bpp-phyl
2.2.0
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Compute WPGMA and UPGMA trees from a distance matrix. More...
#include <Bpp/Phyl/Distance/PGMA.h>
Public Member Functions | |
PGMA (bool weighted=true) | |
PGMA (const DistanceMatrix &matrix, bool weighted=true, bool verbose=true) throw (Exception) | |
Create a (U/W)PGMA object instance. More... | |
virtual | ~PGMA () |
PGMA * | clone () const |
std::string | getName () const |
void | setDistanceMatrix (const DistanceMatrix &matrix) throw (Exception) |
Set the distance matrix to use. More... | |
TreeTemplate< Node > * | getTree () const |
Get the computed tree, if there is one. More... | |
void | setWeighted (bool weighted) |
bool | isWeighted () const |
virtual void | computeTree () throw (Exception) |
Compute the tree corresponding to the distance matrix. More... | |
void | setVerbose (bool yn) |
bool | isVerbose () const |
Protected Member Functions | |
std::vector< size_t > | getBestPair () throw (Exception) |
Get the best pair of nodes to agglomerate. More... | |
std::vector< double > | computeBranchLengthsForPair (const std::vector< size_t > &pair) |
Compute the branch lengths for two nodes to agglomerate. More... | |
double | computeDistancesFromPair (const std::vector< size_t > &pair, const std::vector< double > &branchLengths, size_t pos) |
Actualizes the distance matrix according to a given pair and the corresponding branch lengths. More... | |
void | finalStep (int idRoot) |
Method called when there ar eonly three remaining node to agglomerate, and creates the root node of the tree. More... | |
virtual Node * | getLeafNode (int id, const std::string &name) |
Get a leaf node. More... | |
virtual Node * | getParentNode (int id, Node *son1, Node *son2) |
Get an inner node. More... | |
Protected Attributes | |
bool | weighted_ |
DistanceMatrix | matrix_ |
Tree * | tree_ |
std::map< size_t, Node * > | currentNodes_ |
bool | verbose_ |
bool | rootTree_ |
Compute WPGMA and UPGMA trees from a distance matrix.
WPGMA = Weighted pair group method using arithmetic averaging, is equivalent to the average linkage hierarchical clustering method. The distance between two taxa is the average distance between all individuals in each taxa. The unweighted version (named UPGMA), uses a weighted average, with the number of individuals in a group as a weight.
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inline |
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inline |
Create a (U/W)PGMA object instance.
matrix | Input distance matrix. |
weighted | Tell if we should perform Weighted or Unweighted pair group method. |
verbose | Allow to display extra information, like progress bars. |
Definition at line 84 of file PGMA.h.
References bpp::AbstractAgglomerativeDistanceMethod::computeTree().
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protectedvirtual |
Compute the branch lengths for two nodes to agglomerate.
This method compute l1 and l2 given N1 and N2.
pair | The indices of the nodes to be agglomerated. |
Implements bpp::AbstractAgglomerativeDistanceMethod.
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protectedvirtual |
Actualizes the distance matrix according to a given pair and the corresponding branch lengths.
pair | The indices of the nodes to be agglomerated. |
branchLengths | The corresponding branch lengths. |
pos | The index of the node whose distance ust be updated. |
Implements bpp::AbstractAgglomerativeDistanceMethod.
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virtualinherited |
Compute the tree corresponding to the distance matrix.
This method implements the following algorithm: 1) Build all leaf nodes (getLeafNode method) 2) Get the best pair to agglomerate (getBestPair method) 3) Compute the branch lengths for this pair (computeBranchLengthsForPair method) 4) Build the parent node of the pair (getParentNode method) 5) For each remaining node, update distances from the pair (computeDistancesFromPair method) 6) Return to step 2 while there are more than 3 remaining nodes. 7) Perform the final step, and send a rooted or unrooted tree.
Implements bpp::DistanceMethod.
Reimplemented in bpp::BioNJ.
Definition at line 62 of file AbstractAgglomerativeDistanceMethod.cpp.
References bpp::Node::setDistanceToFather().
Referenced by bpp::HierarchicalClustering::HierarchicalClustering(), bpp::NeighborJoining::NeighborJoining(), and PGMA().
