changing command name classify.shared to classifyrf.shared

[mothur.git] / getotuscommand.cpp

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index 4e8d3198c9b6c560d57ff579b26eb9985e452b35..335ebc4506ca99ac3a0e3dc9a2d068b0f1c41cd7 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -15,13 +15,13 @@
 //**********************************************************************************************************************
 vector<string> GetOtusCommand::setParameters(){        
        try {
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true, true); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true, true); parameters.push_back(plist);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               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);          }
@@ -53,7 +53,22 @@ string GetOtusCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string GetOtusCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "group")       {   pattern = "[filename],[tag],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],pick,[extension]";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetOtusCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){      
        try {
@@ -182,7 +197,7 @@ int GetOtusCommand::execute(){
                groupMap->readMap();
                
                //get groups you want to get
-               if (accnosfile != "") { readAccnos(); }
+               if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
                
                //make sure groups are valid
                //takes care of user setting groupNames that are invalid or setting groups=all
@@ -231,14 +246,20 @@ int GetOtusCommand::readListGroup(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label +  m->getExtension(listfile);
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = label;
+        variables["[extension]"] = m->getExtension(listfile);
+               string outputFileName = getOutputFileName("list", variables);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
                string GroupOutputDir = outputDir;
                if (outputDir == "") {  GroupOutputDir += m->hasPath(groupfile);  }
-               string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label  + m->getExtension(groupfile);
+        variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+               string outputGroupFileName = getOutputFileName("group", variables);
                
                ofstream outGroup;
                m->openOutputFile(outputGroupFileName, outGroup);
@@ -400,29 +421,5 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
        }
 }
 //**********************************************************************************************************************
-void GetOtusCommand::readAccnos(){
-       try {
-               Groups.clear();
-               
-               ifstream in;
-               m->openInputFile(accnosfile, in);
-               string name;
-               
-               while(!in.eof()){
-                       in >> name;
-                       
-                       Groups.push_back(name);
-                       
-                       m->gobble(in);
-               }
-               in.close();             
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GetOtusCommand", "readAccnos");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************