// This sets up the grid (mPara[][]) according to the priors.
/// It calculates the probability of data at each site given w: f(f_h|w).
/// This is calculated using the branch model (NSsites = 0 model = 2), with
/// BayesEB=2 used to force the use of the correct scale factors in GetPMatBranch().
///
///@verbatim
......@@ -113,15 +113,15 @@ private:
///
double getGridParams(const std::vector<double>& aVars, const std::vector<double>& aSiteMultiplicity, size_t aFgBranch, const std::vector<double>& aScales);
/// This gives the indices (ix, iy) and the coordinates (aProbX, aProbY, 1-aProbX-aProbY) for
/// This gives the indices (ix, iy) and the coordinates (aProbX, aProbY, 1-aProbX-aProbY) for
/// the aTriangleIdx-th triangle, with aTriangleIdx from 0, 1, ..., BEB_N1D*BEB_N1D-1.
///
/// The ternary graph (0-1 on each axis) is partitioned into BEB_N1D*BEB_N1D equal-sized triangles.
/// The ternary graph (0-1 on each axis) is partitioned into BEB_N1D*BEB_N1D equal-sized triangles.
/// In the first row (ix=0), there is one triangle (iy=0);
/// In the second row (ix=1), there are 3 triangles (iy=0,1,2);
/// In the i-th row (ix=i), there are 2*i+1 triangles (iy=0,1,...,2*i).
///
/// aProbX rises when ix goes up, but aProbY decreases when iy increases. (aProbX, aProbY) is the
/// aProbX rises when ix goes up, but aProbY decreases when iy increases. (aProbX, aProbY) is the
/// centroid in the ij-th small triangle. aProbX and aProbY each takes on 2*BEB_N1D-1 possible values.
///
/// @param[out] aProbX The p0 value on the X axis of the triangular grid.
......
......@@ -1568,7 +1568,7 @@ void BranchSiteModel::verifyOptimizerAlgo(unsigned int aOptimizationAlgo)
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-01-13 (initial version)
/// @version 1.0
/// @version 1.1
///
///
class MaximizerFunction
......
......@@ -18,7 +18,7 @@ static const double THRESHOLD_FOR_LRT = 1.92072941034706202;
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-12-23 (initial version)
/// @version 1.0
/// @version 1.1
///
class BranchSiteModel
{
......@@ -357,7 +357,7 @@ private:
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-12-23 (initial version)
/// @version 1.0
/// @version 1.1
///
///
class BranchSiteModelNullHyp : public BranchSiteModel
......@@ -448,7 +448,7 @@ private:
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-12-23 (initial version)
/// @version 1.0
/// @version 1.1
///
///
class BranchSiteModelAltHyp : public BranchSiteModel
......
......@@ -206,7 +206,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
{ OPT_NO_PRE_STOP, "--no-pre-stop", SO_NONE, "" },
{ OPT_MAX_ITER, "-mi", SO_REQ_SEP, "Maximum number of iterations for the maximizer (default: 10000)" },
{ OPT_MAX_ITER, "--max-iterations", SO_REQ_SEP, "" },
{OPT_BRANCH_LENGTH, "-bl", SO_NONE, "The length of the branches is fixed (only for KCM and algorithms LBFGS and SLSQP)"},
{OPT_BRANCH_LENGTH, "-bl", SO_NONE, "The length of the brances is fixed"},
{OPT_BRANCH_LENGTH, "--branch-lengths-fixed", SO_NONE, ""},
SO_END_OF_OPTIONS
};
......
......@@ -18,7 +18,7 @@ static const unsigned int MAX_ITERATIONS=10000;
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-12-22 (initial version)
/// @version 1.0
/// @version 1.1
///
///
class CmdLine
......
......@@ -10,7 +10,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS) based on code from Ziheng Yang CodeML.
/// @date 2012-01-11 (initial version)
/// @version 1.0
/// @version 1.1
///
class Ming2
{
......
......@@ -17,7 +17,7 @@ static const double GOOD_CODON_THRESHOLD = 1e-100;
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-10-24 (initial version)
/// @version 1.0
/// @version 1.1
///
class CodonFrequencies
{
......@@ -48,19 +48,19 @@ public:
/// Return a pointer to the codon frequencies array
///
/// @return Pointer to the codon frequencies array
/// @return Pointer to the codon frequencies array
///
const double* getCodonFrequencies(void) const {return &mCodonFrequencies[0];}
/// Return a pointer to the codon square root of frequencies array
///
/// @return Pointer to the codon square root of frequencies array
/// @return Pointer to the codon square root of frequencies array
///
const double* getSqrtCodonFrequencies(void) const {return &mCodonFreqSqrt[0];}
/// Return a pointer to the codon array of inverse of frequencies
///
/// @return Pointer to the codon inverse of frequencies array
/// @return Pointer to the codon inverse of frequencies array
///
const double* getInvCodonFrequencies(void) const {return &mCodonFreqInv[0];}
......@@ -78,7 +78,7 @@ public:
/// Return a pointer to the codon array of inverse frequencies at the n power
///
/// @return Pointer to the codon inverse of frequencies at the n power array
/// @return Pointer to the codon inverse of frequencies at the n power array
///
const double* getCodonFreqInv2(void) const {return &mCodonFreqInv2[0];}
......
