fixes while testing

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 557622db59b1f5480a87fda36050e98cfb9439a9..1ea9c39af69e703f41b0aa7c9e5194eeeb0efcf0 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -26,6 +26,7 @@ vector<string> RemoveLineageCommand::getValidParameters(){
 //**********************************************************************************************************************
 RemoveLineageCommand::RemoveLineageCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -297,7 +298,7 @@ int RemoveLineageCommand::readFasta(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputTypes["fasta"].push_back(outputFileName); 
+               outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); 
                
                return 0;
                
@@ -368,7 +369,7 @@ int RemoveLineageCommand::readList(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputTypes["list"].push_back(outputFileName); 
+               outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName); 
                                
                return 0;
 
@@ -454,7 +455,7 @@ int RemoveLineageCommand::readName(){
                out.close();
 
                if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputTypes["name"].push_back(outputFileName);
+               outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
                                
                return 0;
        }
@@ -498,7 +499,7 @@ int RemoveLineageCommand::readGroup(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputTypes["group"].push_back(outputFileName);
+               outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
                
                return 0;
        }
@@ -552,7 +553,7 @@ int RemoveLineageCommand::readTax(){
                out.close();
                
                if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputTypes["taxonomy"].push_back(outputFileName);
+               outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
                        
                return 0;
 
@@ -642,7 +643,7 @@ int RemoveLineageCommand::readAlign(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputTypes["alignreport"].push_back(outputFileName);
+               outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
                
                return 0;