changing command name classify.shared to classifyrf.shared

[mothur.git] / getlabelcommand.cpp

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index 236eef24acfdb4c0b82d2802abe63562db53ef4a..03bf7ad991829e2afc693db3d15560d66e597a91 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -13,12 +13,11 @@
 //**********************************************************************************************************************
 vector<string> GetlabelCommand::setParameters(){       
        try {
-               CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-               CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
-               CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
-               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);            
-               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","",false,false, true); parameters.push_back(plist);
+               CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
+               CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
+               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);          }
@@ -44,7 +43,7 @@ GetlabelCommand::GetlabelCommand(){
 string GetlabelCommand::getHelpString(){       
        try {
                string helpString = "";
-               helpString += "The get.label command parameters are list, sabund, rabund and shared file. \n";
+               helpString += "The get.label command parameters are list, sabund and rabund file. \n";
                helpString += "The get.label command should be in the following format: \n";
                helpString += "get.label()\n";
                helpString += "Example get.label().\n";
@@ -63,6 +62,7 @@ GetlabelCommand::GetlabelCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -83,13 +83,6 @@ GetlabelCommand::GetlabelCommand(string option)  {
                        if (inputDir == "not found"){   inputDir = "";          }
                        else {
                                string path;
-                               it = parameters.find("shared");
-                               //user has given a template file
-                               if(it != parameters.end()){ 
-                                       path = m->hasPath(it->second);
-                                       //if the user has not given a path then, add inputdir. else leave path alone.
-                                       if (path == "") {       parameters["shared"] = inputDir + it->second;           }
-                               }
                                
                                it = parameters.find("rabund");
                                //user has given a template file
@@ -120,47 +113,38 @@ GetlabelCommand::GetlabelCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else {  format = "list"; inputfile = listfile; }
+                       else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
-                       else {  format = "sabund"; inputfile = sabundfile; }
+                       else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
-                       else {  format = "rabund"; inputfile = rabundfile; }
-                       
-                       sharedfile = validParameter.validFile(parameters, "shared", true);
-                       if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
-                       else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  format = "sharedfile"; inputfile = sharedfile; }
+                       else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
                        
-                       if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
+                       if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?
-                               //give priority to shared, then list, then rabund, then sabund
+                               //give priority to list, then rabund, then sabund
                                //if there is a current shared file, use it
-                               sharedfile = m->getSharedFile(); 
-                               if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+                               
+                               listfile = m->getListFile(); 
+                               if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
                                else { 
-                                       listfile = m->getListFile(); 
-                                       if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+                                       rabundfile = m->getRabundFile(); 
+                                       if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
                                        else { 
-                                               rabundfile = m->getRabundFile(); 
-                                               if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+                                               sabundfile = m->getSabundFile(); 
+                                               if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
                                                else { 
-                                                       sabundfile = m->getSabundFile(); 
-                                                       if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
-                                                       else { 
-                                                               m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); 
-                                                               abort = true;
-                                                       }
+                                                       m->mothurOut("No valid current files. You must provide a list, sabund or rabund file."); m->mothurOutEndLine(); 
+                                                       abort = true;
                                                }
                                        }
                                }
                        }
-                       
                }
 
        }
@@ -184,10 +168,10 @@ int GetlabelCommand::execute(){
                        
                        if (m->control_pressed) { delete input;  delete order; return 0; }
                        
-                       m->mothurOut(label); m->mothurOutEndLine();
-                       
                        label = order->getLabel();      
                        
+                       m->mothurOut(label); m->mothurOutEndLine();
+                       
                        delete order;           
                        order = input->getOrderVector();
                }