X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venncommand.cpp;h=70c35f713bd02a6a1f786668ed00b79784f05293;hb=55bbd10379db27def51cec72a8819d775f73e45b;hp=9c234959f0e96040c2d6655649d69f10c0ee66a6;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git diff --git a/venncommand.cpp b/venncommand.cpp index 9c23495..70c35f7 100644 --- a/venncommand.cpp +++ b/venncommand.cpp @@ -27,6 +27,7 @@ vector VennCommand::setParameters(){ CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc); CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund); CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs); + CommandParameter psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus); CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize); CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); @@ -215,6 +216,9 @@ VennCommand::VennCommand(string option) { temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; } perm = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; } + sharedOtus = m->isTrue(temp); temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; } m->mothurConvert(temp, fontsize); @@ -266,7 +270,7 @@ int VennCommand::execute(){ //if the users entered no valid calculators don't execute command if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; } - venn = new Venn(outputDir, nseqs, inputfile, fontsize); + venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus); input = new InputData(inputfile, format); string lastLabel;