From: westcott <westcott>
Date: Mon, 11 Apr 2011 17:38:56 +0000 (+0000)
Subject: 1.18.0
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=9d6f36294dcaef3ac65a0e69fd8140077c3209e0

1.18.0
---

diff --git a/mothur.cpp b/mothur.cpp
index 3e2a439..45be11d 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -168,7 +168,7 @@ int main(int argc, char *argv[]){
  
 		if(argc>1){
 			input = argv[1];
-			//m->mothurOut("input = " + input); m->mothurOutEndLine();
+			m->mothurOut("input = " + input); m->mothurOutEndLine();
 
 			if (input[0] == '#') {
 				m->mothurOutJustToLog("Script Mode");
diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index c7f67b4..3eb422e 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -189,7 +189,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
 			
 			lineLabel = validParameter.validFile(parameters, "label", false);	if (lineLabel == "not found") { lineLabel = ""; }
 			
-			sensSpecFileName = listFile.substr(0,listFile.find_last_of('.')) + ".sensspec";
+			sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + ".sensspec";
 		}
 	}
 	catch(exception& e) {
diff --git a/setdircommand.cpp b/setdircommand.cpp
index fc411ae..3135b81 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -100,13 +100,15 @@ int SetDirectoryCommand::execute(){
 		
 		commandFactory = CommandFactory::getInstance();
 		
+		m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
+		
 		//redirect output
 		if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 		else if (output == "default") { 
 			string exepath = m->argv;
 			output = exepath.substr(0, (exepath.find_last_of('m')));
 			
-			m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();  
+			m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
 			commandFactory->setOutputDirectory(output);
 		}else {
 			//add / to name if needed
@@ -127,7 +129,7 @@ int SetDirectoryCommand::execute(){
 			}else{
 				out.close();
 				remove(outTemp.c_str());
-				m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();  
+				m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
 				commandFactory->setOutputDirectory(output);
 			}
 		}
@@ -138,7 +140,7 @@ int SetDirectoryCommand::execute(){
 			string exepath = m->argv;
 			input = exepath.substr(0, (exepath.find_last_of('m')));
 			
-			m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();  
+			m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
 			commandFactory->setInputDirectory(input);
 		}else {
 			//add / to name if needed
@@ -159,7 +161,7 @@ int SetDirectoryCommand::execute(){
 			}else{
 				in.close();
 				remove(inTemp.c_str());
-				m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();  
+				m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
 				commandFactory->setInputDirectory(input); 
 			}
 		}
@@ -168,7 +170,7 @@ int SetDirectoryCommand::execute(){
 		if (tempdefault == "clear") {  
 			#ifdef MOTHUR_FILES
 				string temp = MOTHUR_FILES; 
-				m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();  
+				m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();  
 				m->setDefaultPath(temp);
 			#else
 				string temp = ""; 
@@ -180,7 +182,7 @@ int SetDirectoryCommand::execute(){
 			string exepath = m->argv;
 			tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 			
-			m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
+			m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
 			m->setDefaultPath(tempdefault);
 		}else {
 			//add / to name if needed
@@ -191,7 +193,7 @@ int SetDirectoryCommand::execute(){
 				if (lastChar != "\\") { tempdefault += "\\"; }	
 			#endif
 			
-			m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
+			m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
 			m->setDefaultPath(tempdefault);
 		}
 
diff --git a/setlogfilecommand.h b/setlogfilecommand.h
index 0c0347b..ed08180 100644
--- a/setlogfilecommand.h
+++ b/setlogfilecommand.h
@@ -19,7 +19,7 @@ class SetLogFileCommand : public Command {
 	
 public:
 	SetLogFileCommand(string);
-	SetLogFileCommand() { abort = true; calledHelp = true; }
+	SetLogFileCommand() { setParameters(); abort = true; calledHelp = true; }
 	~SetLogFileCommand(){}
 	
 	vector<string> setParameters();
diff --git a/systemcommand.cpp b/systemcommand.cpp
index 6b0a6d0..6a1e355 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -9,7 +9,20 @@
 
 #include "systemcommand.h"
 
-
+//**********************************************************************************************************************
+vector<string> SystemCommand::setParameters(){	
+	try {
+		CommandParameter pcommand("command", "String", "", "", "", "", "",false,false); parameters.push_back(pcommand);
+				
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SystemCommand", "setParameters");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 SystemCommand::SystemCommand(string option)  {
 	try {
@@ -19,8 +32,22 @@ SystemCommand::SystemCommand(string option)  {
 		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
-			if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
-			else { 
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser.getParameters();
+			map<string, string>::iterator it;
+			
+			ValidParameters validParameter;
+			
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			string commandOption = validParameter.validFile(parameters, "command", false);			
+			if (commandOption == "not found") { commandOption = ""; }
+			else { command = commandOption; }
+			
+			if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
+			else if (commandOption == "") { 
 				//check for outputdir and inputdir parameters
 				int commaPos = option.find_first_of(',');
 				
diff --git a/systemcommand.h b/systemcommand.h
index 892ac96..8c959cf 100644
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,10 +18,10 @@ class SystemCommand : public Command {
 	public:
 	
 		SystemCommand(string);	
-		SystemCommand() { abort = true; calledHelp = true; }
+		SystemCommand() { setParameters(); abort = true; calledHelp = true; }
 		~SystemCommand(){}
 	
-		vector<string> setParameters() { return outputNames; } //dummy does not do anything
+		vector<string> setParameters();
 		string getCommandName()			{ return "system";		}
 		string getCommandCategory()		{ return "General";		}
 		string getHelpString();