QString IndexOrganizedTableProperties::generateDdl() const
{
QString ddl;
if(pctThreshold!=-1){
ddl.append(" PCTTHRESHOLD ").append(QString::number(pctThreshold));
}
ddl.append(optionText(mappingTable, " MAPPING TABLE", " NOMAPPING"));
if(keyCompression==1){
ddl.append(" COMPRESS ");
if(keyCompressionPrefixLength!=-1){
ddl.append(QString::number(keyCompressionPrefixLength));
}
}else if(keyCompression==2){
ddl.append(" NOCOMPRESS");
}
if(overflow){
ddl.append(" OVERFLOW");
if(!including.isEmpty()){
ddl.append(" INCLUDING \"").append(including).append("\" ");
}
QString storageParamsDdl=storageParams.generateDdl();
if(!storageParamsDdl.isEmpty()){
ddl.append(" ").append(storageParamsDdl);
}
ddl.append(optionText(logging, " LOGGING ", " NOLOGGING "));
}
return ddl;
}
QString IndexOrganizedTableProperties::generateDiffDdl(const IndexOrganizedTableProperties &other) const
{
QString ddl;
if(pctThreshold!=other.pctThreshold){
ddl.append(" PCTTHRESHOLD ").append(QString::number(pctThreshold));
}
QString overflowDdl;
if(overflow){
if(!including.isEmpty() && including!=other.including){
overflowDdl.append(" INCLUDING \"").append(including).append("\" ");
}
QString storageParamsDdl=storageParams.generateDiffDdl(other.storageParams);
if(!storageParamsDdl.isEmpty()){
overflowDdl.append(storageParamsDdl);
}
if(logging!=other.logging){
overflowDdl.append(optionText(logging, " LOGGING", " NOLOGGING"));
}
if(!other.overflow){
overflowDdl.prepend(" ADD OVERFLOW");
}else if(!overflowDdl.isEmpty()){
overflowDdl.prepend(" OVERFLOW");
}
}
if(!overflowDdl.isEmpty()){
ddl.append(overflowDdl);
}
return ddl;
}
OBBase* OBMol::DoTransformations(const std::map<std::string, std::string>* pOptions, OBConversion* pConv)
{
// Perform any requested transformations
// on a OBMol
//The input map has option letters or name as the key and
//any associated text as the value.
//For normal(non-filter) transforms:
// returns a pointer to the OBMol (this) if ok or NULL if not.
//For filters returns a pointer to the OBMol (this) if there is a match,
//and NULL when not and in addition the OBMol object is deleted NULL.
//This is now a virtual function. The OBBase version just returns the OBMol pointer.
//This is declared in mol.h
//The filter options, s and v allow a obgrep facility.
//Used together they must both be true to allow a molecule through.
//Parse GeneralOptions
if(pOptions->empty())
return this;
// DoOps calls Do() for each of the plugin options in the map
// It normally returns true, even if there are no options but
// can return false if one of the options decides that the
// molecule should not be output. If it is a filtering op, it
// should delete the molecule itself (unlike the -s, --filter options,
// which delete it in this function).
if(!OBOp::DoOps(this, pOptions, pConv))
return (OBBase *)NULL;
bool ret=true;
map<string,string>::const_iterator itr, itr2;
if(pOptions->find("b")!=pOptions->end())
if(!ConvertDativeBonds())
ret=false;
if(pOptions->find("d")!=pOptions->end())
if(!DeleteHydrogens())
ret=false;
if(pOptions->find("h")!=pOptions->end())
if(!AddHydrogens(false, false))
ret=false;
if(pOptions->find("r")!=pOptions->end()) {
StripSalts();
ret = true;
}
itr = pOptions->find("p");
if(itr!=pOptions->end()) {
double pH = strtod(itr->second.c_str(), 0);
if(!AddHydrogens(false, true, pH))
ret=false;
}
if(pOptions->find("c")!=pOptions->end())
Center();
itr = pOptions->find("title"); //Replaces title
if(itr!=pOptions->end())
SetTitle(itr->second.c_str());
itr = pOptions->find("addtotitle"); //Appends text to title
if(itr!=pOptions->end())
{
string title(GetTitle());
title += itr->second;
SetTitle(title.c_str());
}
/* itr = pOptions->find("addformula"); //Appends tab + formula to title
if(itr!=pOptions->end())
{
string title(GetTitle());
title += '\t' + GetSpacedFormula(1,"");//actually unspaced
SetTitle(title.c_str());
}
*/
//Add an extra property to the molecule.
//Parameter has atrribute and value separated by a space
itr = pOptions->find("property");
if(itr!=pOptions->end())
{
string txt(itr->second);
string::size_type pos = txt.find(' ');
if(pos==string::npos)
{
obErrorLog.ThrowError(__FUNCTION__, "Missing property value", obError);
ret=false;
}
else
{
string attr(txt.substr(0,pos)), val(txt.substr(pos+1));
//Update value if it already exists
OBPairData* dp = dynamic_cast<OBPairData*>(GetData(attr));
if(dp) {
dp->SetValue(val);
dp->SetOrigin(userInput);
}
else {
// Pair did not exist; make new one
dp = new OBPairData;
dp->SetAttribute(attr);
dp->SetValue(val);
dp->SetOrigin(userInput);
SetData(dp);
}
}
}
itr = pOptions->find("add"); //adds new properties from descriptors in list
if(itr!=pOptions->end())
OBDescriptor::AddProperties(this, itr->second);
itr = pOptions->find("delete"); //deletes the specified properties
if(itr!=pOptions->end())
OBDescriptor::DeleteProperties(this, itr->second);
itr = pOptions->find("append"); //Appends values of descriptors or properties to title
if(itr!=pOptions->end())
{
string title(GetTitle());
title += OBDescriptor::GetValues(this, itr->second);
if(ispunct(title[0]))
title[0]=' ';//a leading punct char is used only as a separator, not at start
SetTitle(Trim(title).c_str());
}
//Filter using OBDescriptor comparison and (older) SMARTS tests
//Continue only if previous test was true.
bool fmatch = true;
itr = pOptions->find("filter");
if(itr!=pOptions->end())
{
std::istringstream optionText(itr->second);
fmatch = OBDescriptor::FilterCompare(this, optionText, false);
}
if(fmatch)
{
itr = pOptions->find("v");
if(itr!=pOptions->end() && !itr->second.empty())
{
//inverse match quoted SMARTS string which follows
OBSmartsPattern sp;
sp.Init(itr->second);
fmatch = !sp.Match(*this); //(*pmol) ;
}
}
if(fmatch)
{
itr = pOptions->find("s");
if(itr!=pOptions->end() && !itr->second.empty())
{
//SMARTS filter
//If exactmatch option set (probably in fastsearchformat) the
//number of atoms in the pattern (passed as a string in the option text)
//has to be the same as in the molecule.
itr2 = pOptions->find("exactmatch");
if(itr2!=pOptions->end() && NumHvyAtoms()!=atoi(itr2->second.c_str()))
fmatch=false;
else
{
//match quoted SMARTS string which follows
OBSmartsPattern sp;
sp.Init(itr->second.c_str());
fmatch = sp.Match(*this);
}
}
}
if(!fmatch)
{
//filter failed: delete OBMol and return NULL
delete this;
return NULL;
}
else
{
if(ret==false)
{
obErrorLog.ThrowError(__FUNCTION__, "Error executing an option", obError);
delete this; //added 9March2006
return NULL;
}
else
return this;
}
}
