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Trees.cpp
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Trees.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
//##########################################################################
// Trees.cpp
// Member function definitions for class Trees.h
// by whuang gzhou
#ifndef TREES_CPP
#define TREES_CPP
#include "Trees.h"
std::map<String, void ***> StrToDist;
//std::map<String, int ***> StrToIntDist;
//std::map<String, double ***> StrToDoubleDist;
Trees::Trees()
{
String str_matrix("Unweighted RF-distance");
StrToDist["Unweighted RF-distance"] = (void ***) &dist_URF;
str_matrix = (String)("Matching-distance");
StrToDist["Matching-distance"] = (void ***) &dist_match;
str_matrix = (String)("SPR-distance");
StrToDist["SPR-distance"] = (void ***) &dist_SPR;
str_matrix = (String)("Weighted RF-distance");
StrToDist["Weighted RF-distance"] = (void ***) &dist_RF;
str_matrix = (String) "Geodesic-distance";
StrToDist["Geodesic-distance"] = (void ***) &dist_geo;
str_matrix = (String) "File-distance";
StrToDist["File-distance"] = (void ***) &dist_file;
str_matrix = (String) "File-coordinate";
StrToDist["File-coordinate"] = (void ***) &coord_file;
str_matrix = (String)("Covariance Matrix");
StrToDist["Covariance Matrix"] = (void ***) &treecov;
str_matrix = (String)("File-covariance");
StrToDist["File-covariance"] = (void ***) &filecov;
str_matrix = (String) "Affinity-Reciprocal-URF";
StrToDist["Affinity-Reciprocal-URF"] = (void ***) &affi_Recip_URF;
str_matrix = (String) "Affinity-Reciprocal-RF";
StrToDist["Affinity-Reciprocal-RF"] = (void ***) &affi_Recip_RF;
str_matrix = (String) "Affinity-Reciprocal-match";
StrToDist["Affinity-Reciprocal-match"] = (void ***) &affi_Recip_match;
str_matrix = (String) "Affinity-Reciprocal-SPR";
StrToDist["Affinity-Reciprocal-SPR"] = (void ***) &affi_Recip_SPR;
str_matrix = (String) "Affinity-Reciprocal-geodesic";
StrToDist["Affinity-Reciprocal-geodesic"] = (void ***) &affi_Recip_geo;
str_matrix = (String) "Affinity-Reciprocal-filedist";
StrToDist["Affinity-Reciprocal-filedist"] = (void ***) &affi_Recip_file;
str_matrix = (String) "Affinity-Exponential-URF";
StrToDist["Affinity-Exponential-URF"] = (void ***) &affi_Exp_URF;
str_matrix = (String) "Affinity-Exponential-RF";
StrToDist["Affinity-Exponential-RF"] = (void ***) &affi_Exp_RF;
str_matrix = (String) "Affinity-Exponential-match";
StrToDist["Affinity-Exponential-match"] = (void ***) &affi_Exp_match;
str_matrix = (String) "Affinity-Exponential-SPR";
StrToDist["Affinity-Exponential-SPR"] = (void ***) &affi_Exp_SPR;
str_matrix = (String) "Affinity-Exponential-geodesic";
StrToDist["Affinity-Exponential-geodesic"] = (void ***) &affi_Exp_geo;
str_matrix = (String) "Affinity-Exponential-filedist";
StrToDist["Affinity-Exponential-filedist"] = (void ***) &affi_Exp_file;
str_matrix = (String)("File-affinity");
StrToDist["File-affinity"] = (void ***) &fileaffinity;
isrooted = true;
isweighted = false;
treesfilename = "";
n_trees = 0;
treeset = NULL;
// sparse representation of bipartition matrix
sbipartmatrix = NULL;
numberofbipartition = NULL;
bipart_count = NULL;
// bipartcovariance = NULL;
treecov_size = 0;
treecov = NULL;
filecov_size = 0;
filecov = NULL;
dist_URF = NULL;
dist_RF = NULL;
dist_match = NULL;
dist_SPR = NULL;
dist_geo = NULL;
affi_Recip_URF = NULL;
affi_Recip_RF = NULL;
affi_Recip_match = NULL;
affi_Recip_SPR = NULL;
affi_Recip_geo = NULL;
