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NCBI C++ ToolKit: include/algo/cobalt/clusterer.hpp Source File

(

) {m_Elements.clear();}

(

)

{

m_Elements.size();}

FindCenterElement(

& dmatrix)

;

vector<int>&

(

)

{

m_Elements;}

operator[](

index)

;

SetDistMatrix(shared_ptr<TDistMatrix>& dmat);

ComputeClusters(

max_diam,

do_trees =

,

ComputeClustersFromLinks(

);

TSingleCluster& GetSingleCluster(

index)

;

GetClusterId(

elem)

;

GetTrees(vector<TPhyTreeNode*>& trees)

;

ReleaseTrees(vector<TPhyTreeNode*>& trees);

vector<TPhyTreeNode*>&

(

) {

m_Trees;}

SetPrototypes(

);

GetClusterDistMatrix(

index, TDistMatrix& mat)

;

x_JoinClustElem(

cluster_id,

elem,

dist);

x_JoinClusters(

cluster1_id,

cluster2_id,

dist);

x_CreateCluster(

elem);

x_CanAddElem(

cluster_id,

elem,

& dist)

;

x_CanJoinClusters(

cluster1_id,

cluster2_id,

& dist)

;

Exceptions for CClusterer class.

NCBI_EXCEPTION_DEFAULT(CClustererException, CException)

@ eElementOutOfRange

Cluster element is larger than distance matrix size.

@ eElemIndexOutOfRange

Index of cluster element out of range.

@ eClusterIndexOutOfRange

Index of cluster out of range.

@ eNoDistMatrix

Distance matrix not assigned.

CSingleCluster(void)

Create empty cluster.

void SetPrototype(int el)

Set cluster prototype.

const_iterator begin(void) const

void clear(void)

Removes all elements from the cluster.

int GetPrototype(void) const

Get cluster prototype.

size_t size(void) const

Get cluster size.

TPhyTreeNode * m_Tree

Cluster tree root.

void AddElement(int el)

Add element to the cluster.

double m_Diameter

Max distance between elements.

vector< int > m_Elements

List of indeces of cluster elements.

int m_Prototype

Index of cluster representative element.

const vector< int > & GetElements(void) const

Get list of cluster elements.

vector< int >::iterator iterator

vector< int >::const_iterator const_iterator

double GetMaxDistance(void) const

Get maximum distance in cluster.

vector< double > m_DistToRoot

Distances between cluster elements and tree root.

const_iterator end(void) const

void SetMaxDistance(double dist)

Set maximum distance in cluster.

Interface for CClusterer class used for clustering any type of data based on distance matrix.

vector< TPhyTreeNode * > & GetTrees(void)

Get list of trees for clusters.

list< int > m_UnusedEntries

void SetMaxClusterDiameter(double diam)

Set maximum diameter for single cluster.

double GetMaxClusterDiameter(void) const

Get maximum diameter for single cluster.

EClustMethod

Method for clustering from links.

EDistMethod

Method for computing distance between clusters.

shared_ptr< TDistMatrix > m_DistMatrix

CClusterer & operator=(const CClusterer &)

Forbid assignment operator.

void SetReportSingletons(bool b)

Set reporting of single element clusters.

CNcbiMatrix< double > TDistMatrix

EClustMethod GetClustMethod(void) const

Get clustering method for links.

CSingleCluster TSingleCluster

bool GetReportSingletons(void) const

Get reporting mode for single element clusters.

void SetMakeTrees(bool trees)

Set make cluster tree/dendrogram option.

vector< int > m_ClusterId

const TClusters & GetClusters(void) const

Get clusters.

void SetClustMethod(EClustMethod method)

Set clustering method for links.

CClusterer(const CClusterer &)

Forbid copy constructor.

vector< TSingleCluster > TClusters

vector< TPhyTreeNode * > m_Trees

TClusters & SetClusters(void)

Set clusters.

CClusterer(shared_ptr< TDistMatrix > &dmat)

Create clusterer.

EClustMethod m_LinkMethod

void PurgeDistMatrix(void)

Delete distance matrix.

definition of a Culling tree

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

void Run(void)

Enter the main loop.

#define NCBI_COBALT_EXPORT

NCBI C++ auxiliary debug macros.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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