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OpenMS
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AverageLinkage ClusterMethod. More...
#include <OpenMS/ML/CLUSTERING/AverageLinkage.h>
Public Member Functions | |
| AverageLinkage () | |
| default constructor More... | |
| AverageLinkage (const AverageLinkage &source) | |
| copy constructor More... | |
| ~AverageLinkage () override | |
| destructor More... | |
| AverageLinkage & | operator= (const AverageLinkage &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... | |
| virtual | ~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 | setLogger (ProgressLoggerImpl *logger) |
| Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const |
| void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More... | |
Additional Inherited Members | |
| Public Types inherited from ProgressLogger | |
| enum | LogType { CMD , GUI , NONE } |
| Possible log types. 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_ |
AverageLinkage ClusterMethod.
The details of the method can be found in: Backhaus, Erichson, Plinke, Weiber Multivariate Analysemethoden, Springer 2000 and Ellen M. Voorhees: Implementing agglomerative hierarchic clustering algorithms for use in document retrieval. Inf. Process. Manage. 22(6): 465-476 (1986)
| AverageLinkage | ( | ) |
default constructor
| AverageLinkage | ( | const AverageLinkage & | source | ) |
copy constructor
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override |
destructor
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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, will be changed during clustering process, make sure to have a copy or be able to redo |
| cluster_tree | vector< BinaryTreeNode >, represents the clustering, each node contains the next merged clusters (not element indices) and their distance, strict order is kept: left_child < right_child |
| threshold | float value, the minimal distance from which on cluster merging is considered unrealistic. By default set to 1, i.e. complete clustering until only one cluster remains |
| ClusterFunctor::InsufficientInput | thrown if input is <2 The clustering method is average linkage, where the updated distances after merging two clusters are each the average distances between the elements of their clusters. After threshold is exceeded, cluster_tree is filled with dummy clusteringsteps (children: (0,1), distance: -1) to the root. |
Implements ClusterFunctor.
| AverageLinkage& operator= | ( | const AverageLinkage & | source | ) |
assignment operator
1.9.1 