......@@ -11,7 +11,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-05-14 (initial version)
/// @version 1.0
/// @version 1.1
///
class DAGScheduler
{
......@@ -35,7 +35,7 @@ public:
/// @param[in] aDependant The object to be computed only when aDependsOn is ready
///
void loadDependency(unsigned int aCopyId, const void* aDependsOn, const void* aDependant);
/// Signals dependencies load has finished.
///
/// @param[in] aNumCodonSets Number of DAG copies (one for each codon classes)
......@@ -47,13 +47,13 @@ public:
/// @return The next object with all dependencies satisfied. Return NULL if no more objects to be executed.
///
void* getNext(void);
/// Signals finished execution on aItem.
///
/// @param[in] aItem Object on which execution has ended.
///
void setDone(const void* aItem);
/// Reset all dependencies to initial state
///
void resetDependencies(void);
......@@ -61,13 +61,13 @@ public:
/// Dump DAG in textual form
///
void dumpDAG(std::ostream& aOut) const;
private:
std::set<const void*> mNodes; ///< Load the distinct node addresses
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
std::map<const void*, int> mRefCounterSave; ///< Save the reference counter map
};
#endif
......
......@@ -11,7 +11,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-09-31 (initial version)
/// @version 1.0
/// @version 1.1
///
class FatVectorTransform
{
......@@ -53,7 +53,7 @@ public:
mReuseCmds.clear();
mNoTransformations = false;
}
/// Initialize the class instance so can be used if no subtree pruning is present
///
/// @param[in] aNumBranches Number of branches
......
......@@ -27,7 +27,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-02-23 (initial version)
/// @version 1.0
/// @version 1.1
///
class Forest
{
......@@ -48,7 +48,7 @@ public:
mNodeNames.clear();
mBranchLengths.clear();
mProbs.clear();
mSiteMultiplicity.clear();
mSiteMultiplicity.clear();
mTableInternalToBranchID.clear();
#ifdef NEW_LIKELIHOOD
mProbsOut.clear();
......@@ -59,7 +59,7 @@ public:
mVisitTreeParents.clear();
#endif
}
/// Build the forest and reduces the subtrees.
///
/// @param[in] aTree The phylogenetic tree
......@@ -297,8 +297,8 @@ private:
///
void prepareNonRecursiveVisitWalker(ForestNode* aNode,
ForestNode* aParentNode,
unsigned int aSite,
std::vector<ForestNode*>& aVisitList,
unsigned int aSite,
std::vector<ForestNode*>& aVisitList,
std::vector<ForestNode*>& aParentList);
/// Walker for the computation of tree likelihood
......@@ -339,7 +339,7 @@ private:
#ifdef NEW_LIKELIHOOD
/// New loglikelihood computation support
/// The mProbs and mProbsOut layout
///
/// [site0][site1][site2]... [site0][site1][site2]... each is VECTOR_SLOT bytes long (for which only the first N are significant)
......
......@@ -11,7 +11,7 @@ class Forest;
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-02-13 (initial version)
/// @version 1.0
/// @version 1.1
///
class ForestExport
{
......
......@@ -18,7 +18,7 @@ static const unsigned char ALL_CHILDREN_SAME_TREE = 0xFF;
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-11-08 (initial version)
/// @version 1.0
/// @version 1.1
///
struct ForestNodeSupport
{
......@@ -34,7 +34,7 @@ struct ForestNodeSupport
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-02-23 (initial version)
/// @version 1.0
/// @version 1.1
///
struct ForestNode
{
......@@ -65,7 +65,7 @@ struct ForestNode
ForestNode() : mChildrenSameTreeFlags(ALL_CHILDREN_SAME_TREE), mChildrenCount(0), mLeafCodon(-1), mBranchId(0), mOwnTree(0), mParent(NULL), mInternalNodeId(0)
#ifdef NON_RECURSIVE_VISIT
, mFirstChild(false), mChildIdx(0)
#endif
#endif
{
#ifndef NEW_LIKELIHOOD
memset(mProb, 0, Nt*sizeof(double*));
......@@ -256,7 +256,7 @@ struct ForestNode
// Print the name
aOut << '<' << ((mBranchId != UINT_MAX) ? aNodeNames[mBranchId+1] : aNodeNames[0]) << "> ";
// Print the ID
if(mInternalNodeId != UINT_MAX) aOut << '(' << mInternalNodeId << '|' << mBranchId << '|' << mLeafCodon << ") ";
else aOut << '(' << '|' << mBranchId << '|' << mLeafCodon << ") ";
......@@ -346,7 +346,7 @@ struct ForestNode
cnt += 1;
}
}
return cnt;
}
......@@ -386,7 +386,7 @@ struct ForestNode
cost += aCostPtr;
}
}
return cost;
}
......
