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/******************************************************************************/
/* The C Clustering Library.
* Copyright (C) 2002 Michiel Jan Laurens de Hoon.
*
* This library was written at the Laboratory of DNA Information Analysis,
* Human Genome Center, Institute of Medical Science, University of Tokyo,
* 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
* Contact: michiel.dehoon 'AT' riken.jp
*
* Permission to use, copy, modify, and distribute this software and its
* documentation with or without modifications and for any purpose and
* without fee is hereby granted, provided that any copyright notices
* appear in all copies and that both those copyright notices and this
* permission notice appear in supporting documentation, and that the
* names of the contributors or copyright holders not be used in
* advertising or publicity pertaining to distribution of the software
* without specific prior permission.
*
* THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
* WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
* CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
* OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
* OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
* OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
* OR PERFORMANCE OF THIS SOFTWARE.
*
*/
#ifndef min
#define min(x, y) ((x) < (y) ? (x) : (y))
#endif
#ifndef max
#define max(x, y) ((x) > (y) ? (x) : (y))
#endif
#define CLUSTERVERSION "1.59"
/* Chapter 2 */
double clusterdistance(int nrows, int ncolumns, double** data, int** mask,
double weight[], int n1, int n2, int index1[], int index2[], char dist,
char method, int transpose);
void distancematrix(int ngenes, int ndata, double** data, int** mask,
double* weight, char dist, int transpose, double** distances);
/* Chapter 3 */
int getclustercentroids(int nclusters, int nrows, int ncolumns,
double** data, int** mask, int clusterid[], double** cdata, int** cmask,
int transpose, char method);
void getclustermedoids(int nclusters, int nelements, double** distance,
int clusterid[], int centroids[], double errors[]);
void kcluster(int nclusters, int ngenes, int ndata, double** data,
int** mask, double weight[], int transpose, int npass, char method, char dist,
int clusterid[], double* error, int* ifound);
void kmedoids(int nclusters, int nelements, double** distance,
int npass, int clusterid[], double* error, int* ifound);
/* Chapter 4 */
typedef struct {int left; int right; double distance;} Node;
/*
* A Node struct describes a single node in a tree created by hierarchical
* clustering. The tree can be represented by an array of n Node structs,
* where n is the number of elements minus one. The integers left and right
* in each Node struct refer to the two elements or subnodes that are joined
* in this node. The original elements are numbered 0..nelements-1, and the
* nodes -1..-(nelements-1). For each node, distance contains the distance
* between the two subnodes that were joined.
*/
Node* treecluster(int nrows, int ncolumns, double** data, int** mask,
double weight[], int transpose, char dist, char method, double** distmatrix);
int sorttree(const int nnodes, Node* tree, const double order[], int indices[]);
int cuttree(int nelements, const Node* tree, int nclusters, int clusterid[]);
/* Chapter 5 */
void somcluster(int nrows, int ncolumns, double** data, int** mask,
const double weight[], int transpose, int nxnodes, int nynodes,
double inittau, int niter, char dist, double*** celldata,
int clusterid[][2]);
/* Chapter 6 */
int pca(int m, int n, double** u, double** v, double* w);
/* Utility routines, currently undocumented */
void sort(int n, const double data[], int index[]);
double mean(int n, double x[]);
double median (int n, double x[]);
double* calculate_weights(int nrows, int ncolumns, double** data, int** mask,
double weights[], int transpose, char dist, double cutoff, double exponent);
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