medusa.georgios.ClusteringAlgorithms

Class Clustering_NJ_UPGMA

java.lang.Object

medusa.georgios.ClusteringAlgorithms.Clustering_NJ_UPGMA

public class Clustering_NJ_UPGMA
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.ArrayList<java.lang.String>	labels

Constructor Summary

Constructors

Constructor and Description
Clustering_NJ_UPGMA(java.util.ArrayList<java.lang.String> list, int choose_clustering)
Clustering_NJ_UPGMA(float[][] distance_Matrix, java.util.ArrayList<java.lang.String> Leaf_Labels, int choose_clustering)
Clustering_NJ_UPGMA(java.lang.String filename, int choose_clustering)

Method Summary

Modifier and Type	Method and Description
java.lang.String	get_NewickFormat_NeighborJoining()
java.lang.String	get_NewickFormat_NeighborJoining(java.lang.String layer)
java.lang.String	get_NewickFormat_UPGMA()
java.lang.String	get_NewickFormat_UPGMA(java.lang.String layer)
void	read_file_and_create_matrix2(java.lang.String filename)
void	Save_To_File(java.lang.String filename, java.lang.String information)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

labels

public static java.util.ArrayList<java.lang.String> labels

Constructor Detail

Clustering_NJ_UPGMA

public Clustering_NJ_UPGMA(float[][] distance_Matrix,
                           java.util.ArrayList<java.lang.String> Leaf_Labels,
                           int choose_clustering)

Clustering_NJ_UPGMA

public Clustering_NJ_UPGMA(java.lang.String filename,
                           int choose_clustering)

Clustering_NJ_UPGMA

public Clustering_NJ_UPGMA(java.util.ArrayList<java.lang.String> list,
                           int choose_clustering)

Method Detail

get_NewickFormat_UPGMA

public java.lang.String get_NewickFormat_UPGMA()

get_NewickFormat_UPGMA

public java.lang.String get_NewickFormat_UPGMA(java.lang.String layer)

get_NewickFormat_NeighborJoining

public java.lang.String get_NewickFormat_NeighborJoining(java.lang.String layer)

get_NewickFormat_NeighborJoining

public java.lang.String get_NewickFormat_NeighborJoining()

Save_To_File

public void Save_To_File(java.lang.String filename,
                         java.lang.String information)

read_file_and_create_matrix2

public void read_file_and_create_matrix2(java.lang.String filename)