X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=ca8c62d43821652d6bf4ea868e9444d54c256ff4;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=55b752dba4f40e76f11a46d2608e75d43c0de506;hpb=eb4bb52af987ff4df7354d95d60cd763aec537e1;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 55b752d..ca8c62d 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -12,7 +12,8 @@
 //**********************************************************************************************************************
 vector<string> SetDirectoryCommand::setParameters(){	
 	try {
-		CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);	
+		CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
+        CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug);
 		CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
 		CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -34,7 +35,9 @@ string SetDirectoryCommand::getHelpString(){
 		helpString += "The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n";
 		helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
 		helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
-		helpString += "The set.dir command parameters are input, output and tempdefault and one is required.\n";
+        helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
+		helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
+        helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n";
 		helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
 		helpString += "To return the input to the current working directory you may enter: input=clear.\n";
 		helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n";
@@ -81,10 +84,20 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
 			
 			tempdefault = validParameter.validFile(parameters, "tempdefault", false);			
 			if (tempdefault == "not found") {  tempdefault = "";  }
+            
+            bool debug = false;
+            bool nodebug = false;
+            debugOnly = false;
+            string temp = validParameter.validFile(parameters, "debug", false);			
+			if (temp == "not found") {  debug = false;  nodebug=true; }
+            else {  debug = m->isTrue(temp); }
+            m->debug = debug;
+            
+            if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
 				
-			if ((input == "") && (output == "") && (tempdefault == "")) {	
-				m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
-			}
+			if ((input == "") && (output == "") && (tempdefault == "") && nodebug) {	
+				m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true;
+			}else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; }
 		}
 	}
 	catch(exception& e) {
@@ -99,6 +112,8 @@ int SetDirectoryCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
+        if (debugOnly) { return 0; }
+        
 		commandFactory = CommandFactory::getInstance();
 		
 		m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();