affi_Exp_URF = NULL;
affi_Exp_RF = NULL;
affi_Exp_match = NULL;
affi_Exp_SPR = NULL;
affi_Exp_geo = NULL;
affinityfile_size = 0;
fileaffinity = NULL;
file_distsize = 0;
dist_file = NULL;
affi_Recip_file = NULL;
affi_Exp_file = NULL;
file_coordinatesize = 0;
file_coordinatedim = 0;
coord_file = NULL;
covariance_freeid_size = 0;
covariance_freeid = NULL;
covariance_nonfree_id_size = 0;
covariance_nonfree_id = NULL;
com_info = NULL;
com_info_col = 0;
// bipartFreq = NULL;
// bipartFreqIdx = NULL;
}
void Trees::destructor()
{
deletetrees();
deleteConsensustree();
delete [] numberofbipartition;
numberofbipartition = NULL;
delete [] bipart_count;
bipart_count = NULL;
vec_hashrf.hashrfmap_clear();
delete_double_array(treecov, treecov_size);
delete_double_array(filecov, filecov_size);
delete_double_array(dist_URF, n_trees);
delete_double_array(dist_RF, n_trees);
delete_double_array(dist_match, n_trees);
delete_double_array(dist_SPR, n_trees);
delete_double_array(dist_geo, n_trees);
delete_double_array(affi_Recip_URF, n_trees);
delete_double_array(affi_Recip_RF, n_trees);
delete_double_array(affi_Recip_match, n_trees);
delete_double_array(affi_Recip_SPR, n_trees);
delete_double_array(affi_Recip_geo, n_trees);
delete_double_array(affi_Exp_URF, n_trees);
delete_double_array(affi_Exp_RF, n_trees);
delete_double_array(affi_Exp_match, n_trees);
delete_double_array(affi_Exp_SPR, n_trees);
delete_double_array(affi_Exp_geo, n_trees);
delete_double_array(coord_file, file_coordinatesize);
delete_double_array(dist_file, file_distsize);
delete_double_array(affi_Recip_file, file_distsize);
delete_double_array(affi_Exp_file, file_distsize);
delete_double_array(fileaffinity, affinityfile_size);
delete_double_array(com_info, covariance_nonfree_id_size + 4);
delete sbipartmatrix;
sbipartmatrix = NULL;
// delete_double_array(bipartFreq, splits);
// delete [] bipartFreqIdx;
// bipartFreqIdx = NULL;
for(std::map<unsigned long long, Array<char> *>::iterator itr = hash2bitstr.begin(); itr != hash2bitstr.end(); itr++)
{
delete itr->second;
itr->second = NULL;
}
hash2bitstr.clear(); //
// set to be default
isrooted = true;
isweighted = false;
treesfilename = "";
n_trees = 0;
treecov_size = 0;
filecov_size = 0;
file_distsize = 0;
file_coordinatesize = 0;
file_coordinatedim = 0;
affinityfile_size = 0;
delete [] covariance_freeid;
covariance_freeid = NULL;
covariance_freeid_size = 0;
delete [] covariance_nonfree_id;
covariance_nonfree_id = NULL;
covariance_nonfree_id_size = 0;
}
void Trees::deletetrees()
{
//cout << "set address:" << (long) treeset << endl;//----
if(treeset != NULL)
{
for(unsigned int i = 0; i < n_trees; i++)
{
//cout << "i-th tree:" << i << ", address:" << (long) treeset[i] << endl;//----
if(treeset[i] != NULL)
{
TreeOPE::killnewicktree(treeset[i]);
treeset[i] = NULL;
}
}
delete [] treeset;
treeset = NULL;
}
// if(consensustrees.is_empty() == 0)
// {
// for(unsigned int i = 0; i < consensustrees.get_length(); i++)
// {
// TreeOPE::killnewicktree(consensustrees[i]);
// consensustrees[i] = NULL;
// }
// consensustrees.resize(0);
// }
}
void Trees::deleteConsensustree()
{
if(consensustrees.is_empty() == 0)
{
for(unsigned int i = 0; i < consensustrees.get_length(); i++)
{
TreeOPE::killnewicktree(consensustrees[i]);
consensustrees[i] = NULL;
}
consensustrees.resize(0);
}
}
void Trees::deleteBipartitionMatrix()
{
if(treeset != NULL)
{
for(unsigned int i = 0; i < n_trees; i++)
{
if(treeset[i] != NULL)
{