......@@ -10,7 +10,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-12-22 (initial version)
/// @version 1.0
/// @version 1.1
///
class Genes
{
......
......@@ -15,7 +15,7 @@ static const int MASTER_JOB = 0;
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-11-22 (initial version)
/// @version 1.0
/// @version 1.1
///
class HighLevelCoordinator
......
......@@ -22,7 +22,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-02-15 (initial version)
/// @version 1.0
/// @version 1.1
///
class Newick : public PhyloTree
{
......
......@@ -11,7 +11,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-02-21 (initial version)
/// @version 1.0
/// @version 1.1
///
class ParseParameters
{
......
......@@ -10,7 +10,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-02-15 (initial version)
/// @version 1.0
/// @version 1.1
///
///
class Phylip : public Genes
......
......@@ -13,7 +13,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2010-08-30 (initial version)
/// @version 1.0
/// @version 1.1
///
class PhyloTree
{
......
......@@ -21,7 +21,7 @@
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2011-04-05 (initial version)
/// @version 1.0
/// @version 1.1
///
class ProbabilityMatrixSet
{
......@@ -66,7 +66,7 @@ public:
///
/// @param[in] aFgBranch Number of the foreground branch (as branch number not as internal branch number!)
///
void initializeFgBranch(unsigned int aFgBranch) {mFgBranch = static_cast<int>(aFgBranch);}
void initializeFgBranch(unsigned int aFgBranch) {mFgBranch = static_cast<int>(aFgBranch);}
#ifndef NEW_LIKELIHOOD
/// Multiply the aGin vector by the precomputed exp(Q*t) matrix
......@@ -151,7 +151,7 @@ public:
void doTransition(unsigned int aSetIdx, unsigned int aBranch, int aNumSites, const double* aMin, double* aMout) const
{
#ifdef USE_LAPACK
dsymm_("L", "U", &N, &aNumSites, &D1, mMatrices[aSetIdx*mNumMatrices+aBranch], &N, aMin, &VECTOR_SLOT, &D0, aMout, &VECTOR_SLOT);
#ifdef USE_MKL_VML
......@@ -197,7 +197,7 @@ protected:
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-09-07 (initial version)
/// @version 1.0
/// @version 1.1
///
class ProbabilityMatrixSetH0 : public ProbabilityMatrixSet
{
......@@ -215,7 +215,7 @@ public:
void initializeSet(unsigned int aFgBranch);
/// Compute the three sets of matrices for the H0 hypothesis.
/// The sets are (these are the bg and fg matrices):
/// The sets are (these are the bg and fg matrices):
/// - set 0: w0, w0
/// - set 1: w1, w1
/// - set 2: w0, w1
......@@ -270,7 +270,7 @@ private:
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-09-07 (initial version)
/// @version 1.0
/// @version 1.1
///
class ProbabilityMatrixSetH1 : public ProbabilityMatrixSet
{
......@@ -288,7 +288,7 @@ public:
void initializeSet(unsigned int aFgBranch);
/// Compute the four sets of matrices for the H1 hypothesis.
/// The sets are (these are the bg and fg matrices):
/// The sets are (these are the bg and fg matrices):
/// - set 0: w0, w0
/// - set 1: w1, w1
/// - set 2: w0, w2
......@@ -307,7 +307,7 @@ public:
double aSbg,
double aSfg,
const std::vector<double>& aParams);
/// Restore the previous value for the aBranch matrices.
///
/// @param[in] aBranch Branch for which the matrices should be restored
......@@ -347,7 +347,7 @@ private:
///
/// @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
/// @date 2012-09-20 (initial version)
/// @version 1.0
/// @version 1.1
///
class ProbabilityMatrixSetBEB : public ProbabilityMatrixSet
{
......@@ -365,7 +365,7 @@ public:
}
/// Compute the sets of matrices for the BEB computation.
/// The sets are (these are the bg and fg matrices):
/// The sets are (these are the bg and fg matrices):
/// - set 0: w0, w0
/// - set 1: w1, w1
/// - set 2: w0, w2
......
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