X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=venncommand.cpp;h=98796b3466fcc344b5e4c990015316a5ae2a0582;hp=9c234959f0e96040c2d6655649d69f10c0ee66a6;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7

diff --git a/venncommand.cpp b/venncommand.cpp
index 9c23495..98796b3 100644
--- 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);
@@ -45,7 +46,7 @@ vector<string> VennCommand::setParameters(){
 string VennCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, fontsize and label.   shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
+		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";
@@ -57,6 +58,7 @@ string VennCommand::getHelpString(){
 		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, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\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;
@@ -215,6 +217,9 @@ 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 +271,7 @@ 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;