void
aln_init (struct Alignment **aln_loc, unsigned int size)
{
*aln_loc = (struct Alignment *) malloc_util( sizeof(struct Alignment ));
(*aln_loc)->numseqs = size;
(*aln_loc)->seqs = (struct Sequence **) malloc_util( size * sizeof( struct Sequence *));
(*aln_loc)->length = 0;
unsigned int i = 0;
char *buffer = NULL;
for (i=0; i<size; i++) {
(*aln_loc)->seqs[i] = empty_Sequence();
if(asprintf(&buffer, "%d", i) == -1)
fatal_util("asprintf failed");
(*aln_loc)->seqs[i]->name = buffer;
}
return;
}
int main (int argc, char *argv[]) {
FILE *input;
char *fname;
char *optname; /* name of option found by getoption */
char *optarg; /* argument found by getoption */
unsigned int optindex; /* index in argv[] */
/**********************************/
/** process command line options **/
/**********************************/
clock_t start = clock();
while (get_option( argc,
argv,
options,
sizeof(options) / sizeof( struct Option ),
usage,
&optindex,
&optname,
&optarg )){
if (strcmp(optname, "-upgma") == 0) use_upgma = 1;
else if (strcmp(optname, "-kimura") == 0) use_kimura = 1;
else if (strcmp(optname, "-boot") == 0) calc_bootstraps = atoi( optarg );
else if (strcmp(optname, "-in") == 0) {
if (optarg[0] != 'm' && optarg[0] != 'a')
fatal_util("Error: Incorrect use of '-in' optio\n%s\n", usage );
if (optarg[0] == 'm')
input_is_matrix = 1;
else if (optarg[0] == 'a')
input_is_matrix = 0;
}
else if (strcmp(optname, "-out") == 0) {
if (optarg[0] != 'm' && optarg[0] != 't')
fatal_util("Error: Incorrect use of '-out' option\n%s\n", usage );
if (optarg[0] == 'm')
output_is_matrix = 1;
else if (optarg[0] == 't')
output_is_matrix = 0;
}
else if (strcmp(optname, "-h") == 0) {
fprintf( stderr, "%s", usage );
exit(0);
}
}
if (argc - optindex != 1) {
fatal_util("Fatal error: Incorrect number of arguements.\n%s\n", usage );
}
fname = argv[optindex];
/* do some options combination checking - some combinations do not make sense */
if (input_is_matrix && use_kimura)
fatal_util("You can only use kimura when giving an aligment\n%s\n", usage );
if ( (input_is_matrix || output_is_matrix) && calc_bootstraps)
fatal_util("You can't do bootstrapping in matrix mode. You need an alignment\n%s\n", usage );
if ((input = fopen( fname, "r" )) == NULL)
fatal_util( "Could not open file %s for reading", fname );
quicktree( input );
printf("Time elapsed: %f\n", ((double)clock() - start) / CLOCKS_PER_SEC);
exit(0);
}
char *
msa2tree (char **mfa, unsigned int num) {
// fprintf(stderr, "TREELIB: Starting msa2tree [%d]\n", num);
struct DistanceMatrix *mat = NULL;
struct Alignment *aln = NULL;
struct ClusterGroup *group = NULL;
struct Tree *njTree = NULL;
char *treestring = NULL;
assert(num >= 0);
if (num == 0) {
return NULL;
} else if (num == 1) {
if(asprintf(&treestring, "%d;", 0) == -1)
fatal_util("asprintf failed");
return treestring;
} else if (num == 2) {
float dist = jcdist(mfa[0], mfa[1]);
dist *= 0.5;
if(asprintf(&treestring, "(%d:%g, %d:%g)", 0, dist, 1, dist) == -1)
fatal_util("asprintf failed");
return treestring;
}
// fprintf(stderr, "TREELIB: Here is the msa\n");
// unsigned int i = 0;
// for (i=0; i<num; i++) {
// fprintf(stderr, "TREELIB:\t[%s]\n", mfa[i]);
// }
// fprintf(stderr, "TREELIB: Building the distance matrix\n");
mat = mfa2dist(mfa, num);
aln_init(&aln, num);
group = alignment_to_ClusterGroup(aln, 0);
group->matrix = mat;
// print_DistanceMatrix(stderr, mat);
fprintf(stderr, "TREELIB: Building the NJ tree\n");
njTree = neighbour_joining_buildtree(group, 0);
struct Tnode *tmpNode = NULL;
tmpNode = njTree->child[2];
njTree->child[2] = NULL;
// fprintf(stderr, "TREELIB: Rooting the tree\n");
struct Tnode *leftNode = NULL;
leftNode = (struct Tnode *) malloc_util(sizeof(struct Tnode));
leftNode->left = njTree->child[0];
leftNode->right = njTree->child[1];
leftNode->distance = 0.0;
struct Tnode *rootNode = NULL;
rootNode = (struct Tnode *) malloc_util(sizeof(struct Tnode));
rootNode->left = leftNode;
rootNode->right = tmpNode;
njTree->child[0] = rootNode;
njTree->child[1] = NULL;
fprintf(stderr, "TREELIB: Converting tree to string\n");
treestring = tree2string(njTree);
// fprintf(stderr, "TREELIB: [[%s]]\n", treestring);
// fprintf(stderr, "TREELIB: free aln\n");
aln = free_Alignment(aln);
// fprintf(stderr, "TREELIB: free group\n");
group = free_ClusterGroup(group);
// fprintf(stderr, "TREELIB: free njTree\n");
// njTree = free_Tree(njTree);
// fprintf(stderr, "TREELIB: Ending msa2tree\n");
return treestring;
}
