// Constructor
Input(int argc, char **argv)
: ec_(false), shortestOnly_(false), distances_(false), suppressRef_(false),
overlaps_(true), delim_("|"), refFile_(""), nonRefFile_(""), chr_("all") {
typedef Ext::UserError UE;
if ( 1 == argc )
throw(NoInput());
int argcntr = 1;
bool outoption = false; // may choose up to one type of non-default output option
// [Process-Flags]
std::string next = "";
while ( argcntr < argc ) {
next = argv[argcntr];
if ( next == "--help" )
throw(HelpException());
else if ( next == "--version" )
throw(VersionException());
else if ( next == "--ec" || next == "--header" )
ec_ = true;
else if ( next == "--no-overlaps" )
overlaps_ = false;
else if ( next == "--delim" ) {
Ext::Assert<UE>(++argcntr < argc, "No value given for --delim.");
delim_ = argv[argcntr];
}
else if ( next == "--chrom" ) {
Ext::Assert<UE>(++argcntr < argc, "No value given for --chrome.");
chr_ = argv[argcntr];
}
else if ( next == "--closest" ) {
Ext::Assert<UE>(!outoption, "Multiple output options not allowed.");
shortestOnly_ = true;
outoption = true;
}
else if ( next == "--dist" )
distances_ = true;
else if ( next == "--no-ref" )
suppressRef_ = true;
else if ( next == "--help" )
throw(HelpException());
else if ( next == "--shortest" ) { // silently supported for bckwd compatibility
Ext::Assert<UE>(!outoption, "Multiple output options not allowed.");
shortestOnly_ = true;
outoption = true;
} else { // the rest are two input files?
Ext::Assert<UE>(argcntr + 2 == argc, "Unknown option: " + next + ".");
break;
}
++argcntr;
} // while
Ext::Assert<UE>(argcntr + 2 == argc, "Not enough input files given.");
refFile_ = argv[argcntr++];
nonRefFile_ = argv[argcntr];
Ext::Assert<UE>(refFile_.find("--") != 0, "Option given where file expected: " + refFile_ + ".");
Ext::Assert<UE>(nonRefFile_.find("--") != 0, "Option given where file expected: " + nonRefFile_ + ".");
}
/*!
* Throws VersionException, SpecificationPathsNotValid, SpecificationTextNotValid
* exception.
*/
Specification::Specification(const std::string & pathSpecification) :
pathSpecification(pathSpecification) {
std::ifstream _ifstream(pathSpecification.c_str());
if (_ifstream) { // Is true if file exists
hasChanges = false;
int totalQuestions;
_ifstream.ignore(256, ' '); // ignore until space
_ifstream >> version;
if (!(version == 1 || version == 2 || version == 3)) {
throw VersionException(version);
}
version = 3;
_ifstream.ignore(256, ' '); // ignore until space
_ifstream >> iD;
_ifstream.ignore(256, ' '); // ignore until space
_ifstream >> totalQuestions;
questions = new std::vector<Question*>(totalQuestions, nullptr);
try {
for (int i = 1; i <= totalQuestions; i++) {
std::string questionPath_;
_ifstream >> questionPath_;
(*questions)[i - 1] = Question::Initializer(questionPath_,
_ifstream);
}
} catch (const SpecificationTextNotValid & ex) {
_ifstream.close();
clear();
throw; // Rethrow for further handling in upper layers.
}
_ifstream.close();
hasChanges = false;
validateQuestionPaths(); // Throws exception if not valid
} else {
