+++ /dev/null
-/* newick.c 2012-02-09 */
-
-/* Copyright 2007-2008 Vincent Lefort */
-
-/* This file is part of the R-package `ape'. */
-/* See the file ../COPYING for licensing issues. */
-
-#include "me.h"
-
-int nodeCount;
-int edgeCount;
-
-int whiteSpace(char c)
-{
- if ((' ' == c) || ('\t' == c) || ('\n' == c))
- return(1);
- else return(0);
-}
-
-int leaf(node *v)
-{
- int count = 0;
- if (NULL != v->parentEdge)
- count++;
- if (NULL != v->leftEdge)
- count++;
- if (NULL != v->rightEdge)
- count++;
- if (NULL != v->middleEdge)
- count++;
- if (count > 1)
- return(0);
- return(1);
-}
-
-/*decodeNewickSubtree is used to turn a string of the form
- "(v1:d1,v2:d2,(subtree) v3:d3....vk:dk) subroot:d," into a subtree
- rooted at subrooted, with corresponding subtrees and leaves at v1
- through vk. It is called recursively on subtrees*/
-
-node *decodeNewickSubtree(char *treeString, tree *T, int *uCount)
-{
- node *thisNode;
- node *centerNode;
- double thisWeight;
- edge *thisEdge;
-// char label[MAX_LABEL_LENGTH];
- char stringWeight[MAX_LABEL_LENGTH];
- int state;
- int i = 0;
- int j;
- int left,right;
- int parcount;
-// snprintf(label,14,"Default_Label\0");
- left = right = 0;
- parcount = 0;
- state = ReadOpenParenthesis;
- if('(' == treeString[0])
- parcount++;
- //centerNode = makeNode(label,NULL,nodeCount++);
- centerNode = makeNode("",NULL,nodeCount++);
- T->size++;
- while(parcount > 0)
- {
- while(whiteSpace(treeString[i]))
- i++;
- switch(state)
- {
- case(ReadOpenParenthesis):
- if('(' != treeString[0])
- {
- error("error reading subtree");
- }
- i++;
- state = ReadSubTree;
- break;
- case(ReadSubTree):
- if('(' == treeString[i]) /*if treeString[i] is a left parenthesis,
- we scan down the string until we find its partner.
- the relative number of '('s vs. ')'s is counted
- by the variable parcount*/
- {
- left = i++;
- parcount++;
- while(parcount > 1)
- {
- while (('(' != treeString[i]) && (')' != treeString[i]))
- i++; /*skip over characters which are not parentheses*/
- if('(' == treeString[i])
- parcount++;
- else if (')' == treeString[i])
- parcount--;
- i++;
- } /*end while */
- right = i; /*at this point, the subtree string goes from
- treeString[left] to treeString[right - 1]*/
- thisNode = decodeNewickSubtree(treeString + left,T,uCount); /*note that this
- step will put
- thisNode in T*/
- i = right; /*having created the node for the subtree, we move
- to assigning the label for the new node.
- treeString[right] will be the start of this label */
- } /* end if ('(' == treeString[i]) condition */
- else
- {
- //thisNode = makeNode(label,NULL,nodeCount++);
- thisNode = makeNode("",NULL,nodeCount++);
- T->size++;
- }
- state = ReadLabel;
- break;
- case(ReadLabel):
- left = i; /*recall "left" is the left marker for the substring, "right" the right*/
- if (':' == treeString[i]) /*this means an internal node?*/
- {
- //sprintf(thisNode->label,"I%d",(*uCount)++);
- //snprintf(thisNode->label,MAX_LABEL_LENGTH,"I%d",(*uCount)++);
- (*uCount)++;
- right = i;
- }
- else
- {
- while((':' != treeString[i]) && (',' != treeString[i]) && (')' != treeString[i]))
- i++;
- right = i;
- j = 0;
- for(i = left; i < right;i++)
- if(!(whiteSpace(treeString[i])))
- thisNode->label[j++] = treeString[i];
- thisNode->label[j] = '\0';
- }
- if(':' == treeString[right])
- state = ReadWeight;
- else
- {
- state = AddEdge;
- thisWeight = 0.0;
- }
- i = right + 1;
- break;
- case(ReadWeight):
- left = i;
- while
- ((',' != treeString[i]) && (')' != treeString[i]))
- i++;
- right = i;
- j = 0;
- for(i = left; i < right; i++)
- stringWeight[j++] = treeString[i];
- stringWeight[j] = '\0';
- thisWeight = atof(stringWeight);
- state=AddEdge;
- break;
- case(AddEdge):
- //thisEdge = makeEdge(label,centerNode,thisNode,thisWeight);
- thisEdge = makeEdge("",centerNode,thisNode,thisWeight);
- thisNode->parentEdge = thisEdge;
- if (NULL == centerNode->leftEdge)
- centerNode->leftEdge = thisEdge;
- else if (NULL == centerNode->rightEdge)
- centerNode->rightEdge = thisEdge;
- else if (NULL == centerNode->middleEdge)
- centerNode->middleEdge = thisEdge;
- else
- {
- error("node %s has too many (>3) children.", centerNode->label);
- }
- //sprintf(thisEdge->label,"E%d",edgeCount++);
- //snprintf(thisEdge->label,MAX_LABEL_LENGTH,"E%d",edgeCount++);
- edgeCount++;
- i = right + 1;
- if (',' == treeString[right])
- state = ReadSubTree;
- else
- parcount--;
- break;
- }
- }
- return(centerNode);
-}
-
-tree *readNewickString (char *str, int numLeaves)
-{
- tree *T;
- node *centerNode;
- int i = 0;
- int j = 0;
- int inputLength;
- int uCount = 0;
- int parCount = 0;
- char rootLabel[MAX_LABEL_LENGTH];
- nodeCount = edgeCount = 0;
-
- T = newTree();
-
- if ('(' != str[0])
- {
- error("generated tree does not start with '('");
- }
- inputLength = strlen (str)+1;
- for(i = 0; i < inputLength; i++)
- {
- if ('(' == str[i])
- parCount++;
- else if (')' == str[i])
- parCount--;
- if (parCount > 0)
- ;
- else if (0 == parCount)
- {
- i++;
-/* if(';' == str[i])
- sprintf(rootLabel,"URoot");
- else
- {*/
- while(';' != str[i])
- if (!(whiteSpace (str[i++])))
- rootLabel[j++] = str[i-1]; /*be careful here */
- rootLabel[j] = '\0';
-// }
- i = inputLength;
- }
- else if (parCount < 0)
- {
- error("generated tree has too many right parentheses");
- }
- }
- centerNode = decodeNewickSubtree (str, T, &uCount);
- snprintf (centerNode->label, MAX_LABEL_LENGTH, "%s", rootLabel); /* added "%s" following Jos Kafer's suggestion (2010-11-23) */
- T->root = centerNode;
- return(T);
-}
projects / ape.git / blobdiff