TreeOPE::killnewicktreeBitstr(treeset[i]);
}
}
}
delete [] bipart_count;
bipart_count = NULL;
vec_hashrf.hashrfmap_clear();
delete sbipartmatrix;
sbipartmatrix = NULL;
for(std::map<unsigned long long, Array<char> *>::iterator itr = hash2bitstr.begin(); itr != hash2bitstr.end(); itr++)
{
delete itr->second;
itr->second = NULL;
}
hash2bitstr.clear(); //
}
Trees::~Trees()
{
destructor();
}
template<class T>
void Trees::delete_double_array(T ** (&arr), int n)
{
if(arr != NULL)
{
for(int i = 0; i < n; i++)
{
delete [] arr[i];
}
delete [] arr;
arr = NULL;
}
}
template<class T>
void Trees::delete_double_array(T *** arr, int n)
{
if((*arr) != NULL)
{
for(int i = 0; i < n; i++)
{
delete [] (*arr)[i];
}
delete [] (*arr);
(*arr) = NULL;
}
}
void Trees::delete_matrix(String str_matrix)
{
cout << "Deleting: " << str_matrix << "\n\n";
if(str_matrix == (String)"Bipartition Matrix")
{
deleteBipartitionMatrix();
} else if(str_matrix == (String)"Covariance Matrix")
delete_double_array((double ***) StrToDist[str_matrix], treecov_size);
else if(str_matrix == (String)"File-covariance")
delete_double_array((double ***) StrToDist[str_matrix], filecov_size);
else if(str_matrix == (String)"File-distance" || str_matrix == (String)"Affinity-filedist")
delete_double_array((double ***) StrToDist[str_matrix], file_distsize);
else if(str_matrix == (String)"File-coordinate")
delete_double_array((double ***) StrToDist[str_matrix], file_coordinatesize);
else if(str_matrix == (String)"File-affinity")
delete_double_array((double ***) StrToDist[str_matrix], affinityfile_size);
else if(str_matrix == (String)"Matching-distance" || str_matrix == (String)"SPR-distance")
delete_double_array((int ***) StrToDist[str_matrix], n_trees);
else
delete_double_array((double ***) StrToDist[str_matrix], n_trees);
cout << "Done!!\n\n";
}
string Trees::make_DISToutput_name(String str_matrix)
{
String result = treesfilename.c_str();
result = result.before('.');
result += "_";
if(treesfilename != "")
{
if(isrooted)
result += "rooted_";
else
result += "unrooted_";
if(isweighted)
result += "weighted_";
else
result += "unweighted_";
}
if(str_matrix == (String) "Unweighted RF-distance")
result += "RF-distance";
else if(str_matrix == (String) "Weighted RF-distance")
result += "RF-distance";
else if(str_matrix == (String) "Covariance Matrix")
result += "Covariance_Matrix";
else
{
result += (char *) str_matrix;
}
result += ".out";
return (char *) result;
}
template<class T>
void Trees::print_double_array(T *** arr, int n, string outfile)
{
ofstream fout;
if (outfile != "")
fout.open(outfile.c_str());
if((*arr) != NULL)
{
fout << setw(5) << "tree" << ' ';
for (int i = 0, c = 1; i < n; i++, c++)
fout << setw(5) << c << "\t" << ' ';
fout << endl;
for (int i = 0, c = 1; i < n; i++, c++)
{
fout << setw(5) << c << "\t" << ' ';
for (int j = 0; j <= i; j++)
{
fout << setw(5) << (*arr)[i][j] << "\t" << ' ';
}
fout << endl;
}
}
if (outfile != "")
fout.close();
}
template<class T>
void Trees::print_coordinate_matrix(T *** arr, int n, int m, string outfile)
{
ofstream fout;
if (outfile != "")
fout.open(outfile.c_str());
if((*arr) != NULL)
{
for(int i = 0; i < n; i++)
{
for(int j = 0; j < m; j++)
{
fout << setw(5) << (*arr)[i][j] << "\t";
}
fout << endl;
}
}
if (outfile != "")
fout.close();
}
void Trees::print_matrix(String str_matrix, string outfile)
{
if (str_matrix == (String)"Covariance Matrix")
print_double_array((double ***) StrToDist[str_matrix], treecov_size, outfile);
