indentation.

mgescan/nonltr/hmm/hmm.h

@@ -40,7 +40,6 @@
 #define RT_CRE 31
 #define RT_R2 32
 
-
 #define A_H_KD 0.0703
 #define A_H_WW 0.0976
 #define A_H_HH 0.0639
@@ -62,22 +61,17 @@
 
 #define CODE 1
 
-
-
 typedef struct {
-  int N;          /* number of states;  Q={1,2,...,N} */
-  int M;          /* number of observation symbols; V={1,2,...,M}*/
-  double  **A;    /* A[1..N][1..N]. a[i][j] is the transition prob                                                                     
-                           of going from state i at time t to state j                                                                        
-                           at time t+1 */
-  double  **B;    /* B[1..N][1..M]. b[j][k] is the probability of                                                                      
-		     of observing symbol k in state j */
-  double  *pi;    /* pi[1..N] pi[i] is the initial state distribution. */
+	int N;          /* number of states;  Q={1,2,...,N} */
+	int M;          /* number of observation symbols; V={1,2,...,M}*/
+	double  **A;    /* A[1..N][1..N]. a[i][j] is the transition prob                                                                     
+			   of going from state i at time t to state j                                                                        
+			   at time t+1 */
+	double  **B;    /* B[1..N][1..M]. b[j][k] is the probability of                                                                      
+			   of observing symbol k in state j */
+	double  *pi;    /* pi[1..N] pi[i] is the initial state distribution. */
 } HMM;
 
-
-
-
 void print_hmm(HMM *hmm_ptr);
 void get_hmm_from_file(FILE *fp, HMM *hmm_ptr);
 void free_hmm(HMM *hmm);
@@ -90,4 +84,4 @@ double dist_rt(int dist);
 double dist_id(int dist);
 double dist_ie(int dist);
 double get_prob(int state, int start, int end,  char *O, char *hmmerv);
- 
+

mgescan/nonltr/hmm/main.c

@@ -0,0 +1,89 @@
+#include <ctype.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <unistd.h>
+#include <string.h>
+#include "hmm.h"
+
+int main (int argc, char **argv){
+
+	int c;
+	char *hmm_file, *seq_file, *sig1_file, *sig2_file, *out_file, *phmm_dir, *out_dir, *hmmerv;
+	int debug=1;
+	FILE *fp;
+	HMM hmm;
+
+	int i,j;
+	int num_seqs;
+	char **obs_seqs;
+
+	char *O;
+	int T;
+	double **alpha, **beta;
+	double pprob;
+	int *vpath;
+
+	/* read command line argument */
+	while ((c=getopt(argc, argv, "m:s:r:a:o:p:d:v:")) != -1){
+
+		switch (c){
+			case 'm':
+				hmm_file = optarg;   /* HMM */
+				break;
+
+			case 's':
+				seq_file = optarg;   /* DNA SEQ */
+				break;      
+
+			case 'a':
+				sig1_file = optarg;   /* APE */
+				break;      
+
+			case 'r':
+				sig2_file = optarg;   /* RT */
+				break;      
+
+			case 'o':
+				out_file = optarg;   /* output */
+				break;      
+
+			case 'p':
+				phmm_dir = optarg;   /* program main dir */
+				break;      
+
+			case 'd':  
+				out_dir = optarg;   /* out1 dir */ 
+				break; 
+
+			case 'v':
+				hmmerv = optarg;   /* hmmer version */
+				break;
+
+		}
+	}
+
+	/* read initial model */
+	fp = fopen(hmm_file, "r");
+	get_hmm_from_file(fp, &hmm);
+	fclose(fp);
+	/*print_hmm(&hmm);*/
+
+	/* read observation seq */
+	fp = fopen(seq_file, "r");
+	read_obs_seq_from_file(fp, &num_seqs, &obs_seqs);
+	fclose(fp);
+
+	/* test */
+	for (i=0; i<num_seqs; i++){
+		T = strlen(obs_seqs[i]);
+		viterbi(&hmm, T, obs_seqs[i], &pprob, vpath, sig1_file, sig2_file, out_file, phmm_dir, out_dir, hmmerv); 
+	}
+	/* free memory */
+	free_hmm(&hmm);
+	for (i=0; i<num_seqs; i++){
+		free(obs_seqs[i]);
+	}
+	free(obs_seqs);
+
+}

mgescan/nonltr/hmm/makefile

@@ -1,6 +1,6 @@
 CC =	gcc
 CFLAGS = -O3 -Wall -w # -g -O0 for gdb
-SRCS =	util_lib.c hmm_lib.c test_hmm.c
+SRCS =	util_lib.c hmm_lib.c main.c
 OBJS = $(SRCS:.c=.o)
 MAIN = MGEScan