int SensSpecCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int startTime = time(NULL);
//create list file with only unique names, saves time and memory by removing redundant names from list file that are not in the distance file.
string newListFile = preProcessList();
if (newListFile != "") { listFile = newListFile; }
setUpOutput();
outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
if(format == "phylip") { processPhylip(); }
else if(format == "column") { processColumn(); }
//remove temp file if created
if (newListFile != "") { m->mothurRemove(newListFile); }
if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
m->mothurOut("It took " + toString(time(NULL) - startTime) + " to run sens.spec."); m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SensSpecCommand", "execute");
exit(1);
}
}
int SensSpecCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
setUpOutput();
outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
if(format == "phylip") { processPhylip(); }
else if(format == "column") { processColumn(); }
if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SensSpecCommand", "execute");
exit(1);
}
}