Empty trees allowed

Author: muffato

best.c

@@ -223,30 +223,25 @@ Tree *best_core(BestConfig *bo)
 
 	if (!bo->is_skip_mmerge) {
 		c_begin = clock();
+		Tree *forest[7];
+		forest[1] = t_nj_ds;
+		forest[3] = t_nj_dn;
+		forest[4] = t_nj_mm;
 		if (bo->is_phyml) { /* tree merge */
-			Tree *forest[7];
-			forest[0] = t_phyml_nt; forest[1] = t_nj_ds;
-			forest[2] = t_phyml_aa; forest[3] = t_nj_dn;
-			forest[4] = t_nj_mm;
-			if (bo->ctree == 0) {
-				t_final = tr_mmerge(5, forest);
-			} else {
-				forest[5] = t_nj_dn_cons;
-				forest[6] = t_nj_mm_cons;
-				t_final = tr_mmerge(7, forest);
-			}
+			forest[0] = t_phyml_nt;
+			forest[2] = t_phyml_aa;
 		} else {
-			Tree *forest[5];
-			forest[0] = t_nj_mm;
-			forest[1] = t_nj_dn; forest[2] = t_nj_ds;
-			if (bo->ctree == 0) {
-				t_final = tr_mmerge(3, forest);
-			} else {
-				forest[3] = t_nj_dn_cons;
-				forest[4] = t_nj_mm_cons;
-				t_final = tr_mmerge(5, forest);
-			}
+			forest[0] = NULL;
+			forest[2] = NULL;
+		}
+		if (bo->ctree == 0) {
+			forest[5] = NULL;
+			forest[6] = NULL;
+		} else {
+			forest[5] = t_nj_dn_cons;
+			forest[6] = t_nj_mm_cons;
 		}
+		t_final = tr_mmerge(7, forest);
 		if (bo->is_debug) fprintf(stderr, "tree merge: %.2fs\n", (float)(clock() - c_begin) / CLOCKS_PER_SEC);
 
 	} else {

mmerge.cc

@@ -244,7 +244,11 @@ static MMergeGlobal *initialize_G_space(int n, Tree **forest)
 	AllNodeHash *all_node;
 	all_node = g->hash = new AllNodeHash;
 
-	tree = forest[0];
+	int k = 0;
+	// Allows to pad the array with NULLs, to always have the same trees at the same indices
+	while (!forest[k]) k++;
+
+	tree = forest[k];
 	n_leaf = tree->n_leaf;
 	g->n_leaf = n_leaf;
 	g->n_tree = n;
@@ -257,8 +261,13 @@ static MMergeGlobal *initialize_G_space(int n, Tree **forest)
 	insert_single_leaf(all_node, n_leaf, name);
 	root_an = 0;
 	tree_index = 1;
-	for (int k = 0; k < n; ++k, tree_index<<=1) {
+	for (k = 0; k < n; ++k, tree_index<<=1) {
 		tree = forest[k];
+		// Allows to pad the array with NULLs, to always have the same trees at the same indices
+		if (!tree) {
+			fprintf(stderr, "[initialize_G_space] tree %d is NULL\n", k);
+			continue;
+		}
 		// QC
 		if (tree->n_leaf != n_leaf) {
 			fprintf(stderr, "[initialize_G_space] tree %d has different number of leaves (%d!=%d)\n", k, tree->n_leaf, n_leaf);