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#include<string>
#include<vector>
#include<cassert>
#include "ncl/nxscxxdiscretematrix.h"
#include "ncl/nxsmultiformat.h"
bool gCullGapped = false;
int main(int argc, char * argv[])
{
/* Usually it is easiest to surround interactions with NCL in a try block
that catches NxsException instances.
Reading files can certainly generate these errors, but even queries
after the parse can result in these exceptions.
*/
std::string filename;
for (int argi = 1; argi < argc; ++argi)
{
if (strlen(argv[argi]) > 1 && argv[argi][0] == '-')
{
if (argv[argi][1] == 'h')
{
std::cerr << "Takes a arguments: The path to a NEXUS file with a single characters block. Optional arguments: -g to cull positions with gaps or missing data\n";
return 0;
}
else if (argv[argi][1] == 'g')
gCullGapped = true;
else
{
std::cerr << "Option flag -" << argv[argi][1] << " is not supported\n.";
return 1;
}
}
else if (filename.empty())
filename.assign(argv[argi]);
else
{
std::cerr << "Expecting one file name as an argument.\n";
return 1;
}
}
if (filename.empty())
{
std::cerr << "Expecting one arguments: a file name\n";
return 1;
}
try {
int blocksToRead = (PublicNexusReader::NEXUS_TAXA_BLOCK_BIT
| PublicNexusReader::NEXUS_CHARACTERS_BLOCK_BIT
| PublicNexusReader::NEXUS_ASSUMPTIONS_BLOCK_BIT
| PublicNexusReader::NEXUS_SETS_BLOCK_BIT
);
MultiFormatReader nexusReader(blocksToRead, NxsReader::WARNINGS_TO_STDERR);
/* See discussion in "Making NCL less strict" */
NxsCharactersBlock * charsB = nexusReader.GetCharactersBlockTemplate();
NxsDataBlock * dataB = nexusReader.GetDataBlockTemplate();
charsB->SetAllowAugmentingOfSequenceSymbols(true);
dataB->SetAllowAugmentingOfSequenceSymbols(true);
/* End of code related to the section on making NCL less strict */
std::cerr << "Reading " << filename << "\n";
try {
nexusReader.DemoteBlocks();
nexusReader.ReadFilepath(filename.c_str(), MultiFormatReader::NEXUS_FORMAT);
}
catch(const NxsException &x)
{
std::cerr << "Error:\n " << x.msg << std::endl;
if (x.line > 0 || x.pos > 0)
std::cerr << "at line " << x.line << ", column (approximately) " << x.col << " (and file position "<< x.pos << ")" << std::endl;
return 2;
}
catch(...)
{
nexusReader.DeleteBlocksFromFactories();
std::cerr << "Exiting with an unknown error" << std::endl;
return 1;
}
const unsigned numTaxaBlocks = nexusReader.GetNumTaxaBlocks();
if (numTaxaBlocks != 1)
{
std::cerr << "Expecting a file with exactly 1 TAXA block, but found " << numTaxaBlocks << " in the file " << filename << ".\n";
return 2;
}
NxsTaxaBlock * taxaBlock = nexusReader.GetTaxaBlock(0);
const unsigned nCharBlocks = nexusReader.GetNumCharactersBlocks(taxaBlock);
if (nCharBlocks != 1)
{
std::cerr << "Expecting a file with exactly 1 CHARACTERS/DATA block, but found " << nCharBlocks << " in the file " << filename << ".\n";
return 3;
}
NCL_COULD_BE_CONST NxsCharactersBlock * charBlock = nexusReader.GetCharactersBlock(taxaBlock, 0);
std::vector<const NxsDiscreteDatatypeMapper *> mappers = charBlock->GetAllDatatypeMappers();
if (mappers.size() != 1)
{
std::cerr << "Expecting an unmixed characters block, but found a matrix with datatype = mixed or a datatype with augmented symbols\n";
return 4;
}
const NxsDiscreteDatatypeMapper * dm = mappers[0];
ScopedTwoDMatrix<NxsCDiscreteStateSet> compressedMatrix;
std::vector<unsigned> patternCounts;
std::vector<double> patternWeights;
bool hasWeights = true;
bool hasIntWeights = true;
