removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 54197174e1fa3da14861614734b1dc58314a466a..dbdcc36300f2fd5d3f5ea6135dbc8666f328bba0 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -95,14 +95,13 @@ string Engine::findMothursPath(){
 
 InteractEngine::InteractEngine(string path){
 
-       globaldata = GlobalData::getInstance();
        
        string temppath = path.substr(0, (path.find_last_of("othur")-5));
        
        //this will happen if you set the path variable to contain mothur's exe location
        if (temppath == "") { path = findMothursPath(); }
        
-       globaldata->argv = path;
+       mout->argv = path;
 }
 
 /***********************************************************************/
@@ -250,7 +249,6 @@ string Engine::getCommand()  {
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
        try {
-               globaldata = GlobalData::getInstance();
        
                openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
                
@@ -259,7 +257,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
                //this will happen if you set the path variable to contain mothur's exe location
                if (temppath == "") { path = findMothursPath(); }
                
-               globaldata->argv = path;
+               mout->argv = path;
                                
        }
        catch(exception& e) {
@@ -406,7 +404,6 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 //This function opens the batchfile to be used by BatchEngine::getInput.
 ScriptEngine::ScriptEngine(string path, string commandString){
        try {
-               globaldata = GlobalData::getInstance();
                
                //remove quotes
                listOfCommands = commandString.substr(1, (commandString.length()-1));
@@ -416,7 +413,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
                //this will happen if you set the path variable to contain mothur's exe location
                if (temppath == "") { path = findMothursPath(); }
                
-               globaldata->argv = path;
+               mout->argv = path;
                                
        }
        catch(exception& e) {