//**********************************************************************************************************************
DistanceCommand::DistanceCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
Estimators.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
int DistanceCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int startTime = time(NULL);
//delete filename;
if (pid == 0) { //you are the root process
-
+
//do your part
string outputMyPart;
delete distCalculator;
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("phylip");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ }
+
+ //set column file as new current columnfile
+ itTypes = outputTypes.find("column");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
m->mothurOut(outputFile); m->mothurOutEndLine();
remove(outputFile.c_str()); //temp file is bad because file mismatch above
}
+ return good;
+
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "sanityCheck");