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TreeOPE.cpp
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//##########################################################################
//# This software is part of the Treescaper i
//# -- Version 0.1
//# Copyright (C) 2010 Wen Huang
//#
//# This program is free software; you can redistribute it and/or
//# modify it under the terms of the GNU General Public License
//# as published by the Free Software Foundation; either version 2
//# of the License, or (at your option) any later version.
//#
//# This program is distributed in the hope that it will be useful,
//# but WITHOUT ANY WARRANTY; without even the implied warranty of
//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//# GNU General Public License for more details.
//# http://www.gnu.org/copyleft/gpl.html
//##########################################################################
// TreeOPE.cpp
// Member function definitions for class TreeOPE.h
// by whuang gzhou
#ifndef TREEOPE_CPP
#define TREEOPE_CPP
#include "TreeOPE.h"
#define __HALF_MAX_SIGNED(type) ((type)1 << (sizeof(type)*8-2))
#define __MAX_SIGNED(type) (__HALF_MAX_SIGNED(type) - 1 + __HALF_MAX_SIGNED(type))
#define __MIN_SIGNED(type) (-1 - __MAX_SIGNED(type))
#define __MIN(type) ((type)-1 < 1?__MIN_SIGNED(type):(type)0)
#define __MAX(type) ((type)~__MIN(type))
//#ifndef _WIN32
#define assign(dest,src) ({ \
typeof(src) __x=(src); \
typeof(dest) __y=__x; \
(__x==__y && ((__x<1) == (__y<1)) ? (void)((dest)=__y),0:1); \
})
#define add_of(c,a,b) ({ \
typeof(a) __a=a; \
typeof(b) __b=b; \
(__b)<1 ? \
((__MIN(typeof(c))-(__b)<=(__a)) ? assign(c,__a+__b):1) : \
((__MAX(typeof(c))-(__b)>=(__a)) ? assign(c,__a+__b):1); \
})
//#else
//// This is not correct and need to be rewitten.
// template<typename T1, typename T2, typename T3>
// T3 assign(T1 dest, T2 src)
// {
// return dest;
// }
// template<typename T1, typename T2, typename T3>
// T1 add_of(T1 c, T2 a, T3 b)
// {
// return a+b;
// }
// #define assign(dest,src) ({ \
// typeid(src) __x=(src); \
// typeid(dest) __y=__x; \
// (__x==__y && ((__x<1) == (__y<1)) ? (void)((dest)=__y),0:1); \
// })
// #define add_of(c,a,b) ({ \
// typeid(a) __a=a; \
// typeid(b) __b=b; \
// (__b)<1 ? \
// ((__MIN(typeid(c))-(__b)<=(__a)) ? assign(c,__a+__b):1) : \
// ((__MAX(typeid(c))-(__b)>=(__a)) ? assign(c,__a+__b):1); \
// })
//#endif
/*
load a newick tree from a file
Params: fname - path to file
error - return for error code
Returns: the loaded object on success, 0 on fail
Error codes: -1 out of memory
-2 parse error
-3 can't open file
*/
NEWICKTREE *TreeOPE::loadnewicktree(char *fname, int *error)
{
NEWICKTREE *answer = NULL;
FILE *fp = NULL;
int err;
fp = fopen(fname, "r");
if(!fp)
{
err = -3;
goto error_exit;
}
answer = floadnewicktree(fp, &err);
if(!answer)
goto error_exit;
if(error)
*error = 0;
return answer;
error_exit:
if(error)
*error = err;
return 0;
}
NEWICKTREE *TreeOPE::loadnewicktree2(FILE *fp, int *error)
