+//**********************************************************************************************************************
+vector<string> VennCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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", "Multiple", "1-2-3-4", "4", "", "", "","",false,false); parameters.push_back(ppermute); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string VennCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, sharedotus, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n";
+ helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n";
+ helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
+ helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
+ helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
+ helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n";
+ helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n";
+ helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n";
+ helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
+ helpString += "If you have more than 4 groups, you can use the permute parameter to set the number of groups you would like mothur to divide the samples into to draw the venn diagrams for all possible combos. Default=4.\n";
+ helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
+ helpString += "The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.\n";
+ helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string VennCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "svg") { pattern = "[filename],svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getOutputPattern");
+ exit(1);
+ }
+}