else {
//valid paramters for this command
- string AlignArray[] = {"groups","label","calc", "abund"};
+ string AlignArray[] = {"groups","label","calc", "abund","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); mothurOutEndLine(); abort = true;
}
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
}
}
- venn = new Venn();
+ venn = new Venn(outputDir);
}
}
}
if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
venn->getPic(lookup, vennCalculators);
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
}
if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = sabund->getLabel();
+
delete sabund;
sabund = input->getSAbundVector(lastLabel);
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
+
+ //restore real lastlabel to save below
+ sabund->setLabel(saveLabel);
}
lastLabel = sabund->getLabel();