{
NEWICKTREE *answer = NULL;
// FILE *fp;
int err;
// fp = fopen(fname, "r");
// if(!fp)
// {
// err = -3;
// goto error_exit;
// }
answer = floadnewicktree(fp, &err);
if(!answer)
goto error_exit;
if(error)
*error = 0;
return answer;
error_exit:
if(error)
*error = err;
return 0;
}
/*
load newick tree from an opened stream
Params: fp - input stream
error - return for error
Returns: pointer to object, 0 on fail
Error codes -1 out of memory
-2 parse error
Notes: format allows several trees to be stored in a file
*/
NEWICKTREE *TreeOPE::floadnewicktree(FILE *fp, int *error)
{
NEWICKTREE *answer = NULL;
int err;
int ch;
answer = (NEWICKTREE *) malloc(sizeof(NEWICKTREE));
if(!answer)
{
err = -1;
goto error_exit;
}
skipspace(fp);
ch = fgetc(fp);
if(ch == '(' )
{
answer->root = loadnode(fp, &err);
if(!answer->root || err != 0)
goto error_exit;
}
skipspace(fp);
ch = fgetc(fp);
if(ch != ';')
{
err = -2;
goto error_exit;
}
if(error)
*error = 0;
return answer;
error_exit:
killnewicktree(answer);
if(error)
*error = err;
return 0;
}
/*
newick tree destructor
*/
void TreeOPE::killnewicktree(NEWICKTREE *tree)
{
// rewind(stdin);
// setbuf(stdout, NULL);
if(tree)
{
killnoder(tree->root);
free(tree);
}
}
/*
node destructor (recursive)
*/
void TreeOPE::killnoder(NEWICKNODE *node)
{
if(!node)
return;
for(int i = 0;i < node->Nchildren; i++)
{
killnoder(node->child[i]);
}
setbuf(stdout, NULL);
free(node->label);
if(node->bitstr != NULL)
{
delete node->bitstr;
node->bitstr = NULL;
}
free(node->child);
free(node);
}
void TreeOPE::killnewicktreeBitstr(NEWICKTREE *tree)
{
if(tree)
{
killnoderBitstr(tree->root);
}
}
/*
node bitstr destructor (recursive)
*/
void TreeOPE::killnoderBitstr(NEWICKNODE *node)
{
for(int i = 0;i < node->Nchildren; i++)
{
killnoderBitstr(node->child[i]);
}
if(node->bitstr != NULL)
{
delete node->bitstr;
node->bitstr = NULL;
}
}
/*
turns a string into a label suitable for use in the tree
Params: str - the string
Returns: modified string, 0 on out of memory
Notes: strings containing spaces have them replaced by underscores
strings contianing illegal characters are quoted
null pointer is returned as the empty string ""
*/
char *TreeOPE::makenewicklabel(const char *str)
{
const char *cptr = NULL;
char *vptr = NULL;
int needsquote = 0;
char *answer = NULL;
if(!str)
return mystrdup("");
cptr = str;
while(*cptr)
{
if(strchr("\'()[]:;,", *cptr))
needsquote = 1;
if(isspace(*cptr) && *cptr != ' ')
needsquote = 1;
cptr++;
}
if(needsquote)
{
answer = (char *) malloc(strlen(str) + 2 + mystrcount(str, '\''));
vptr = answer;
*vptr++ = '\'';
while(*str)
{
*vptr = *str;
if(*str == '\'')
{
vptr++;
*vptr = '\'';
}
vptr++;
str++;
}
*vptr++ = '\'';
*vptr = 0;
}
else
{
answer = mystrdup(str);
vptr = answer;
while(*vptr)
{
if(*vptr == ' ' )
*vptr = '_';
vptr++;
}
}
delete cptr;
free(vptr);
return answer;
}
/*
load a node from the file
Params: fp - the input stream
error - return for error
Returns: node loaded.
