cluster.h

一个通用的隐性马尔可夫C代码库 开发环境:C语言 简要说明:这是一个通用的隐性马尔可夫C代码库

/*******************************************************************************
  author       : Bernd Wichern
  filename     : ghmm/ghmm/cluster.h
  created      : TIME: 11:17:55     DATE: Tue 02. June 1998
  $Id: cluster.h,v 1.7 2001/07/20 13:16:48 disa Exp $ 

Copyright (C) 1998-2001, ZAIK/ZPR, Universit鋞 zu K鰈n

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA


*********************************************************************************/

#ifndef CLUSTER_H
#define CLUSTER_H
#include <ghmm/sequence.h>
#include <ghmm/model.h>

#ifdef __cplusplus
extern "C" {
#endif

/**
 @name cluster
 */

/*@{ */

/**
 */
struct cluster_t{
  /** 
    Vector of HMM-Model pointers */
  model **mo;
  /** 
    Vector of sequence_t pointers: for saving the sequence data
    that belongs to the models
  */
  sequence_t **mo_seq;
  /** 
    Number of models read in */
  int mo_number;
};
/**
*/
typedef struct cluster_t cluster_t;

/**
   Writess out the final models.
   @return 0 for success; -1 for error
   @param cl cluster of models to write
   @param sq 
   @param outfile output file
   @param out_filename name of the output file
 */
int cluster_out(cluster_t *cl, sequence_t *sq, FILE *outfile,
		    char *out_filename);

/**
   Prevents that empty models are sent out (no associated seqences) by 
   associating a random sequence. Since it's possible to produce an empty model
   in this way, the sequences are shifted until a nonempty model is produced. (This 
   could be a never-ending process and therefore it's only done 100 times).
   @return 0 for success; -1 for error
   @param seq_label vector of labels for the sequences
   @param seq_number number of sequences
   @param mo_number number of models
 */
int cluster_avoid_empty_model(long *seq_label, long seq_number, int mo_number);

/**
   Makes a cluster and reestimates the HMMs.
   @return 0 for success; -1 for error
   @param seq_file file of sequences
   @param mo_file file of initial models
   @param out_file output file
 */
int cluster_hmm(char *seq_file, char *mo_file, char *out_file);

/**
   Updates the cluster with additional sequences.
   @return 0 for success; -1 for error
   @param cl cluster to update
   @param sq sequences to update the cluster with
 */
int cluster_update(cluster_t *cl, sequence_t *sq);

/**
   Updates a label
   @return number of changes made
   @param oldlabel label to update
   @param up to date label for comparison
   @param seq_number number of sequences
 */
long cluster_update_label(long *oldlabel, long *seq_label, long seq_number);

/**
   Prints out the likelihood values for the cluster.
   @param outfile output file
   @param cl cluster of models and sequences
 */
void cluster_print_likelihood(FILE *outfile, cluster_t *cl);

/*@} cluster documentation */

#ifdef __cplusplus
}
#endif


#endif /* CLUSTER_H */