fix to summary.tax for 1.28.0

[mothur.git] / getotuscommand.cpp

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index b94b42a8a37038d188bf19a430a7ee8951f2f86c..8d20e63b65b9a99b6476608fe4a108ce233718f0 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -53,7 +53,27 @@ string GetOtusCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string GetOtusCommand::getOutputFileNameTag(string type, string inputName=""){ 
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "group")            {   outputFileName = "pick" + m->getExtension(inputName);  }
+            else if (type == "list")        {   outputFileName = "pick" + m->getExtension(inputName);  }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetOtusCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){      
        try {
@@ -182,12 +202,14 @@ 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
                SharedUtil* util = new SharedUtil();
-               util->setGroups(Groups, groupMap->namesOfGroups);
+               vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
+               util->setGroups(Groups, gNamesOfGroups);
+               groupMap->setNamesOfGroups(gNamesOfGroups);
                delete util;
                
                if (m->control_pressed) { delete groupMap; return 0; }
@@ -229,14 +251,14 @@ 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);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
                
                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);
+               string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
                
                ofstream outGroup;
                m->openOutputFile(outputGroupFileName, outGroup);
@@ -398,29 +420,5 @@ 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);
-       }
-}
-//**********************************************************************************************************************