Notes: recursive. Expects the opening parenthesis to have been eaten
*/
NEWICKNODE *TreeOPE::loadnode(FILE *fp, int *error)
{
NEWICKNODE *answer = NULL;
int err;
NEWICKNODE *child = 0;
int ch;
answer = (NEWICKNODE *) malloc(sizeof(NEWICKNODE));
//printf("sizeof(NEWICKNODE) = %d\n", sizeof(NEWICKNODE));
if(!answer)
{
err = -1;
goto error_exit;
}
answer->Nchildren = 0;
answer->label = 0;
answer->child = 0;
answer->hv1 = 0;
answer->hv2 = 0;
answer->bitstr = NULL;
skipspace(fp);
do
{
ch = fgetc(fp);
if(ch == '(')
{
child = loadnode(fp, &err);
if(!child)
goto error_exit;
if(addchild(answer, child ) == -1)
{
err = -1;
goto error_exit;
}
child = 0;
}
else
{
ungetc(ch, fp);
child = loadleaf(fp, &err);
if(!child)
goto error_exit;
if(addchild(answer, child) == -1)
{
err = -1;
goto error_exit;
}
child = 0;
}
skipspace(fp);
ch = fgetc(fp);
} while(ch == ',');
if(ch == ')')
{
answer->label = readlabelandweight(fp, &answer->weight, &err);
if(err)
goto error_exit;
}
else
{
err = -2;
goto error_exit;
}
if(error)
*error = 0;
return answer;
error_exit:
if(child)
killnoder(child);
killnoder(answer);
if(error)
*error = err;
return 0;
}
/*
add a child to a node
Params: parent - parent node
child - child to add
Returns: 0 on success, -1 on fail
*/
int TreeOPE::addchild(NEWICKNODE *parent, NEWICKNODE *child)
{
NEWICKNODE **temp = NULL;
temp = (NEWICKNODE **) realloc(parent->child, (parent->Nchildren + 1) * sizeof(NEWICKNODE *));
// std::cout << "addchild:" << (long) temp << std::endl;//-- WHtest
// if(child->label != '\0')
// std::cout << "cname:" << child->label << std::endl;//--- WHtest
if(!temp)
return -1;
parent->child = temp;
parent->child[parent->Nchildren] = child;
parent->Nchildren++;
return 0;
}
/*
load a leaf node
Params: fp - the input stream
error - return for error
Returns: node object
*/
NEWICKNODE *TreeOPE::loadleaf(FILE *fp, int *error)
{
NEWICKNODE *answer = NULL;
int err;
answer = (NEWICKNODE *) malloc(sizeof(NEWICKNODE));
if(!answer)
{
err = -1;
goto error_exit;
}
answer->Nchildren = 0;
answer->child = 0;
answer->label = readlabelandweight(fp, &answer->weight, &err);
answer->bitstr = NULL;
if(err)
goto error_exit;
return answer;
error_exit:
if(error)
*error = err;
if(answer)
{
free(answer->label);
free(answer);
}
return 0;
}
/*
read label, colon and associated weight
Params: fp - the input stream
weight - return for weight
error - return for error
Returns: the label
Notes: a null label is not an error
*/
char *TreeOPE::readlabelandweight(FILE *fp, double *weight, int *error)
{
char *answer = NULL;
int ch;
*weight = 0;
answer = readlabel(fp);
if(!answer)
{
*error = -1;
return 0;
}
skipspace(fp);
ch = fgetc(fp);
if(ch == ':')
{
if( fscanf(fp, "%lf", weight) != 1)
{
*error = -2;
free(answer);
return 0;
}
}
else
ungetc(ch, fp);
if(*answer == 0)
{
free(answer);
answer = 0;
}
*error = 0;
return answer;
}
/*
readlabel - read a label from stream
Params: fp - the input stream
Returns: allocarted label
Notes: null label is the null string ""
*/
char *TreeOPE::readlabel(FILE *fp)
{
char *answer = NULL;
int ch;
