some changes while testing 1.9

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 4ad63da5655b4bb6118d09b339f3be0f3651dd04..30dc55343d46e0656c7123aba7afddea7f4b3a77 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -34,7 +34,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                       
+       
                        globaldata->newRead();
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -156,18 +156,17 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        }
                        
                        globaldata->allLines = allLines;
-                       
+               
                        orderfile = validParameter.validFile(parameters, "order", true);
                        if (orderfile == "not open") { abort = true; }  
                        else if (orderfile == "not found") { orderfile = ""; }
                        else {  globaldata->setOrderFile(orderfile);    }
                        
-                       
+                               
                        if (abort == false) {
                                //gets whichever one of the above is set
                                filename = globaldata->inputFileName;
                        }
-
                }
 
        }
@@ -204,17 +203,14 @@ void ReadOtuCommand::help(){
 
 
 //**********************************************************************************************************************
-
-ReadOtuCommand::~ReadOtuCommand(){
-       }
-
+ReadOtuCommand::~ReadOtuCommand(){}
 //**********************************************************************************************************************
 
 int ReadOtuCommand::execute(){
        try {
        
                if (abort == true) {    return 0;       }
-               
+       
                if (globaldata->getFormat() == "shared") {
                        
                        shared = new SharedCommand(outputDir);
@@ -225,11 +221,11 @@ int ReadOtuCommand::execute(){
                                globaldata->setListFile("");
                                globaldata->setGroupFile("");
                                globaldata->setSharedFile("");
-                       }else {
-                               m->mothurOutEndLine();
-                               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-                               m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();       
-                               m->mothurOutEndLine();
+                       }else { //shared command outputs the filenames
+                               //m->mothurOutEndLine();
+                               //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+                               //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();     
+                               //m->mothurOutEndLine();
                        }
                        
                        delete shared;