std::vector<NxsCharacterPattern> compressedTransposedMatrix;
if (true)
{
std::vector<int> originalIndexToCompressed;
std::vector<std::set<unsigned> > compressedIndexToOriginal;
if (true)
{
NxsCXXDiscreteMatrix cxxMat(*charBlock, false, 0L, false);
hasWeights = cxxMat.hasWeights();
hasIntWeights = cxxMat.hasIntWeights();
NxsCompressDiscreteMatrix(cxxMat, compressedTransposedMatrix, &originalIndexToCompressed, &compressedIndexToOriginal);
}
std::vector<double> * wtsPtr = (hasWeights ? &patternWeights : 0L);
NxsTransposeCompressedMatrix(compressedTransposedMatrix, compressedMatrix, &patternCounts, wtsPtr);
}
NxsCDiscreteStateSet ** matrixAlias = compressedMatrix.GetAlias();
const unsigned ntaxTotal = charBlock->GetNTaxTotal();
const unsigned numPatterns = patternCounts.size();
std::set<unsigned> culledSet;
if (gCullGapped)
{
unsigned ind = 0;
for (std::vector<NxsCharacterPattern>::const_iterator ctmIt = compressedTransposedMatrix.begin();
ctmIt != compressedTransposedMatrix.end();
++ctmIt, ++ind)
{
if (!ctmIt->StateCodesAreNonNegative())
culledSet.insert(ind);
}
}
const unsigned numCulled = culledSet.size();
std::cout << "#NEXUS\nBEGIN DATA;\n\tDimensions ntax = " << ntaxTotal << " nchar = " << numPatterns - numCulled << ";\n\t";
charBlock->WriteFormatCommand(std::cout);
std::cout << "Matrix\n";
const unsigned width = taxaBlock->GetMaxTaxonLabelLength();
for (unsigned i = 0; i < ntaxTotal; i++)
{
const std::string currTaxonLabel = NxsString::GetEscaped(taxaBlock->GetTaxonLabel(i));
std::cout << currTaxonLabel;
unsigned currTaxonLabelLen = (unsigned)currTaxonLabel.size();
unsigned diff = width - currTaxonLabelLen;
for (unsigned k = 0; k < diff+5; k++)
std::cout << ' ';
NxsCDiscreteStateSet * matrixRow = matrixAlias[i];
/*
for (unsigned j = 0; j < numPatterns; ++j)
std::cout << ' ' << (int) matrixRow[j] ;
std::cout << '\n';
*/
for (unsigned j = 0; j < numPatterns; ++j)
{
if (culledSet.find(j) == culledSet.end())
dm->WriteStateCodeAsNexusString(std::cout, matrixRow[j], true);
}
/*
for (unsigned j = 0; j < numPatterns; ++j)
std::cout << ' ' << (int) matrixRow[j];
*/
std::cout << '\n';
}
const char * sp = (hasWeights ? " " : " * ");
unsigned ind = 0;
std::cout << ";\nEND;\nBEGIN ASSUMPTIONS;\n\tWTSET" << sp << " counts ( vector ) =";
for (std::vector<unsigned>::const_iterator cIt = patternCounts.begin(); cIt != patternCounts.end(); ++cIt, ++ind)
{
if (culledSet.find(ind) == culledSet.end())
std::cout << ' ' << *cIt;
}
std::cout << ";\n";
if (hasWeights)
{
std::cout << "\tWTSET * sum_of_weights ( vector ) =";
if (hasIntWeights)
{
for (std::vector<double>::const_iterator cIt = patternWeights.begin(); cIt != patternWeights.end(); ++cIt, ++ind)
{
int w = int(0.01 + *cIt);
if (culledSet.find(ind) == culledSet.end())
std::cout << ' ' << w;
}
}
else
for (std::vector<double>::const_iterator cIt = patternWeights.begin(); cIt != patternWeights.end(); ++cIt, ++ind)
{
if (culledSet.find(ind) == culledSet.end())
std::cout << ' ' << *cIt;
}
std::cout << ";\n";
}
std::cout << "END;\n";
nexusReader.DeleteBlocksFromFactories();
}
catch(const NxsException &x)
{
std::cerr << "Error:\n " << x.msg << std::endl;
if (x.line > 0 || x.pos > 0)
std::cerr << "at line " << x.line << ", column (approximately) " << x.col << " (and file position "<< x.pos << ")" << std::endl;
return 2;
}
catch(...)
{
std::cerr << "Exiting with an unknown error" << std::endl;
return 1;
}
return 0;
}
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