else if(str_matrix == (String)"File-covariance")
print_double_array((double ***) StrToDist[str_matrix], filecov_size, outfile);
else if(str_matrix == (String)"Matching-distance" || str_matrix == (String)"SPR-distance")
print_double_array((int ***) StrToDist[str_matrix], n_trees, outfile);
else if(str_matrix == (String)"File-distance" || str_matrix == (String)"Affinity-filedist")
print_double_array((double ***) StrToDist[str_matrix], file_distsize, outfile);
else if(str_matrix == (String)"File-coordinate")
print_coordinate_matrix((double ***) StrToDist[str_matrix], file_coordinatesize, file_coordinatedim, outfile);
else if(str_matrix == (String)"File-affinity")
print_double_array((double ***) StrToDist[str_matrix], affinityfile_size, outfile);
else
{
print_double_array((double ***) StrToDist[str_matrix], n_trees, outfile);
}
}
void Trees::initialTrees(string fname)
{
treesfilename = fname;
treeformat = CheckTreeFormat();
n_trees = 0;
if(treeformat == NEXUS)
{
leaveslabelsmaps.clear();
ifstream treefile(treesfilename.c_str(), ios::binary);
string line;
int num_line,Line_taxa_begin,count;
int a;
string b;
char namebuff[256];
while (!treefile.eof())
{
for (num_line = 0; getline(treefile, line); num_line++)
{
if (line.find_first_not_of("\t\n ") == string::npos) continue;
if (line.find("Translate", 0) != string::npos || line.find("TRANSLATE", 0) != string::npos || line.find("translate", 0) != string::npos)
{
Line_taxa_begin = num_line;
for (count = Line_taxa_begin + 1; getline(treefile, line); count++)
{
if (line.find_first_not_of("\t\n ") == string::npos) continue;
if ((line.find(";", 0) == string::npos) || (line.find("(") == string::npos
&& find_if(line.begin(), line.end(), (int(*)(int))std::isdigit) != line.end()))
{
istringstream iss(line);
iss >> a >> b;
b.erase(remove(b.begin(),b.end(),','),b.end());
b.erase(remove(b.begin(),b.end(),';'),b.end());
if(b.length() > 255)
{
cout << "The longest name only can include 255 chars!\n\n";
exit(0);
}
strcpy(namebuff, b.c_str());
namebuff[b.length()] = NULL;
leaveslabelsmaps.push(string (namebuff));
}
else if(line.find("(",0) != string::npos)
{
n_trees++;
}
}
}
}
}
treefile.close();
} else
if(treeformat == NEWICK)
{
// ofstream outNexus;
FILE *fp = NULL;
string line, s;
fp = fopen(treesfilename.c_str(), "r");
// unsigned int Num_tree = 0;
int err, count;
NEWICKTREE *newickTree = NULL;
ifstream treeFile(treesfilename.c_str(), ios::out);
if (treeFile)
{
while (getline(treeFile, line) && (line.find_first_not_of("\t\n ") != string::npos))
{
n_trees ++;
}
}
newickTree = TreeOPE::loadnewicktree2(fp, &err);
if (!newickTree)
{
switch (err)
{
case -1:
printf("Out of memory \n");
break;
case -2:
printf("Pase error \n");
break;
case -3:
printf("Cannot load file \n");
break;
default:
printf("Error %d\n", err);
}
}
try {
leaveslabelsmaps.clear();
TreeOPE::GetTaxaLabels(newickTree->root, leaveslabelsmaps);
}
catch (LabelMap::AlreadyPushedEx ex) {
cerr << "Error : The label ' " << ex.label << "' appeared twice!\n\n";
exit(2);
}
TreeOPE::killnewicktree(newickTree);
fclose(fp);
treeFile.close();
} else
{
cout << "Warning: Unregonized file format!\n\n";
}
selected_trees.resize(n_trees + 1);
selected_trees[0] = -1;
}
void Trees::Settreeroottype(bool isrt)
{
isrooted = isrt;
}
void Trees::Settreeweighttype(bool iswt)
{
isweighted = iswt;
}
Treefileformat Trees::CheckTreeFormat()
{
int num_line;
string line,first_line;
