added kruskal.wallis command. added worked on make.lefse. working of lefse command...

[mothur.git] / setlogfilecommand.cpp

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 593664e3569d0ef8f9faeb31df9379ab2cafed41..41c8e743122399563b8367fda6a9d4a94f9bda86 100644 (file)
--- a/setlogfilecommand.cpp
+++ b/setlogfilecommand.cpp
@@ -9,19 +9,52 @@
 
 #include "setlogfilecommand.h"
 
+
+//**********************************************************************************************************************
+vector<string> SetLogFileCommand::setParameters(){     
+       try {
+               CommandParameter pappend("append", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pappend);
+               CommandParameter pname("name", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pname);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+               
+               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, "SetLogFileCommand", "setParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+string SetLogFileCommand::getHelpString(){     
+       try {
+               string helpString = "";
+               helpString += "The set.logfile command can be used to provide a specific name for your logfile and/or to append the log generated by mothur to an existing file.\n";
+               helpString += "The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n";
+               helpString += "The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n";
+               helpString += "Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n";
+               return helpString;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SetLogFileCommand", "getHelpString");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 SetLogFileCommand::SetLogFileCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"name","append","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();
@@ -36,7 +69,7 @@ SetLogFileCommand::SetLogFileCommand(string option)  {
                        if (name == "not found") {  m->mothurOut("name is a required parameter for the set.logfile command."); abort = true; } 
                        
                        string temp = validParameter.validFile(parameters, "append", false);            if (temp == "not found") {  temp = "F";  }
-                       append = isTrue(temp);
+                       append = m->isTrue(temp);
                }
        }
        catch(exception& e) {
@@ -44,35 +77,22 @@ SetLogFileCommand::SetLogFileCommand(string option)  {
                exit(1);
        }
 }
-//**********************************************************************************************************************
-
-void SetLogFileCommand::help(){
-       try {
-               m->mothurOut("The set.logfile command can be used to provide a specific name for your logfile and/or to append the log generated by mothur to an existing file.\n");
-               m->mothurOut("The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n");
-               m->mothurOut("The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n");
-               m->mothurOut("Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SetLogFileCommand", "help");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-
-SetLogFileCommand::~SetLogFileCommand(){}
 
 //**********************************************************************************************************************
 
 int SetLogFileCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
-               
-               commandFactory = CommandFactory::getInstance();
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               commandFactory->setLogfileName(name, append);
+        commandFactory = CommandFactory::getInstance();
+        
+        string directory = m->hasPath(name);
+        if (directory == "") {
+            commandFactory->setLogfileName(name, append);
+        }else if (m->dirCheck(directory)) {
+             commandFactory->setLogfileName(name, append);
+        }
                
                return 0;
        }