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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* 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. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#include "matree.h"
void MaTree::printBrInfo(ostream& out) {
//to store internal branch lengths
DoubleVector inner;
//to store external branch lengths
DoubleVector outer;
//to store all branch lengths
DoubleVector all;
//convert the tree into split graph (vector of split*)
SplitGraph mySg;
convertSplits(mySg);
//get information about the branch length based on this SplitGraph
for ( SplitGraph::iterator it = mySg.begin(); it != mySg.end(); it++)
{
(*it)->report(cout);
//the split is an external branch
if ( (*it)->countTaxa() == 1 )
outer.push_back((*it)->getWeight());
else //the split is an internal branch
inner.push_back((*it)->getWeight());
//a branch
all.push_back((*it)->getWeight());
}
//sort the three vectors of branch lengths
sort(inner.begin(),inner.end());
sort(outer.begin(),outer.end());
sort(all.begin(),all.end());
//for the statistics
int noInner = inner.size();
int noOuter = outer.size();
int noBr = all.size();
double aveInner = 0;
double aveOuter = 0;
double treeLen = 0;
for ( int i = 0; i < noInner; i++ )
aveInner += inner[i];
for ( int i = 0; i < noOuter; i++ )
aveOuter += outer[i];
for ( int i = 0; i < noBr; i++ )
treeLen += all[i];
aveInner /= (double)noInner;
aveOuter /= (double)noOuter;
out << "minInter maxInter aveInter minExter maxExter aveExter minBr maxBr treeLen noBr" << endl;
out << inner[0] << " " << inner[noInner-1] << " " << aveInner << " " << outer[0] << " " << outer[noOuter-1] << " " << aveOuter << " " << all[0] << " " << all[noBr-1] << " " << treeLen << " " << noBr << endl;
}
void MaTree::comparedTo (MTreeSet &trees, DoubleMatrix &brLenMatrix, IntVector &RFs, DoubleVector &BSDs) {
//for consistency reason
NodeVector taxa;
getTaxa(taxa);
sort(taxa.begin(), taxa.end(), nodenamecmp);
int i;
NodeVector::iterator it;
for (it = taxa.begin(), i = 0; it != taxa.end(); it++, i++)
(*it)->id = i;
//convert the tree into SplitIntMap
SplitIntMap sim;
Split *sp = new Split(leafNum);
convertSplitIntMap(sim, sp, 0);
//output to test
/* for ( SplitIntMap::iterator it = sim.begin(); it != sim.end(); it++ ){
cout << (*it).second << "\t";
(*it).first->report(cout);
}*/
// get the taxa name
vector<string> taxname;
taxname.resize(leafNum);
getTaxaName(taxname);
int noTree = trees.size();
if (noTree == 0 ) return;
RFs.resize(noTree);
BSDs.resize(noTree);
//now check if it is consistent (rooting, same leaf set) with the input trees
MTree *tree = trees.front();
// if (tree->rooted != rooted)
// outError("Rooted and unrooted trees are mixed up");
if (tree->leafNum != leafNum)
outError("Tree has different number of taxa!");
vector<string> taxname1;
taxname1.resize(leafNum);
tree->getTaxaName(taxname1);
vector<string>::iterator strit;
for (strit = taxname1.begin(), i = 0; strit != taxname1.end(); strit++, i++) {
if ((*strit) != taxname[i])
outError("Tree has different taxa names!");
}
MTreeSet::iterator tit;
for ( tit = trees.begin(), i=0; tit != trees.end(); tit++, i++ )
{
DoubleVector brVec(nodeNum,-2);
SplitGraph *sg = new SplitGraph;
SplitIntMap *hs = new SplitIntMap;
(*tit)->convertSplits(taxname,*sg);
// make sure that taxon 0 is included
for (SplitGraph::iterator sit = sg->begin(); sit != sg->end(); sit++) {
if (!(*sit)->containTaxon(0)) (*sit)->invert();
// (*sit)->report(cout);
hs->insertSplit((*sit), 1);
}
int rf = 0;
double bsd = 0;
//go through each split in this tree (not the compared tree)
for ( SplitIntMap::iterator tsit = sim.begin(); tsit != sim.end(); tsit++ )
{
Split* fSplit = hs->findSplit(tsit->first); // check whether the compared tree contains this split
if (fSplit) { //yes
brVec[tsit->second] = fSplit->getWeight(); //update brVec
bsd += (fSplit->getWeight() - tsit->first->getWeight()) * (fSplit->getWeight() - tsit->first->getWeight()); //update bsd
}
else {
brVec[tsit->second] = -1;
rf++;
bsd += tsit->first->getWeight() * tsit->first->getWeight();
}
}
//go through each split in the compared tree
for ( SplitIntMap::iterator fsit = hs->begin(); fsit != hs->end(); fsit++ )
{
Split* fSplit = sim.findSplit(fsit->first);
if (!fSplit) {
rf++;
bsd += fsit->first->getWeight() * fsit->first->getWeight();
}
}
//insert the result
RFs[i] = rf;
BSDs[i] = bsd;
brLenMatrix.push_back(brVec);
delete sg;
delete hs;
}
}
//void MaTree::convertSplitIntMap(SplitIntMap &sim){}
void MaTree::convertSplitIntMap(SplitIntMap &sim, Split *resp, const int taxonID, Node *node, Node *dad) {
if (!node) node = root;
ASSERT(resp->getNTaxa() == leafNum);
ASSERT (taxonID >= 0 && taxonID < leafNum);
bool has_child = false;
FOR_NEIGHBOR_IT(node, dad, it) {
//vector<int> taxa;
//getTaxaID((*it)->node, node, taxa);
Split *sp = new Split(leafNum, (*it)->length);
convertSplitIntMap(sim, sp, taxonID,(*it)->node, node);
*resp += *sp;
if (!sp->containTaxon(taxonID))
sp->invert();
//sg.push_back(sp);
if ( node == root)
sim.insertSplit(sp,node->id);
else
sim.insertSplit(sp,(*it)->node->id);
has_child = true;
}
if (!has_child)
resp->addTaxon(node->id);
}
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