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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "RootedClusterTree.h"
#include "../../general/OutputFile.h"
#include "UPGMAAlgorithm.h"
#include "RootedTreeOutput.h"
//#include "../RandomGenerator.h"
namespace clustalw
{
auto_ptr<AlignmentSteps> RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr,
int seq1, int nSeqs, string& phylipName)
{
OutputFile phylipPhyTreeFile;
auto_ptr<AlignmentSteps> progSteps;
try
{
// Test to see if the inputs are valid
if(seq1 < 1 || nSeqs < 1)
{
cerr << "Invalid inputs into treeFromDistMatrix \n"
<< "seq1 = " << seq1 << " nSeqs = " << nSeqs << "\n"
<< "Need to end program!\n";
exit(1);
return progSteps;
}
float dist;
string path;
verbose = false;
firstSeq = seq1;
lastSeq = firstSeq + nSeqs - 1;
SeqInfo info;
info.firstSeq = firstSeq;
info.lastSeq = lastSeq;
info.numSeqs = nSeqs;
utilityObject->getPath(userParameters->getSeqName(), &path);
if(nSeqs >= 2)
{
string name = phylipName;
if(!phylipPhyTreeFile.openFile(&name,
"\nEnter name for new GUIDE TREE file ", &path, "dnd",
"Guide tree"))
{
return progSteps;
}
phylipName = name;
}
else
{
return progSteps;
}
RootedTreeOutput outputTree(&info);
ofstream* ptrToFile = phylipPhyTreeFile.getPtrToFile();
if (nSeqs == 2)
{
dist = (*distMat)(firstSeq, firstSeq + 1) / 2.0;
if(ptrToFile->is_open())
{
(*ptrToFile) << "(" << alignPtr->getName(firstSeq) << ":"
<< setprecision(5)
<< dist << "," << alignPtr->getName(firstSeq + 1) << ":"
<< setprecision(5) << dist <<");\n";
}
progSteps.reset(new AlignmentSteps);
vector<int> groups;
groups.resize(nSeqs + 1, 0);
groups[1] = 1;
groups[2] = 2;
}
else
{
UPGMAAlgorithm clusAlgorithm;
progSteps = clusAlgorithm.generateTree(phyloTree, distMat, &info, false);
outputTree.printPhylipTree(phyloTree, ptrToFile, alignPtr, distMat);
}
return progSteps;
}
catch(const exception &ex)
{
cerr << "ERROR: Error has occurred in treeFromDistMatrix. "
<< "Need to terminate program.\n"
<< ex.what();
exit(1);
}
catch(...)
{
cerr << "ERROR: Error has occurred in treeFromDistMatrix. "
<< "Need to terminate program.\n";
exit(1);
}
}
void RootedClusterTree::treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr)
{
try
{
OutputFile phylipPhyTreeFile;
OutputFile clustalPhyTreeFile;
OutputFile distancesPhyTreeFile;
OutputFile nexusPhyTreeFile;
OutputFile pimFile;
RootedGuideTree phyloTree;
string path;
int j;
int overspill = 0;
int totalDists;
numSeqs = alignPtr->getNumSeqs(); // NOTE class variable
/**
* Check if numSeqs is ok
*/
if(!checkIfConditionsMet(numSeqs, 2))
{
return;
}
firstSeq = 1;
lastSeq = numSeqs;
// The SeqInfo struct is passed to reduce the number of parameters passed!
SeqInfo info;
info.firstSeq = firstSeq;
info.lastSeq = lastSeq;
info.numSeqs = numSeqs;
RootedTreeOutput outputTree(&info); // No bootstrap!
utilityObject->getPath(userParameters->getSeqName(), &path);
/**
* Open the required output files.
*/
if(!openFilesForTreeFromAlignment(&clustalPhyTreeFile, &phylipPhyTreeFile,
&distancesPhyTreeFile, &nexusPhyTreeFile, &pimFile, treeNames, &path))
{
return; // Problem opeing one of the files, cannot continue!
}
int _lenFirstSeq = alignPtr->getSeqLength(firstSeq);
bootPositions.clear();
bootPositions.resize(_lenFirstSeq + 2);
for (j = 1; j <= _lenFirstSeq; ++j)
{
bootPositions[j] = j;
}
/**
* Calculate quickDist and overspill
*/
overspill = calcQuickDistMatForAll(clustalPhyTreeFile.getPtrToFile(),
phylipPhyTreeFile.getPtrToFile(), nexusPhyTreeFile.getPtrToFile(),
pimFile.getPtrToFile(), distancesPhyTreeFile.getPtrToFile(), alignPtr);
// check if any distances overflowed the distance corrections
if (overspill > 0)
{
totalDists = (numSeqs *(numSeqs - 1)) / 2;
overspillMessage(overspill, totalDists);
}
if (userParameters->getOutputTreeClustal())
{
verbose = true;
}
// Turn on file output
if (userParameters->getOutputTreeClustal() ||
userParameters->getOutputTreePhylip()
|| userParameters->getOutputTreeNexus())
{
UPGMAAlgorithm clusAlgorithm;
clusAlgorithm.setVerbose(true);
clusAlgorithm.generateTree(&phyloTree, quickDistMat.get(), &info, false,
clustalPhyTreeFile.getPtrToFile());
clusAlgorithm.setVerbose(false);
}
if (userParameters->getOutputTreePhylip())
{
outputTree.printPhylipTree(&phyloTree, phylipPhyTreeFile.getPtrToFile(), alignPtr,
quickDistMat.get());
}
if (userParameters->getOutputTreeNexus())
{
outputTree.printNexusTree(&phyloTree, nexusPhyTreeFile.getPtrToFile(), alignPtr,
quickDistMat.get());
}
/** Free up resources!!!!! */
treeGaps.clear();
bootPositions.clear();
}
catch(const exception& ex)
{
cerr << ex.what() << endl;
utilityObject->error("Terminating program. Cannot continue\n");
exit(1);
}
}
}
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