added sharedotu parameter to venn command. working of make.contigs.

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 9c234959f0e96040c2d6655649d69f10c0ee66a6..70c35f713bd02a6a1f786668ed00b79784f05293 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -27,6 +27,7 @@ vector<string> 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;