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#include<string>
#include<vector>
#include<cassert>
#include "ncl/nxsmultiformat.h"
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.
*/
if (argc < 3)
{
std::cerr << "Expecting two arguments: a file name and a TaxSet/CharSetName\n";
return 1;
}
if (argv[1][0] == '-' && argv[1][1] == 'h' && argv[1][2] == '\0' )
{
std::cerr << "Takes two arguments: a file name and a TaxSet/CharSetName\n Prints a NEXUS file that contains only the TaxSet/CharSet indicated. Also suppresses taxa that do not have any unambiguous characters for the indicated charset.\n";
return 0;
}
std::string filename(argv[1]);
std::string setName(argv[2]);
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);
const unsigned totalNumTaxa = taxaBlock->GetNTax();
const unsigned totalNumChars = charBlock->GetNCharTotal();
NxsUnsignedSet taxaToInclude;
NxsUnsignedSet charsToInclude;
unsigned nTaxaInSet = taxaBlock->GetIndexSet(setName, &taxaToInclude);
unsigned nCharInSet = charBlock->GetIndexSet(setName, &charsToInclude);
if (nTaxaInSet + nCharInSet == 0)
{
std::cerr << "Expecting \"" << setName << "\" to refer to a TaxSet or CharSet.\n";
return 3;
}
if (nTaxaInSet == 0)
{
for (unsigned i = 0; i < totalNumTaxa; ++i)
taxaToInclude.insert(i);
nTaxaInSet = taxaToInclude.size();
}
if (nCharInSet == 0)
{
for (unsigned i = 0; i < totalNumChars; ++i)
charsToInclude.insert(i);
nCharInSet = charsToInclude.size();
}
NxsUnsignedSet taxaWithUnambigData;
NxsUnsignedSet::const_iterator taxIter = taxaToInclude.begin();
std::vector<std::string> escapedNamesVec;
size_t maxLabelLen = 0;
std::vector<const NxsDiscreteDatatypeMapper *> mapperVec = charBlock->GetAllDatatypeMappers();
if (mapperVec.size() != 1)
{
std::cerr << "Expecting the characters block to contain one type of data (MIXED datatype is not supported).\n";
return 3;
}
const NxsDiscreteDatatypeMapper *mapper = mapperVec[0];
NxsDiscreteStateCell numStates = (NxsDiscreteStateCell)mapper->GetNumStates();
for (; taxIter != taxaToInclude.end(); ++taxIter)
{
const NxsDiscreteStateRow & row = charBlock->GetDiscreteMatrixRow(*taxIter);
bool hasData = false;
for (NxsUnsignedSet::const_iterator cIt = charsToInclude.begin(); cIt != charsToInclude.end(); ++cIt)
{
NxsDiscreteStateCell c = row[*cIt];
if (c >= 0 && c < numStates)
{
hasData = true;
break;
}
}
if (hasData)
{
taxaWithUnambigData.insert(*taxIter);
NxsString lab = taxaBlock->GetTaxonLabel(*taxIter);
std::string e = NxsString::GetEscaped(lab);
size_t ll = e.length();
if (ll > maxLabelLen)
maxLabelLen = ll;
escapedNamesVec.push_back(e);
}
}
if (taxaWithUnambigData.empty())
{
std::cerr << "No selected taxa had unambiguous data for the selected characters!\n";
return 5;
}
std::ostream & out = std::cout;
out << "#NEXUS\nbegin TAXA;\n Dimensions ntax = " << taxaWithUnambigData.size() << "\n; TaxLabels\n ";
std::vector<std::string>::const_iterator nIt = escapedNamesVec.begin();
for (; nIt != escapedNamesVec.end(); ++nIt)
{
out << ' ' << *nIt;
}
out << ";\nEND;\nBegin CHARACTERS;\n Dimensions nchar = " << nCharInSet << ";\n";
charBlock->WriteFormatCommand(out);
out << "\n Matrix\n";
taxIter = taxaWithUnambigData.begin();
nIt = escapedNamesVec.begin();
for (; nIt != escapedNamesVec.end(); ++nIt, ++taxIter)
{
const std::string & e = *nIt;
std::string s(maxLabelLen + 2 - e.length(), ' ');
out << e << s << ' ';
const NxsDiscreteStateRow & row = charBlock->GetDiscreteMatrixRow(*taxIter);
for (NxsUnsignedSet::const_iterator cIt = charsToInclude.begin(); cIt != charsToInclude.end(); ++cIt)
{
mapper->WriteStateCodeAsNexusString(out, row[*cIt]);
}
out << '\n';
}
out << ";\nEND;\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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