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protectedvirtual |
Method called when there ar eonly three remaining node to agglomerate, and creates the root node of the tree.
idRoot | The id of the root node. |
Implements bpp::AbstractAgglomerativeDistanceMethod.
Definition at line 115 of file PGMA.cpp.
References bpp::Node::addSon(), and bpp::Node::setDistanceToFather().
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protectedvirtual |
Get the best pair of nodes to agglomerate.
Define the criterion to chose the next pair of nodes to agglomerate. This criterion uses the matrix_ distance matrix.
Exception | If an error occured. |
Implements bpp::AbstractAgglomerativeDistanceMethod.
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protectedvirtual |
Get a leaf node.
Create a new node with the given id and name.
id | The id of the node. |
name | The name of the node. |
Reimplemented from bpp::AbstractAgglomerativeDistanceMethod.
Definition at line 132 of file PGMA.cpp.
References bpp::PGMAInfos::numberOfLeaves, bpp::NodeTemplate< NodeInfos >::setInfos(), and bpp::PGMAInfos::time.
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inlinevirtual |
Implements bpp::DistanceMethod.
Definition at line 95 of file PGMA.h.
References weighted_.
Get an inner node.
Create a new node with the given id, and set its sons.
id | The id of the node. |
son1 | The first son of the node. |
son2 | The second son of the node. |
Reimplemented from bpp::AbstractAgglomerativeDistanceMethod.
Definition at line 142 of file PGMA.cpp.
References bpp::Node::addSon(), bpp::Node::getDistanceToFather(), bpp::PGMAInfos::numberOfLeaves, and bpp::PGMAInfos::time.
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Get the computed tree, if there is one.
Reimplemented from bpp::AbstractAgglomerativeDistanceMethod.
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inlinevirtualinherited |
Implements bpp::DistanceMethod.
Definition at line 149 of file AbstractAgglomerativeDistanceMethod.h.
References bpp::AbstractAgglomerativeDistanceMethod::verbose_.
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inline |
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inlinevirtual |
Set the distance matrix to use.
matrix | The matrix to use. |
Exception | In case an incorrect matrix is provided (eg smaller than 3). |
Reimplemented from bpp::AbstractAgglomerativeDistanceMethod.
Definition at line 97 of file PGMA.h.
References bpp::AbstractAgglomerativeDistanceMethod::setDistanceMatrix().
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inlinevirtualinherited |
yn | Enable/Disable verbose mode. |
Implements bpp::DistanceMethod.
Definition at line 148 of file AbstractAgglomerativeDistanceMethod.h.
References bpp::AbstractAgglomerativeDistanceMethod::verbose_.
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inline |
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protectedinherited |
Definition at line 69 of file AbstractAgglomerativeDistanceMethod.h.
Referenced by bpp::AbstractAgglomerativeDistanceMethod::operator=().
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protectedinherited |
Definition at line 66 of file AbstractAgglomerativeDistanceMethod.h.
Referenced by bpp::AbstractAgglomerativeDistanceMethod::operator=().
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protectedinherited |
Definition at line 71 of file AbstractAgglomerativeDistanceMethod.h.
Referenced by bpp::AbstractAgglomerativeDistanceMethod::operator=().
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protectedinherited |
Definition at line 67 of file AbstractAgglomerativeDistanceMethod.h.
Referenced by bpp::AbstractAgglomerativeDistanceMethod::AbstractAgglomerativeDistanceMethod(), bpp::AbstractAgglomerativeDistanceMethod::getTree(), bpp::AbstractAgglomerativeDistanceMethod::operator=(), and bpp::AbstractAgglomerativeDistanceMethod::~AbstractAgglomerativeDistanceMethod().
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protectedinherited |
Definition at line 70 of file AbstractAgglomerativeDistanceMethod.h.
Referenced by bpp::AbstractAgglomerativeDistanceMethod::isVerbose(), bpp::AbstractAgglomerativeDistanceMethod::operator=(), and bpp::AbstractAgglomerativeDistanceMethod::setVerbose().
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protected |
Definition at line 70 of file PGMA.h.
Referenced by getName(), isWeighted(), and setWeighted().