src/hg/instinct/inc/cluster.h 1.2

Index: src/hg/instinct/inc/cluster.h
===================================================================
RCS file: src/hg/instinct/inc/cluster.h
diff -N src/hg/instinct/inc/cluster.h
--- src/hg/instinct/inc/cluster.h	18 Jan 2008 19:58:51 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,92 +0,0 @@
-/******************************************************************************/
-/* The C Clustering Library for cDNA microarray data.
- * 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: mdehoon 'AT' gsc.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 CALL 
-# define CALL
-#endif
-
-#ifndef min
-#define min(x, y)	((x) < (y) ? (x) : (y))
-#endif
-#ifndef max
-#define	max(x, y)	((x) > (y) ? (x) : (y))
-#endif
-
-
-/* Chapter 2 */
-double CALL 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);
-double** CALL distancematrix (int ngenes, int ndata, double** data,
-  int** mask, double* weight, char dist, int transpose);
-
-/* 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 CALL 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 CALL 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* CALL treecluster (int nrows, int ncolumns, double** data, int** mask,
-  double weight[], int transpose, char dist, char method, double** distmatrix);
-void cuttree (int nelements, Node* tree, int nclusters, int clusterid[]);
-
-/* Chapter 5 */
-void CALL 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 */
-void CALL svd(int m, int n, double** u, double w[], double** v, int* ierr);
-
-/* Utility routines, currently undocumented */
-void CALL sort(int n, const double data[], int index[]);
-double CALL mean(int n, double x[]);
-double CALL 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);