conversion tree -> phylo

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@14 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/src/tree_phylo.c b/src/tree_phylo.c
new file mode 100644 (file)
index 0000000..63f677d
--- /dev/null
+++ b/src/tree_phylo.c
@@ -0,0 +1,71 @@
+/* tree_phylo.c    2008-01-14 */
+
+/* Copyright 2008 Emmanuel Paradis */
+
+/* This file is part of the R-package `ape'. */
+/* See the file ../COPYING for licensing issues. */
+
+#include "me.h"
+
+/* from newick.c */
+int leaf(node *v);
+
+static int curnod, curtip, iedge;
+
+#define DO_EDGE\
+       el[iedge] = EDGE->distance;\
+       if (leaf(EDGE->head)) {\
+               edge2[iedge] = curtip;\
+               strncpy(tl[curtip - 1], EDGE->head->label, 6);\
+               iedge++;\
+               curtip++;\
+       } else {\
+               edge2[iedge] = curnod;\
+               iedge++;\
+               subtree2phylo(EDGE->head, edge1, edge2, el, tl);\
+       }
+
+void subtree2phylo(node *parent, int *edge1, int *edge2, double *el, char **tl)
+{
+       edge *EDGE; int localnode;
+
+       EDGE = parent->leftEdge;
+/* 'localnode' keeps a copy of the node ancestor # between
+   the two (recursive) calls of subtree2phylo */
+       localnode = edge1[iedge] = curnod;
+       curnod++;
+       DO_EDGE
+
+       EDGE = parent->rightEdge;
+       edge1[iedge] = localnode;
+       DO_EDGE
+}
+
+/*
+transforms a 'tree' struc of pointers into an object of class "phylo"
+assumes the tree is unrooted and binary, so there are 2n - 3 edges
+assumes labels are 6-char long
+*/
+void tree2phylo(tree *T, int *edge1, int *edge2, double *el, char **tl, int n)
+{
+       edge *EDGE;
+       curnod = n + 1; /* the root for ape */
+
+/* there's in fact only one edge from the "root" which is
+   a tip in ape's terminology (i.e., a node of degree 1) */
+
+       EDGE = T->root->leftEdge;
+       edge1[0] = curnod;
+       edge2[0] = 1; /* <- the 1st tip */
+       strncpy(tl[0], T->root->label, 6);
+       el[0] = EDGE->distance;
+       /* now can initialize these two: */
+       curtip = 2; /* <- the 2nd tip */
+       iedge = 1; /* <- the 2nd edge */
+       edge1[iedge] = curnod;
+
+/* 'T->root->leftEdge->head' is the root for ape,
+   so don't need to test if it's a leaf */
+
+       subtree2phylo(EDGE->head, edge1, edge2, el, tl);
+}