X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venncommand.cpp;h=70c35f713bd02a6a1f786668ed00b79784f05293;hb=55bbd10379db27def51cec72a8819d775f73e45b;hp=1b4e3bc70848d7511c1dcd136fb4c320e4265b11;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/venncommand.cpp b/venncommand.cpp
index 1b4e3bc..70c35f7 100644
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -20,17 +20,18 @@
 //**********************************************************************************************************************
 vector<string> VennCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); 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 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);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		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", "Boolean", "", "F", "", "", "","",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);		}
@@ -66,6 +67,21 @@ string 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);
+    }
+}
 
 //**********************************************************************************************************************
 VennCommand::VennCommand(){	
@@ -200,6 +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);
@@ -229,8 +248,7 @@ int VennCommand::execute(){
 					}else if (Estimators[i] == "chao") { 
 						vennCalculators.push_back(new Chao1());
 					}else if (Estimators[i] == "ace") {
-						if(abund < 5)
-							abund = 10;
+						if(abund < 5) { abund = 10; }
 						vennCalculators.push_back(new Ace(abund));
 					}
 				}
@@ -252,7 +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;