bool constructSafeLabels(const NxsTaxaBlock & tb, std::vector<std::string> * vs, std::set<std::string> & safeLabelSet)
{
if (vs == 0L)
return false;
const unsigned numTaxa = tb.GetNTaxTotal();
bool changed = false;
for (unsigned i = 0; i < numTaxa; ++i)
{
NxsString oldName = tb.GetTaxonLabel(i);
unsigned oldOffset = 0;
unsigned newOffset = 0;
std::string prefix;
for (; newOffset < 10 && oldOffset < oldName.length(); ++oldOffset)
{
char c = oldName[oldOffset];
if ((isgraph(c)) && (strchr("!@#$%^&*.?|()[]{}/\\,;:=*\'\"`-+<>", c) == NULL))
{
if (newOffset == 0 && isdigit(c))
{
prefix.append(1, 't');
newOffset += 1;
}
prefix.append(1, toupper(c));
newOffset += 1;
}
}
std::string newLabel = assignUniqueName(prefix, 10, safeLabelSet);
safeLabelSet.insert(newLabel);
vs->push_back(newLabel);
if (newLabel != oldName)
changed = true;
}
return changed;
}
NxsNexmlTaxa::NxsNexmlTaxa( NxsTaxaBlock nTax ){
vector< Otu* > otus = vector< Otu* >();
for ( unsigned i = 0; i < nTax.GetNTaxTotal(); ++i ){
otus.push_back( new Otu( Glib::ustring( nTax.GetTaxonLabel( i ).c_str() ) ) );
}
this->otus_ = new Otus( otus );
this->block_name_ = "Taxa Block";
//<------data-model-------------------------------->
this->inactive_taxa_ = set< unsigned int >();
this->active_taxa_ = set< unsigned int >();
this->partitions_ = map< string, NxsPartition >();
this->index_sets_ = map< string, NxsUnsignedSet >();
}
bool substituteSafeTaxaLabels(PublicNexusReader &nexusReader, std::string filepath, bool evenTrivial)
{
std::ostream * outStrPtr = 0L;
std::ofstream outStream;
const unsigned nTaxaBlocks = nexusReader.GetNumTaxaBlocks();
bool someChanged = false;
std::set<std::string> safeNameSet;
try
{
for (unsigned t = 0; t < nTaxaBlocks; ++t)
{
NxsTaxaBlock * tb = nexusReader.GetTaxaBlock(t);
std::vector<std::string> safeLabelsVec;
bool changed = constructSafeLabels(*tb, &safeLabelsVec, safeNameSet);
someChanged = someChanged | changed;
if (changed || evenTrivial)
{
if (outStrPtr == 0L)
{
outStream.open(filepath.c_str());
if (!outStream.good())
{
NxsString eMessage;
eMessage << "Could not open the file \"" << filepath << "\"";
throw NxsException(eMessage);
}
outStrPtr = &outStream;
outStream << "#NEXUS\n";
}
tb->WriteAsNexus(*outStrPtr);
std::vector<NxsString> oldNameVec;
const unsigned numTaxa = tb->GetNTaxTotal();
for (unsigned i = 0; i < numTaxa; ++i)
{
NxsString oldName = tb->GetTaxonLabel(i);
oldNameVec.push_back(oldName);
NxsString newName;
newName << safeLabelsVec[i];
tb->ChangeTaxonLabel(i, newName);
}
NxsString title;
title << tb->GetTitle();
NxsString nt;
nt << "Renamed " << title;
tb->SetTitle(nt, false);
tb->WriteAsNexus(*outStrPtr);
// We can't just create a TaxaAssociationBlock instance here,
// and call WriteAsNexus because it first and second taxa block pointers
// would refer to the same instance...
NxsString taTitle;
taTitle << "Renaming " << title;
*outStrPtr << "BEGIN TaxaAssociation;\n Title " << NxsString::GetEscaped(taTitle) << " ;\n";
*outStrPtr << " Taxa " << NxsString::GetEscaped(title) << " , " << NxsString::GetEscaped(nt) << " ;\n";
*outStrPtr << " Associates ";
for (unsigned i = 0; i < numTaxa; ++i)
{
if (i > 0)
*outStrPtr << " ,\n ";
*outStrPtr << NxsString::GetEscaped(oldNameVec[i]) << " / " << NxsString::GetEscaped(safeLabelsVec[i]);
}
*outStrPtr << " ;\nEND;\n" ;
}
}
}
catch (...)
{
if (outStrPtr != 0L)
outStream.close();
throw;
}
if (outStrPtr != 0L)
outStream.close();
return someChanged;
}