ifstream treefile(treesfilename.c_str(), ios::binary);
Treefileformat format;
if (!treefile)
{
cout << "Unable to open the file!\n\n";
exit(0);
}
while (!treefile.eof())
{
for (num_line = 0; getline(treefile, line); num_line++)
if (num_line == 0)
{
istringstream iss(line);
iss >> first_line;
if (first_line.compare("#NEXUS") == 0)
format = NEXUS;
else
format = NEWICK;
}
}
treefile.close();
return format;
};
void Trees::ReadTrees() // newick nexus
{
deletetrees();
treeset = new NEWICKTREE *[n_trees];
int error;
// fixed a leaf to be one side of the root
std::string leafroot = "1";//--leaveslabelsmaps.name(0); // normalized unrooted tree by WH
NEWICKNODE *lrpt = NULL; // normalized unrooted tree by WH
int indexchild = -1; // normalized unrooted tree by WH
if(treeformat == NEXUS)
{
ifstream treefile(treesfilename.c_str(), ios::binary);
string line;
int num_line, Line_taxa_begin, count;
int treesetidx = 0;
while (!treefile.eof())
{
for (num_line = 0; getline(treefile, line); num_line++)
{
if (line.find_first_not_of("\t\n ") == string::npos) continue;
if (line.find("Translate", 0) != string::npos || line.find("TRANSLATE", 0) != string::npos || line.find("translate", 0) != string::npos)
{
Line_taxa_begin = num_line;
for (count = Line_taxa_begin + 1; getline(treefile, line); count++)
{
if (line.find_first_not_of("\t\n ") == string::npos) continue;
if(line.find("(",0) != string::npos)
{
size_t tstart = line.find_first_of("(", 0);
if(line.find(":", 0) != string::npos)
{
char *btree = new char[line.substr(tstart).length() + 1];
strcpy(btree, line.substr(tstart).c_str());
btree[line.substr(tstart).length()] = NULL;
treeset[treesetidx] = TreeOPE::parsetree(btree, &error, NULL);
delete btree;
}
else
{
//----------- make it weighted string ----------------
char *btree = new char[2 * line.substr(tstart).length() + 1];
int idx = 0;
// const char *stree = line.substr(tstart).c_str(); // For Some reason this did not work for some file types in CLV (MAC)
char *stree = new char[line.substr(tstart).length() + 1];
strcpy(stree, line.substr(tstart).c_str());
stree[line.substr(tstart).length()] = '\0';
for(int i = 0; i < line.substr(tstart).length(); i++)
{
if((stree[i] == ')' || stree[i] == ',') && i < line.substr(tstart).length() - 1)
{
btree[idx++] = ':';
btree[idx++] = '1';
}
btree[idx++] = stree[i];
}
btree[idx] = '\0';
//-------------work but not good way-------------
treeset[treesetidx] = TreeOPE::parsetree(btree, &error, NULL);
delete btree;
}
if(!isrooted)
{
lrpt = TreeOPE::findleaf(leafroot, treeset[treesetidx]->root, NULL, &indexchild); // normalized unrooted tree by WH
TreeOPE::normailzedTree(lrpt, treeset[treesetidx], indexchild); // normalized unrooted tree by WH
}
treesetidx++;
}
}
}
}
}
treefile.close();
} else
if(treeformat == NEWICK)
{
string s;
// fp = fopen(fileNames.c_str(), "r");
int count = 0;
ifstream treeFile(treesfilename.c_str(), ios::out);
int NN = 10000;
char *gzbuff = (char*)malloc(NN);
treeFile.clear();
treeFile.seekg(0);
while (getline(treeFile, s) && (s.find_first_not_of("\t\n ") != string::npos))
{
// std::cout << "count:" << count << std::endl;//-- WHtest
gzbuff[0] = NULL;
if(s.find(":", 0) != string::npos)
{
char *btree = new char[s.length() + 1];
strcpy(btree, s.c_str());
btree[s.length()] = NULL;
treeset[count] = TreeOPE::parsetree(btree, &error, NULL);
delete btree;
}
else
{
//----------- make it weighted string ----------------
char *btree = new char[2 * s.length() + 1];
int idx = 0;
