void GDEFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
string& secStructName, int &structPenalties, int length)
{
+ bool guigetss = false;
+ if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1())
+ guigetss = true;
+ if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2())
+ guigetss = true;
+
char _title[MAXLINE + 1];
char _line[MAXLINE + 1];
char _lin2[MAXLINE + 1];
utilityObject->blankToUnderscore(_sname);
secStructName = string(_sname);
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title, "Found secondary structure in alignment file: ");
strcat(_title, _sname);
{
(*_lin2) = 'y';
}
- if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+ if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = SECST;
for (i = 0; i < length; i++)
utilityObject->blankToUnderscore(_sname);
secStructName = string(_sname);
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title, "Found gap penalty mask in alignment file: ");
strcat(_title, _sname);
{
(*_lin2) = 'y';
}
- if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+ if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = GMASK;
for (i = 0; i < length; i++)