added filter.shared command. fixed lci and uci for thetayc calc

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 1b4e3bc70848d7511c1dcd136fb4c320e4265b11..70c35f713bd02a6a1f786668ed00b79784f05293 100644 (file)
--- 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;