SingleLinkageClusterer (biojava 6.0.0 API)

java.lang.Object
- org.biojava.nbio.core.util.SingleLinkageClusterer

```
public class SingleLinkageClusterer
extends Object
```
An implementation of a single linkage clusterer See http://en.wikipedia.org/wiki/Single-linkage_clustering

Author:

Jose Duarte

Constructor Summary

Constructors
Constructor	Description
`SingleLinkageClusterer(double[][] matrix, boolean isScoreMatrix)`	Constructs a new SingleLinkageClusterer Subsequently use `getDendrogram()` to get the full tree or `getClusters(double)` to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Map<Integer,Set<Integer>>`	`getClusters(double cutoff)`	Get the clusters by cutting the dendrogram at given cutoff
`org.biojava.nbio.core.util.SingleLinkageClusterer.LinkedPair[]`	`getDendrogram()`	Get the full dendrogram (size n-1) result of the hierarchical clustering

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SingleLinkageClusterer
```
public SingleLinkageClusterer(double[][] matrix,
                              boolean isScoreMatrix)
```
    Constructs a new SingleLinkageClusterer Subsequently use getDendrogram() to get the full tree or getClusters(double) to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure. A copy must be made before by the user if needing to use the original matrix further.
    
    Parameters:
    
    matrix - the distance matrix with distance values in j>i half, all other values will be ignored
    
    isScoreMatrix - if false the matrix will be considered a distance matrix: lower values (distances) mean closer objects, if true the matrix will be considered a score matrix: larger values (scores) mean closer objects
    
    Throws:
    
    IllegalArgumentException - if matrix not square
- Method Detail
  - getDendrogram
```
public org.biojava.nbio.core.util.SingleLinkageClusterer.LinkedPair[] getDendrogram()
```
    Get the full dendrogram (size n-1) result of the hierarchical clustering
    
    Returns:
  - getClusters
```
public Map<Integer,Set<Integer>> getClusters(double cutoff)
```
    Get the clusters by cutting the dendrogram at given cutoff
    
    Parameters:
    
    cutoff -
    
    Returns:
    
    Map from cluster numbers to indices of the cluster members