X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fme.c;h=21a23968364c3dca6ecacdfd6888e6ca63cfae74;hb=24fc6c03893f85a3f9ab3d088201b3731f3035b4;hp=5b383f33b2c685f0fd8887ada72514bb94e2b09c;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git

diff --git a/src/me.c b/src/me.c
index 5b383f3..21a2396 100644
--- a/src/me.c
+++ b/src/me.c
@@ -1,26 +1,39 @@
+/* me.c    2008-01-14 */
+
+/* Copyright 2007-2008 Olivier Gascuel, Rick Desper,
+   R port by Vincent Lefort, me_*() below modified by Emmanuel Paradis */
+
+/* This file is part of the R-package `ape'. */
+/* See the file ../COPYING for licensing issues. */
+
 #include "me.h"
 
 //functions from me_balanced.c
-tree *BMEaddSpecies(tree *T,node *v, double **D, double **A);
+tree *BMEaddSpecies(tree *T, node *v, double **D, double **A);
 void assignBMEWeights(tree *T, double **A);
 void makeBMEAveragesTable(tree *T, double **D, double **A);
 //functions from me_ols.c
-tree *GMEaddSpecies(tree *T,node *v, double **D, double **A);
+tree *GMEaddSpecies(tree *T, node *v, double **D, double **A);
 void assignOLSWeights(tree *T, double **A);
 void makeOLSAveragesTable(tree *T, double **D, double **A);
 //functions from bNNI.c
 void bNNI(tree *T, double **avgDistArray, int *count, double **D, int numSpecies);
 //functions from NNI.c
 void NNI(tree *T, double **avgDistArray, int *count, double **D, int numSpecies);
+//functions from SPR.c
+void SPR(tree *T, double **D, double **A, int *count);
+//functions from TBR.c
+void TBR(tree *T, double **D, double **A);
 
 
-void me_b(double *X, int *N, char **labels, char **treeStr, int *nni)
+void me_b(double *X, int *N, char **labels,
+	  int *nni, int *spr, int *tbr,
+	  int *edge1, int *edge2, double *el, char **tl)
 {
   double **D, **A;
   set *species, *slooper;
   node *addNode;
   tree *T;
-  char *str;
   int n, nniCount;
 
   n = *N;
@@ -29,53 +42,37 @@ void me_b(double *X, int *N, char **labels, char **treeStr, int *nni)
   species = (set *) malloc(sizeof(set));
   species->firstNode = NULL;
   species->secondNode = NULL;
-  str = (char *)R_alloc(MAX_INPUT_SIZE, sizeof(char));
-  /* added by EP */
-  if (strlen(str))
-    strncpy(str, "", strlen(str));
-  /* end */
-  D = loadMatrix (X, labels, n, species);
-  A = initDoubleMatrix(2 * n - 2);
+  D = loadMatrix(X, labels, n, species);
+  A = initDoubleMatrix(2*n - 2);
 
   for(slooper = species; NULL != slooper; slooper = slooper->secondNode)
   {
     addNode = copyNode(slooper->firstNode);
-    T = BMEaddSpecies(T,addNode,D,A);
+    T = BMEaddSpecies(T, addNode, D, A);
   }
   // Compute bNNI
-  if (*nni == 1)
-    bNNI(T,A,&nniCount,D,n);
+  if (*nni) bNNI(T, A, &nniCount, D, n);
   assignBMEWeights(T,A);
 
-  NewickPrintTreeStr(T,str);
+  if (*spr) SPR(T, D, A, &nniCount);
+  if (*tbr) TBR(T, D, A);
 
-  if (strlen (str) < MAX_INPUT_SIZE -1)
-    {
-      *treeStr = (char *)R_alloc(MAX_INPUT_SIZE, sizeof(char));
-      /* added by EP */
-      if (strlen(*treeStr))
-	strncpy(*treeStr, "", strlen(*treeStr));
-      /* end */
-      strncpy (*treeStr, str, strlen(str));
-    }
+  tree2phylo(T, edge1, edge2, el, tl, n);
 
-/*   free (str); */
   freeMatrix(D,n);
   freeMatrix(A,2*n - 2);
   freeSet(species);
   freeTree(T);
   T = NULL;
-
-  /* return; */
 }
 
-void me_o(double *X, int *N, char **labels, char **treeStr, int *nni)
+void me_o(double *X, int *N, char **labels, int *nni,
+	  int *edge1, int *edge2, double *el, char **tl)
 {
   double **D, **A;
   set *species, *slooper;
   node *addNode;
   tree *T;
-  char *str;
   int n, nniCount;
 
   n = *N;
@@ -84,11 +81,6 @@ void me_o(double *X, int *N, char **labels, char **treeStr, int *nni)
   species = (set *) malloc(sizeof(set));
   species->firstNode = NULL;
   species->secondNode = NULL;
-  str = (char *)R_alloc(MAX_INPUT_SIZE, sizeof(char));
-  /* added by EP */
-  if (strlen(str))
-    strncpy(str, "", strlen(str));
-  /* end */
 
   D = loadMatrix (X, labels, n, species);
   A = initDoubleMatrix(2 * n - 2);
@@ -100,30 +92,17 @@ void me_o(double *X, int *N, char **labels, char **treeStr, int *nni)
   }
   makeOLSAveragesTable(T,D,A);
   // Compute NNI
-  if (*nni == 1)
+  if (*nni)
     NNI(T,A,&nniCount,D,n);
   assignOLSWeights(T,A);
 
-  NewickPrintTreeStr(T,str);
-
-  if (strlen (str) < MAX_INPUT_SIZE -1)
-    {
-      *treeStr = (char *)R_alloc(MAX_INPUT_SIZE, sizeof(char));
-      /* added by EP */
-      if (strlen(*treeStr))
-	strncpy(*treeStr, "", strlen(*treeStr));
-      /* end */
-      strncpy (*treeStr, str, strlen (str));
-    }
+  tree2phylo(T, edge1, edge2, el, tl, n);
 
- /*  free (str); */
   freeMatrix(D,n);
   freeMatrix(A,2*n - 2);
   freeSet(species);
   freeTree(T);
   T = NULL;
-
-  return;
 }
 
 /*************************************************************************
@@ -516,4 +495,3 @@ void freeSubTree(edge *e)
   e->head = NULL;
   free(e);
 }
-