skipspace(fp);
ch = fgetc(fp);
ungetc(ch, fp);
if(ch == '\'')
answer = readquotedlabel(fp);
else
answer = readplainlabel(fp);
return answer;
}
/*
read a quoted label from stream
Params: fp - the input stream
Returns: the label. null string is ""
*/
char *TreeOPE::readquotedlabel(FILE *fp)
{
char *answer = NULL;
char *temp = NULL;
int capacity = 32 * sizeof(char);
int len = 0;
int ch;
answer = (char *) malloc(capacity);
if(!answer)
return 0;
ch = fgetc(fp);
while( (ch = fgetc(fp)) != EOF)
{
if(ch == '\'')
{
ch = fgetc(fp);
if(ch == '\'')
answer[len++] = (char) ch;
else
{
ungetc(ch, fp);
answer[len] = 0;
return answer;
}
}
else
answer[len++] = (char) ch;
if(len == capacity - 1)
{
temp = (char *) realloc(answer, capacity * 2);
if(!temp)
{
free(answer);
return 0;
}
answer = temp;
capacity = capacity * 2;
}
}
answer[len] = 0;
return answer;
}
/*
read aplian (unquoted) label
Params: fp - the open file
Returns: the label, null string is ""
*/
char *TreeOPE::readplainlabel(FILE *fp)
{
char *answer = NULL;
char *temp = NULL;
int len = 0;
int capacity = 32 * sizeof(char);
int ch;
answer = (char *) malloc(capacity);
if(!answer)
return 0;
while( (ch = fgetc(fp)) != EOF)
{
if(isspace(ch) || strchr(" ()[]\':;,", ch))
{
ungetc(ch, fp);
answer[len] = 0;
return answer;
}
if(ch == '_')
ch = '_'; // ssj
answer[len++] = (char) ch;
if(len == capacity - 1)
{
temp = (char *) realloc(answer, capacity * 2);
if(!temp)
{
free(answer);
return 0;
}
answer = temp;
capacity = capacity * 2;
}
}
answer[len] = 0;
return answer;
}
/*
consume space in input stream.
Params: fp - the input stream
*/
void TreeOPE::skipspace(FILE *fp)
{
int ch;
while( (ch = fgetc(fp)) != EOF )
if(!isspace(ch))
{
ungetc(ch, fp);
break;
}
}
/*
strduo implemetation
*/
char *TreeOPE::mystrdup(const char *str)
{
char *answer = NULL;
answer = (char *) malloc(strlen(str) + 1);
if(answer)
strcpy(answer, str);
return answer;
}
/*
count the number of instances of ch in the string
Params: str - serach string
ch - character.
Returns: number of times ch appears in str.
*/
int TreeOPE::mystrcount(const char *str, int ch)
{
int answer = 0;
while(*str)
if(*str++ == ch)
answer++;
return answer;
}
/*
print out a node (test function)
Parmas: node - node to print
indent - indent level
Notes: recursive
*/
void TreeOPE::printnewicknode(NEWICKNODE *node, int indent)
{
int i;
for(i=0;i<indent;i++)
cout << " ";
cout << (long) node << ":";
if(node->label == NULL)
cout << "NULL";
else
cout << node->label;
cout << " : " << node->weight << " : " << node->Nchildren << endl;
for(i=0;i<node->Nchildren;i++)
printnewicknode(node->child[i], indent + 5);
}
void TreeOPE::printnewicktree(const NEWICKTREE *tree)
{
printnewicknode(tree->root, 0);
}
int TreeOPE::newickmain(int argc, char **argv)
{
NEWICKTREE *tree = NULL;
int err;
char *label = NULL;
if(argc != 2)
fprintf(stderr, "Newick tree loader\n");
else
{
tree = loadnewicktree(argv[1], &err);
if(!tree)
{
switch(err)
{
case -1: printf("Out of memory\n"); break;
case -2: printf("parse error\n"); break;
case -3: printf("Can't load file\n"); break;
