changing command name classify.shared to classifyrf.shared

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 4dc20634c1e53d774348559447c736f736ff4e69..a4d7b83397f83bf6ae3dd21627566252035b328f 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> GetListCountCommand::setParameters(){   
        try {
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "",false,false); parameters.push_back(parasort);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otu",false,true, true); parameters.push_back(plist);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "","",false,false); parameters.push_back(parasort);
+               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);          }
@@ -49,6 +49,21 @@ string GetListCountCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string GetListCountCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "otu") {  pattern = "[filename],[tag],otu"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetListCountCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 GetListCountCommand::GetListCountCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -114,6 +129,7 @@ GetListCountCommand::GetListCountCommand(string option)  {
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                
                        //check for optional parameter and set defaults
@@ -148,7 +164,7 @@ int GetListCountCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -156,7 +172,7 @@ int GetListCountCommand::execute(){
                        
                                process(list);
                                
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -170,7 +186,7 @@ int GetListCountCommand::execute(){
                                
                                process(list);
                                
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
 
                                                                                                        
                                processedLabels.insert(list->getLabel());
@@ -207,7 +223,7 @@ int GetListCountCommand::execute(){
                                
                        process(list);  
                        
-                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                        
                        delete list;  
                }
@@ -233,7 +249,11 @@ void GetListCountCommand::process(ListVector* list) {
        try {
                string binnames;
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = list->getLabel();
+               string outputFileName = getOutputFileName("otu", variables);
+               
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);