const char *stree = s.c_str();
for(int i = 0; i < s.length(); i++)
{
if((stree[i] == ')' || stree[i] == ',') && i < s.length() - 1)
{
btree[idx++] = ':';
btree[idx++] = '1';
}
btree[idx++] = stree[i];
}
btree[idx] = NULL;
//-------------work but not good way-------------
treeset[count] = TreeOPE::parsetree(btree, &error, NULL);
delete btree;
}
// cout << count << ":!!" << btree << "!!" << endl;//---
TreeOPE::Label_strint((treeset[count])->root, leaveslabelsmaps);
if(!isrooted)
{
lrpt = TreeOPE::findleaf(leafroot, treeset[count]->root, NULL, &indexchild); // normalized unrooted tree by WH
TreeOPE::normailzedTree(lrpt, treeset[count], indexchild); // normalized unrooted tree by WH
}
count++;
}
free(gzbuff);
treeFile.close();
}
}
void Trees::compute_numofbipart()
{
if(numberofbipartition != NULL)
delete [] numberofbipartition;
numberofbipartition = new int [n_trees];
for (int i = 0; i < n_trees; i++)
{
numberofbipartition[i] = TreeOPE::sumofdegree(treeset[i]->root, isrooted);
numberofbipartition[i] = numberofbipartition[i]/2-leaveslabelsmaps.size();
}
}
void Trees::WriteTrees(string &outfile, Treefileformat tf) // newick nexus
{
if(tf == NEWICK)
{
ofstream outNewick;
int NN = 10000;
char *gzbuff = (char*) malloc(NN);
outNewick.open(outfile.c_str());
char **taxa_str = new char*[leaveslabelsmaps.size()];
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
string temp = leaveslabelsmaps.name(i);
taxa_str[i] = new char[temp.length()+1];
for (int j = 0; j < temp.length(); j++)
taxa_str[i][j] = temp[j];
taxa_str[i][temp.length()] = '\0';
}
for(int i = 0; i < n_trees; i++)
{
gzbuff[0] = NULL;
TreeOPE::printTree_new(treeset[i]->root, taxa_str, gzbuff, 0, NN);
outNewick << gzbuff << ";" << endl;
}
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
delete[] taxa_str[i];
taxa_str[i] = NULL;
}
delete[] taxa_str;
taxa_str = NULL;
free(gzbuff);
outNewick.close();
} else
if(tf == NEXUS)
{
ofstream outNexus;
outNexus.open(outfile.c_str());
outNexus << "#NEXUS" << endl;
outNexus << "BEGIN TAXA;" << endl;
outNexus << " dimensions ntax=" << leaveslabelsmaps.size() << ";" << endl;
outNexus << " taxlabels ";
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
outNexus<< leaveslabelsmaps.name(i) <<" ";
}
outNexus << ";" << endl;
outNexus << "END;" << endl;
outNexus << "BEGIN TREES;" << endl;
outNexus << " dimension ntree=" << n_trees << ";" << endl;
outNexus << " " << "Translate" << endl;
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
if (i < leaveslabelsmaps.size() - 1)
outNexus << " " << i+1 << " " << leaveslabelsmaps.name(i) << "," << endl;
else
outNexus << " " << i+1 << " " << leaveslabelsmaps.name(i) << endl;
}
outNexus << " ;" << endl;
char **taxa_str = new char*[leaveslabelsmaps.size()];
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
string temp = leaveslabelsmaps.name(i);
taxa_str[i] = new char[temp.length()+1];
for (int j = 0; j < temp.length(); j++)
taxa_str[i][j] = temp[j];
taxa_str[i][temp.length()] = NULL;
}
int NN = 10000;
char *gzbuff = (char*)malloc(NN);
for(int count = 0; count < n_trees; count++)
{
gzbuff[0] = NULL;
TreeOPE::printTree_nex(treeset[count]->root, leaveslabelsmaps.size(), gzbuff, 0, NN);
outNexus << "TREE tree " << count << " = " << gzbuff << ";" << endl;
}
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
delete[] taxa_str[i];
taxa_str[i] = NULL;
}
delete[] taxa_str;
taxa_str = NULL;
free(gzbuff);
outNexus << "End;" << endl;
outNexus.close();
}
}
