Fixed edge-case bug of tree comprising a single cluster of identical sequences (produced bad Newick format)

Author: Kevin Howe

include/version.h

@@ -22,6 +22,6 @@
 #define _VERSION
 
 #define VERSION_MAJOR	2
-#define VERSION_MINOR	4
+#define VERSION_MINOR	5
 
 #endif

src/tree.c

@@ -931,7 +931,6 @@ void write_newhampshire_Tree( FILE *handle, struct Tree *thetree,
     if (thetree->child[0] != NULL) {
       if (thetree->child[1] == NULL) {
 	/* draw rooted tree */
-
 	if (thetree->child[0]->left != NULL && thetree->child[0]->right != NULL) {
 	  fprintf( handle, "(\n");
 	  write_newhampshire_Tnode( handle, thetree->child[0]->left, show_bootstraps );
@@ -944,26 +943,18 @@ void write_newhampshire_Tree( FILE *handle, struct Tree *thetree,
 	     or a cluser of sequences. If this leaf contains a single sequence,
 	     then we have a tree of one sequence, in which case we print an
 	     error, because trees of one sequence do not make sense */
-	  
 	  if (thetree->child[0]->clust->clustersize == 1) 
 	    fatal_util( "Cannot build a tree with a single sequence %s",
 		     thetree->child[0]->clust->members[0]->name);
 	  else {
-	    unsigned int i;
-	    
-	    for (i=0; i < thetree->child[0]->clust->clustersize - 1; i++)
-	      fprintf( handle, "(\n%s:%.5f,\n", thetree->child[0]->clust->members[i]->name, 0.0 ); 
-
-	    fprintf( handle, "%s:%.5f", thetree->child[0]->clust->members[i]->name, 0.0);
-
-	    for (i=0; i < thetree->child[0]->clust->clustersize - 2; i++) 
-	      fprintf( handle, ")\n:%.5f)\n", 0.0 ); 
-
+	    fprintf( handle, "(\n"); 
+            write_newhampshire_Cluster( handle, thetree->child[0]->clust, 0, thetree->child[0]->clust->clustersize - 1);
 	    fprintf( handle, ");\n"); 
 	  }
 	}
       }
       else {
+
 	fprintf( handle, "(\n");
 	write_newhampshire_Tnode( handle, thetree->child[0], show_bootstraps );
 	fprintf( handle, ",\n");