OpenMS
2.6.0
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SingleLinkage ClusterMethod. More...
#include <OpenMS/COMPARISON/CLUSTERING/SingleLinkage.h>
Public Member Functions | |
SingleLinkage () | |
default constructor More... | |
SingleLinkage (const SingleLinkage &source) | |
copy constructor More... | |
~SingleLinkage () override | |
destructor More... | |
SingleLinkage & | operator= (const SingleLinkage &source) |
assignment operator More... | |
void | operator() (DistanceMatrix< float > &original_distance, std::vector< BinaryTreeNode > &cluster_tree, const float threshold=1) const override |
clusters the indices according to their respective element distances More... | |
Public Member Functions inherited from ClusterFunctor | |
ClusterFunctor () | |
default constructor More... | |
ClusterFunctor (const ClusterFunctor &source) | |
copy constructor More... | |
virtual | ~ClusterFunctor () |
destructor More... | |
ClusterFunctor & | operator= (const ClusterFunctor &source) |
assignment operator More... | |
Public Member Functions inherited from ProgressLogger | |
ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Static Public Member Functions | |
static ClusterFunctor * | create () |
creates a new instance of a SingleLinkage object More... | |
static const String | getProductName () |
get the identifier for this object More... | |
Static Public Member Functions inherited from ClusterFunctor | |
static void | registerChildren () |
registers all derived products More... | |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Static Protected Member Functions inherited from ProgressLogger | |
static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
Protected Attributes inherited from ProgressLogger | |
LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Static Protected Attributes inherited from ProgressLogger | |
static int | recursion_depth_ |
SingleLinkage ClusterMethod.
The details of the method can be found in: SLINK: An optimally efficient algorithm for the single-link cluster method, The Computer Journal 1973 16(1):30-34; doi:10.1093/comjnl/16.1.30
SingleLinkage | ( | ) |
default constructor
SingleLinkage | ( | const SingleLinkage & | source | ) |
copy constructor
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override |
destructor
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static |
creates a new instance of a SingleLinkage object
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static |
get the identifier for this object
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overridevirtual |
clusters the indices according to their respective element distances
original_distance | DistanceMatrix<float> containing the distances of the elements to be clustered |
cluster_tree | vector< BinaryTreeNode >, represents the clustering, each node contains the next two clusters merged and their distance, strict order is kept: left_child < right_child |
threshold | float value to meet Base class interface, will not be used because algorithm used is considerably fast and does not work by growing distances |
ClusterFunctor::InsufficientInput | thrown if input is <2 The clustering method is single linkage, where the updated distances after merging two clusters are each the minimal distance between the elements of their clusters. |
Implements ClusterFunctor.
SingleLinkage& operator= | ( | const SingleLinkage & | source | ) |
assignment operator