X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venncommand.cpp;h=c918500270a537ac909326f3edc10ad068dc3ac5;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=b5b401de349fcf9d57253582d7c68d9c6cd3f99a;hpb=0718c426add1df69adcc24444ef45550fb262ca7;p=mothur.git

diff --git a/venncommand.cpp b/venncommand.cpp
index b5b401d..c918500 100644
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -66,6 +66,27 @@ string VennCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+
+string VennCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "svg")            {   outputFileName =  "svg";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "VennCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************
 VennCommand::VennCommand(){	
@@ -193,7 +214,7 @@ VennCommand::VennCommand(string option)  {
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "nseqs", false);		if (temp == "not found"){	temp = "f";				}
 			nseqs = m->isTrue(temp); 
@@ -202,7 +223,7 @@ VennCommand::VennCommand(string option)  {
 			perm = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "fontsize", false);		if (temp == "not found") { temp = "24"; }
-			convert(temp, fontsize);
+			m->mothurConvert(temp, fontsize);
 
 		}
 				
@@ -229,8 +250,7 @@ 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));
 					}
 				}