added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / getgroupcommand.cpp

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 9014031d5a58556493b712282fbf4bfc5535d5e2..c754f8eb1bb2ba79daf77c3a060a0ebf770252dd 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -19,7 +19,21 @@ GetgroupCommand::GetgroupCommand(string option){
                if(option == "help") { help(); abort = true; }
                
                else {
-                       if (option != "") { mothurOut("There are no valid parameters for the get.group command."); mothurOutEndLine(); abort = true; }
+                       //valid paramters for this command
+                       string Array[] =  {"outputdir","inputdir"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
+                       //check to make sure all parameters are valid for command
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = "";         }
                        
                        if ((globaldata->getSharedFile() == "")) { mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); mothurOutEndLine(); abort = true; }
                                
@@ -29,7 +43,8 @@ GetgroupCommand::GetgroupCommand(string option){
                                openInputFile(sharedfile, in);
                
                                //open output file
-                               outputFile = getRootName(sharedfile) + "bootGroups";
+                               if (outputDir == "") { outputDir += hasPath(sharedfile); }
+                               outputFile = outputDir + getRootName(getSimpleName(sharedfile)) + "bootGroups";
                                openOutputFile(outputFile, out);
 
                        }