void Trees::WriteConsensusTree(string &outfile, Treefileformat tf)
{
if(tf == NEWICK)
{
ofstream outNewick;
int NN = 10000;
char *gzbuff = (char*) malloc(NN);
outNewick.open(outfile.c_str());
char **taxa_str = new char*[leaveslabelsmaps.size()];
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
string temp = leaveslabelsmaps.name(i);
taxa_str[i] = new char[temp.length()+1];
for (int j = 0; j < temp.length(); j++)
taxa_str[i][j] = temp[j];
taxa_str[i][temp.length()] = '\0';
}
for(int i = 0; i < consensustrees.get_length(); i++)
{
gzbuff[0] = NULL;
TreeOPE::printTree_new(consensustrees[i]->root, taxa_str, gzbuff, 0, NN);
outNewick << gzbuff << ";" << endl;
}
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
delete[] taxa_str[i];
taxa_str[i] = NULL;
}
delete[] taxa_str;
taxa_str = NULL;
free(gzbuff);
outNewick.close();
} else
if(tf == NEXUS)
{
ofstream outNexus;
outNexus.open(outfile.c_str());
outNexus << "#NEXUS" << endl;
outNexus << "BEGIN TAXA;" << endl;
outNexus << " dimensions ntax=" << leaveslabelsmaps.size() << ";" << endl;
outNexus << " taxlabels ";
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
outNexus<< leaveslabelsmaps.name(i) <<" ";
}
outNexus << ";" << endl;
outNexus << "END;" << endl;
outNexus << "BEGIN TREES;" << endl;
outNexus << " dimension ntree=" << n_trees << ";" << endl;
outNexus << " " << "Translate" << endl;
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
if (i < leaveslabelsmaps.size() - 1)
outNexus << " " << i+1 << " " << leaveslabelsmaps.name(i) << "," << endl;
else
outNexus << " " << i+1 << " " << leaveslabelsmaps.name(i) << endl;
}
outNexus << " ;" << endl;
char **taxa_str = new char*[leaveslabelsmaps.size()];
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
string temp = leaveslabelsmaps.name(i);
taxa_str[i] = new char[temp.length()+1];
for (int j = 0; j < temp.length(); j++)
taxa_str[i][j] = temp[j];
taxa_str[i][temp.length()] = NULL;
}
int NN = 10000;
char *gzbuff = (char*)malloc(NN);
for(int count = 0; count < consensustrees.get_length(); count++)
{
gzbuff[0] = NULL;
TreeOPE::printTree_nex(consensustrees[count]->root, leaveslabelsmaps.size(), gzbuff, 0, NN);
outNexus << "TREE tree " << count << " = " << gzbuff << ";" << endl;
}
for (int i = 0; i < leaveslabelsmaps.size(); i++)
{
delete[] taxa_str[i];
taxa_str[i] = NULL;
}
delete[] taxa_str;
taxa_str = NULL;
free(gzbuff);
outNexus << "End;" << endl;
outNexus.close();
}
}
string Trees::WriteTreesFilename(string fname, string type)
{
string result;
string rawname = fname.substr(0, fname.find_last_of("."));
result = rawname;
result += "_";
if(isrooted)
result += "rooted_";
else
result += "unrooted_";
if (isweighted)
result += "weighted_";
else
result += "unweighted_";
type.erase(remove( type.begin(), type.end(), ' ' ), type.end() );
result += type;
result += ".out";
return result;
}
string Trees::WriteConsensusTreeFilename(string fname, string type)
{
string result;
string rawname = fname.substr(0, fname.find_last_of("."));
result = rawname;
result += "_";
if(isrooted)
result += "rooted_";
else
result += "unrooted_";
if (isweighted)
result += "weighted_";
else
result += "unweighted_";
result += "Consensus_tree_";
type.erase(remove( type.begin(), type.end(), ' ' ), type.end() );
result += type;
result += ".out";
return result;
}
void Trees::Printf(int *idx, int length)
{
for(int i = 0; i < length; i++)
{
TreeOPE::printnewicktree(treeset[idx[i]]);
cout << endl;
}
}
void Trees::Compute_Hash()
{