void insert(struct trie *root, char *window, int start, char *seqname, int which){
struct trie *current = root;
int i;
int loc;
for (i=0;i<strlen(window);i++){
loc = cindex(window[i]);
if (current->kids[loc] == NULL){
if (VERBOSE)
printf("alloc for %c - %d\n", window[i], loc);
alloc_trie(&(current->kids[loc]));
}
current = current->kids[loc];
}
/* not a leaf node any more */
if (current->freq == INTERNALNODE)
current->freq = 0;
if (which == 1)
current->freq++;
else
current->freq--;
// we're at the leaf now; fix this for multiple hits.
// insert_sloc(&(current->location), start, seqname);
//strcpy(current->seq, seqname);
if (VERBOSE)
printf("inserted %d\n", start);
//current->location = start;
}
Trie *init_trie(CalcPrefixFunc addPrefixFunc, CalcPrefixFunc findPrefixFunc) {
Trie *trie = alloc_trie();
trie->root = alloc_trie_node();
trie->table = init_table();
trie->addPrefixFunc = addPrefixFunc;
trie->findPrefixFunc = findPrefixFunc;
return trie;
}
int main(int argc, char **argv){
int i, j;
FILE *fasta;
FILE *treefile;
struct trie *root;
char fname[SEQ_LENGTH*2];
char idxname[SEQ_LENGTH];
char command[SEQ_LENGTH*5];
char fgnuplot[SEQ_LENGTH*5];
FILE *gnuplot;
int filestat;
int LOADED;
char searchFile[SEQ_LENGTH];
char seqname[SEQ_LENGTH];
char gnuseq[SEQ_LENGTH];
int gnufreq;
FILE *freqFile;
FILE *freqList;
struct timeval start, end;
struct timezone tz;
/* directory stuff */
DIR *dp;
struct dirent *ep;
triemem = 0;
slocmem = 0;
identifier = 0;
DUMPTREE = 0;
VERBOSE = 0;
SAVEINDEX = 0;
LOADED = 0;
MINWIN = 1;
THREADS = 1;
idxname[0] = 0;
genomelen = 0;
allocs = 0;
frees = 0;
if (argc < 3){
help(argv[0]);
return 0;
}
fname[0] = 0;
searchFile[0] = 0;
QUALFILE[0] = 0;
pthread_mutex_init(&logMutex, NULL);
pthread_mutex_init(&readMutex, NULL);
INDEXSTART = 0;
seqname[0] = 0;
for (i=1;i<argc;i++){
if (!strcmp(argv[i], "-ws"))
WINDOW_SIZE = atoi(argv[i+1]);
else if (!strcmp(argv[i], "-ss"))
SLIDE_SIZE = atoi(argv[i+1]);
else if (!strcmp(argv[i], "-nr"))
NOREV = 1;
else if (!strcmp(argv[i], "-uniq"))
UNIQ = 1;
else if (!strcmp(argv[i], "-v"))
VERBOSE=1;
else if (!strcmp(argv[i], "-f"))
strcpy(fname, argv[i+1]);
else if (!strcmp(argv[i], "-seqname"))
strcpy(seqname, argv[i+1]);
}
if (fname[0] == 0){
help(argv[0]);
return 0;
}
alloc_trie(&root);
if (fname[0] != 0)
fprintf(stderr,"\tfile:\t\t%s\n",fname);
fprintf(stderr,"\twindow size:\t%d\n\tslide size:\t%d\n", WINDOW_SIZE, SLIDE_SIZE);
if (VERBOSE)
fprintf(stderr,"\tverbose:\t\ton\n");
filestat = do_file(fname, root, 1);
if (filestat == 0)
return 0;
if (WINDOW_SIZE == 0){
fprintf(stderr, "Strange ws.\n");
return 0;
}
fprintf(stderr, "Total memory for the trie: %lld bytes = %6.2f Kbytes = %4.2f Mbytes\n", triemem, (float)triemem/1024.0, (float)triemem/1024.0/1024.0);
slocmem = 0;
allocs = 0;
frees = 0;
callocs = 0;
cfrees = 0;
clallocs = 0;
clfrees = 0;
sprintf(idxname, "%s.k%d.txt", fname, WINDOW_SIZE);
saveTrie(root, idxname);
return 1;
}