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

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 94437fddfa766efe0bf25233914fe59befd9f204..fcc42ced634b80790d6aa3f5977ea6ef3121f77a 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -22,21 +22,39 @@ GetListCountCommand::GetListCountCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"list","label"};
+                       string AlignArray[] =  {"list","label","outputdir","inputdir"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();
                        
                        ValidParameters validParameter;
-               
+                       map<string, string>::iterator it;
+                       
                        //check to make sure all parameters are valid for command
-                       for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
                        string ranRead = globaldata->getListFile();
                        
+                       //if the user changes the input directory command factory will send this info to us in the output parameter 
+                       string inputDir = validParameter.validFile(parameters, "inputdir", false);              
+                       if (inputDir == "not found"){   inputDir = "";          }
+                       else {
+                               string path;
+                               it = parameters.find("list");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["list"] = inputDir + it->second;             }
+                               }
+                       }
+
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
+                       
                        //check for required parameters
                        listfile = validParameter.validFile(parameters, "list", true);
                        if ((listfile == "not found") && (globaldata->getListFile() == ""))  { mothurOut("You must read a listfile before running the get.listcount command.");  mothurOutEndLine(); abort = true; }
@@ -179,7 +197,8 @@ int GetListCountCommand::execute(){
 void GetListCountCommand::process(ListVector* list) {
        try {
                string binnames, name, sequence;
-               string outputFileName = getRootName(listfile) + list->getLabel() + ".otu";
+               if (outputDir == "") { outputDir += hasPath(listfile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + list->getLabel() + ".otu";
                openOutputFile(outputFileName, out);
                
                mothurOut(list->getLabel()); mothurOutEndLine();