From fc23a549d88857c3f4c82b4e0a9ced45af2ecc57 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Mon, 14 Jan 2008 13:34:37 +0000
Subject: [PATCH] conversion tree -> phylo

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@14 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 src/tree_phylo.c | 71 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 src/tree_phylo.c

diff --git a/src/tree_phylo.c b/src/tree_phylo.c
new file mode 100644
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);
+}
-- 
2.39.2