Sequence* free_Alignment ( Alignment *LA)
{
/* Does not free the A->S field (sequences of A)*/
Sequence *S;
//aln_stack checks the alignment has not already been freed
if ( LA==NULL || !aln_stack(LA,FREE_ALN)){return NULL;}
S=LA->S;
free_char ( LA->file, -1);
free_char ( LA->seq_al, -1);
free_int ( LA->seq_cache, -1);
free_int ( LA->cdna_cache, -1);
free_char ( LA->name,-1);
free_char ( LA->tree_order,-1);
vfree ( LA->generic_comment);
free_char ( LA->seq_comment, -1);
free_char ( LA->aln_comment, -1);
free_int ( LA->order, -1);
vfree ( LA->score_seq);
vfree ( LA->len);
free_profile (LA->P);
if ( LA->A){free_Alignment (LA->A);LA->A=NULL;}
vfree ( LA);
return S;
}
Sequence* free_aln ( Alignment *LA){ return free_Alignment(LA);}
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;
}
