void NxsTaxaBlockSurrogate::ResetSurrogate()
{
if (ownsTaxaBlock)
{
if (!passedRefOfOwnedBlock)
{
if (taxa != NULL && nxsReader != NULL)
{
NxsTaxaBlockFactory * factory = nxsReader->GetTaxaBlockFactory();
if (factory)
{
factory->BlockError(taxa);
taxa = NULL;
}
}
if (taxa)
delete taxa;
}
taxa = NULL; /*potential memory leak, but a reference should be held, by the nexus reader.*/
ownsTaxaBlock = false;
taxaLinkStatus = NxsBlock::BLOCK_LINK_UNINITIALIZED;
}
newtaxa = false;
passedRefOfOwnedBlock = false;
}
bool NxsTaxaBlockSurrogate::SurrogateSwapEquivalentTaxaBlock(NxsTaxaBlockAPI * tb)
{
NxsTaxaBlockFactory * tbf = nxsReader->GetTaxaBlockFactory();
if (this->taxa && this->ownsTaxaBlock && tbf)
tbf->BlockError(taxa);
this->SetTaxaBlockPtr(tb, NxsBlock::BLOCK_LINK_EQUIVALENT_TO_IMPLIED);
return true;
}
void NxsTaxaBlockSurrogate::AssureTaxaBlock(bool allocBlock, NxsToken &token, const char *cmd)
{
if (!allocBlock)
{
if (taxa != NULL)
return;
if (!nxsReader)
{
NxsString errormsg = "API Error: No nxsReader during parse in NxsTaxaBlockSurrogate::AssureTaxaBlock";
throw NxsNCLAPIException(errormsg, token);
}
unsigned nTb;
NxsTaxaBlockAPI * cb = nxsReader->GetTaxaBlockByTitle(NULL, &nTb);
if (cb == NULL)
{
NxsString errormsg = "TAXA Block has been not been read, but a ";
if (cmd)
errormsg += cmd;
errormsg += " command (which requires a TAXA block) has been encountered. Either add a TAXA block or (for blocks other than the TREES block) you may use a \"DIMENSIONS NEWTAXA NTAX= ...\" command to introduces taxa.";
throw NxsException(errormsg, token);
}
if (nTb > 1)
{
NxsString errormsg = "Multiple TAXA Blocks have been read (or implied using NEWTAXA in other blocks) and a";
if (cmd)
errormsg += cmd;
errormsg += " command (which requires a TAXA block) has been encountered.\nA \"LINK TAXA=<title here>;\" command must be used to specify which TAXA block is needed.";
cb->WarnDangerousContent(errormsg, token);
}
taxa = cb;
return;
}
if (nxsReader != NULL)
{
NxsTaxaBlockFactory * tbf = nxsReader->GetTaxaBlockFactory();
if (tbf)
{
std::string s("TAXA");
taxa = tbf->GetBlockReaderForID(s, nxsReader, &token);
ownsTaxaBlock = true;
passedRefOfOwnedBlock = false;
taxaLinkStatus = NxsBlock::BLOCK_LINK_TO_IMPLIED_BLOCK;
}
}
if (taxa == NULL)
{
taxa = new NxsTaxaBlock();
ownsTaxaBlock = true;
passedRefOfOwnedBlock = false;
taxaLinkStatus = NxsBlock::BLOCK_LINK_TO_IMPLIED_BLOCK;
}
}
/* This function is called by derived classes right before they start to parse a command
that requires a Taxa block.
If a taxa block has not been set at this point, and one cannot be created then
a NxsException will be generated.
This enables lazy initialization of the taxa field.
*/
void NxsTaxaBlockSurrogate::AssureTaxaBlock(bool allocBlock, NxsToken &token, const char *cmd)
{
if (!allocBlock)
{
if (taxa != NULL)
return;
if (!nxsReader)
{
NxsString errormsg = "API Error: No nxsReader during parse in NxsTaxaBlockSurrogate::AssureTaxaBlock";
throw NxsNCLAPIException(errormsg, token);
}
unsigned nTb;
NxsTaxaBlockAPI * cb = nxsReader->GetTaxaBlockByTitle(NULL, &nTb);
if (cb == NULL)
{
NxsString errormsg = "TAXA Block has been not been read, but a ";
if (cmd)
errormsg += cmd;
errormsg += " command (which requires a TAXA block) has been encountered. Either add a TAXA block or (for blocks other than the TREES block) you may use a \"DIMENSIONS NEWTAXA NTAX= ...\" command to introduces taxa.";
throw NxsException(errormsg, token);
}
if (nTb > 1)
{
NxsString errormsg = "Multiple TAXA Blocks have been read (or implied using NEWTAXA in other blocks) and a ";
if (cmd)
errormsg += cmd;
errormsg += " command (which requires a TAXA block) has been encountered";
std::string bn = token.GetBlockName();
if (!bn.empty())
{
errormsg += " in a ";
errormsg += bn;
errormsg += " block.";
}
errormsg += ".\nThis can be caused by reading multiple files. It is possible that\neach file is readable separately, but cannot be read unambiguously when read in sequence.\n";
errormsg += "One way to correct this is to use the\n TITLE some-unique-name-here ;\ncommand in the TAXA block and an accompanying\n LINK TAXA=the-unique-title-goes here;\n";
errormsg += "command to specify which TAXA block is needed.";
cb->WarnDangerousContent(errormsg, token);
}
taxa = cb;
return;
}
if (nxsReader != NULL)
{
NxsTaxaBlockFactory * tbf = nxsReader->GetTaxaBlockFactory();
if (tbf)
{
std::string s("TAXA");
taxa = tbf->GetBlockReaderForID(s, nxsReader, &token);
ownsTaxaBlock = true;
passedRefOfOwnedBlock = false;
taxaLinkStatus = NxsBlock::BLOCK_LINK_TO_IMPLIED_BLOCK;
}
}
if (taxa == NULL)
{
taxa = new NxsTaxaBlock();
ownsTaxaBlock = true;
passedRefOfOwnedBlock = false;
taxaLinkStatus = NxsBlock::BLOCK_LINK_TO_IMPLIED_BLOCK;
}
}