changing command name classify.shared to classifyrf.shared

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 980c886cc0cb79f51f892ee13fe4dc2c3061b812..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; 
@@ -234,7 +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);