default:
printf("Error %d\n", err);
}
}
else
{
printf("Loaded\n");
printnewicktree(tree);
}
killnewicktree(tree);
}
label = makenewicklabel("My name is \'Fred()\'");
printf("***%s***\n", label);
free(label);
return 0;
}
void TreeOPE::GetTaxaLabels(NEWICKNODE *node, LabelMap &lm)
{
if (node->Nchildren == 0)
{
std::string temp(node->label);
lm.push(temp);
}
else
for (int i = 0; i<node->Nchildren; i++)
GetTaxaLabels(node->child[i], lm);
};
void TreeOPE::dfs_compute_hash(
NEWICKNODE* startNode,
LabelMap &lm,
HashRFMap &vec_hashrf,
unsigned treeIdx,
unsigned &numBitstr,
unsigned long long m1,
unsigned long long m2,
bool WEIGHTED,
unsigned int NUM_Taxa,
map<unsigned long long, Array<char> *> &hash2bitstr,
int numofbipartions)
{
// If the node is leaf node, just set the place of the taxon name in the bit string to '1'
// push the bit string into stack
/*cout << "output test========" << endl;//---
for(int i = 0; i < 16; i++)
{
Array<char> *arr = new Array<char> (16);
arr->SetBitArray(i+1);
arr->printbits(16);
cout << endl;//---
delete arr;
}*/
int btlength = (int) ((NUM_Taxa + 7) / 8);
if (startNode->Nchildren == 0)
{
// leaf node
// string temp(startNode->label);
// unsigned int idx = lm[temp];
unsigned int idx = atoi(startNode->label) - 1;
// Implicit BPS
// Set the hash value for each leaf node
startNode->hv1 = vec_hashrf._HF.getA1(idx);
startNode->hv2 = vec_hashrf._HF.getA2(idx);
// std::cout << "l:" << startNode->bitstr.get_length() << ", idx:" << idx << std::endl;//--
startNode->bitstr = new Array<char> (btlength);
// for(int i = 0; i < btlength; i++)
// {
// std::cout << "s i:" << i << std::endl;//--
// startNode->bitstr[i] = NULL;
// }
// cout << "ith:" << idx + 1 << endl;//----
if(! startNode->bitstr->SetBitArray(idx + 1))
std::cout << "Warning: Errors in setting bit string" << std::endl;
// startNode->bitstr->printbits(12);//--
// cout << endl;//---
}
else
{
for (int i = 0; i < startNode->Nchildren; ++i)
{
dfs_compute_hash(startNode->child[i], lm, vec_hashrf,
treeIdx, numBitstr, m1, m2,WEIGHTED,NUM_Taxa, hash2bitstr, numofbipartions);
}
// For weighted RF
float dist = 0.0;
if (WEIGHTED)
dist = startNode->weight;
else
dist = 1;
++ numBitstr;
// Implicit BPS
// After an internal node is found, compute hv1 and hv2
unsigned long long temphv1 = 0;
unsigned long long temphv2 = 0;
startNode->bitstr = new Array<char> (btlength);
for (int i = 0; i < startNode->Nchildren; ++i)
{
// cout << "i:" << i << ",child:" << endl;///---
// startNode->child[i]->bitstr->printbits(12);//---
Array<char> bitstrleft = *(startNode->bitstr);
Array<char> bitstrright = *(startNode->child[i]->bitstr);
startNode->bitstr->ORbitOPE(bitstrleft, bitstrright);
// cout << endl;//--
// cout << "results:";
// startNode->bitstr->printbits(12);//----
// cout << endl;//----
unsigned long long t1 = temphv1;
unsigned long long t2 = temphv2;
unsigned long long h1 = startNode->child[i]->hv1;
unsigned long long h2 = startNode->child[i]->hv2;
if (add_of(temphv1, t1, h1))
{
cout << "ERROR : ullong add overflow !\n\n";
