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- /* The MIT License
-
- Copyright (c) 2016 Genome Research Ltd.
-
- Author: Petr Danecek <pd3@sanger.ac.uk>
-
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
-
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
-
- */
-
- /*
- Simple hierarchical clustering
- */
-
- #ifndef __HCLUST_H__
- #define __HCLUST_H__
-
- #include <stdio.h>
-
- typedef struct _hclust_t hclust_t;
-
- typedef struct
- {
- float dist;
- int nmemb, *memb;
- }
- cluster_t;
-
- #define PDIST(mat,a,b) (mat)[((a)>(b)?((a)*((a)-1)/2+(b)):((b)*((b)-1)/2+(a)))]
-
- /*
- * hclust_init() - init and run clustering
- * @n: number of elements
- * @pdist: pairwise distances. The array will be modified by hclust and
- * must exist until hclust_destroy() is called
- */
- hclust_t *hclust_init(int n, float *pdist);
- void hclust_destroy(hclust_t *clust);
-
- /*
- * hclust_create_list() - returns a list of clusters
- * @min_inter_dist: minimum inter-cluster distance. If smaller, elements are considered
- * homogenous, belonging to the same cluster.
- * @max_intra_dist: maximum intra-cluster distance allowed. If smaller than 0,
- * the threshold can be heuristically lowered, otherwise considered
- * a fixed cutoff. The pointer will be filled to the cutoff actually used.
- */
- cluster_t *hclust_create_list(hclust_t *clust, float min_inter_dist, float *max_intra_dist, int *nclust);
- void hclust_destroy_list(cluster_t *clust, int nclust);
-
- /*
- * Access debugging data used in the decision making process. Note that this
- * must be called immediately after hclust_create_list because other calls,
- * such as hclust_create_dot(), invalidate the temporary data structures.
- */
- char **hclust_explain(hclust_t *clust, int *nlines);
-
- char *hclust_create_dot(hclust_t *clust, char **labels, float th);
-
- #endif
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