cout << "t1 = " << t1 << "h1 = " << h1 << "t1 + h1 = " << t1+h1 << endl;
exit(0);
}
if (add_of(temphv2, t2, h2))
{
cout << "ERROR : ullong add overflow !\n";
cout << "t2 = " << t2 << "h2 = " << h2 << "t2 + h2 = " << t2+h2 << endl;
exit(0);
}
}
// startNode->bitstr->printbits(12);//---
// cout << endl;//---
// Check overflow
unsigned long long temp1 = temphv1 % m1;
unsigned long long temp2 = temphv2 % m2;
startNode->hv1 = temp1;
startNode->hv2 = temp2;
Array<char> *btpt = NULL;
btpt = new Array<char> (*startNode->bitstr);
if(hash2bitstr[startNode->hv2] != NULL)
{
delete hash2bitstr[startNode->hv2];
hash2bitstr[startNode->hv2] = btpt;
}
else
{
hash2bitstr[startNode->hv2] = btpt;
}
// Store bitstring in hash table
if (numBitstr <= numofbipartions)
{
vec_hashrf.hashing_bs_without_type2_nbits(treeIdx, NUM_Taxa, startNode->hv1, startNode->hv2, dist, WEIGHTED);
}
}
};
void TreeOPE::bipart(NEWICKNODE * const startnode, unsigned int &treeIdx,
unsigned long long *matrix_hv,
unsigned int *matrix_treeIdx,
double *matrix_weight, int &idx, int depth, bool isrooted)
{
depth++;
if (isrooted)
{
if(depth > 1 && startnode->Nchildren > 0)
{
matrix_hv[idx] = startnode->hv2;
matrix_treeIdx[idx] = treeIdx+1;
matrix_weight[idx] = startnode->weight;
idx++;
}
}
else
{ if(depth > 2 && startnode->Nchildren > 0)
{
matrix_hv[idx] = startnode->hv2;
matrix_treeIdx[idx] = treeIdx+1;
matrix_weight[idx] = startnode->weight;
idx++;
}
}
for (int i = 0; i < startnode->Nchildren; i++)
if(startnode->child[i]->Nchildren > 0)
bipart(startnode->child[i], treeIdx, matrix_hv, matrix_treeIdx, matrix_weight, idx, depth, isrooted);
};
NEWICKTREE *TreeOPE::parsetree(char *str, int *error, NEWICKTREE *testtree)
{
NEWICKTREE *answer = NULL;
int err;
char *ch = NULL;
int i = 0, idx = 0;
answer = (NEWICKTREE *) malloc(sizeof(NEWICKTREE));
// skip space
char *str_copy = (char *) malloc(sizeof(char) * (strlen(str) + 2));
for(i = 0; i < strlen(str) + 1; i++)
{
if((*(str + i)) != ' ')
{
*(str_copy + idx) = *(str + i);
idx++;
}
if(*(str + i) == '\0')
break;
}
*(str_copy + idx) = '\0';
if (!answer)
{
err = -1;
goto error_exit;
}
ch = str_copy;
if (*ch == '(')
{
ch++;
answer->root = parsenode(&ch, &err);
if (!answer->root || err != 0)
goto error_exit;
}
if(testtree != NULL)
{
cout << "in2-----" << endl;
TreeOPE::printnewicktree(testtree);
}
if (*ch != ';')
{
err = -2; // parse error
goto error_exit;
}
if (error)
*error = 0;
free(str_copy);
// std::cout << "root->child:" << (long) answer->root->child << std::endl;//-- WHtest
return answer;
error_exit:
cout << "Qrong in parsetree()!\n\n";//----
free(str_copy);
killnewicktree(answer);
if (error)
*error = err;
return NULL;
}
NEWICKNODE *TreeOPE::parsenode(char **str, int *error)
{
NEWICKNODE *answer = NULL;
int err;
NEWICKNODE *child = NULL;
answer = (NEWICKNODE *) malloc(sizeof(NEWICKNODE));
if (!answer)
{
err = -1;
goto error_exit;
}
answer->Nchildren = 0;
answer->label = NULL;
answer->child = NULL;
answer->hv1 = 0;
answer->hv2 = 0;
answer->bitstr = NULL;
if (**str == '(')
{
(*str)++;
child = parsenode(str, &err);
if (!child)
goto error_exit;