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

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index f2de77bbeed121a53d670e99ff203b5336cd1d9c..97d633278f4d43dc8b30a5e95298d2897bdabca7 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -35,7 +35,7 @@ RareFactCommand::RareFactCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"iters","freq","label","calc","abund"};
+                       string Array[] =  {"iters","freq","label","calc","abund","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -48,6 +48,12 @@ RareFactCommand::RareFactCommand(string option){
                                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 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
+                               outputDir = ""; 
+                               outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                       }
+
                        //make sure the user has already run the read.otu command
                        if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund, rabund or shared file before you can use the rarefact.single command."); mothurOutEndLine(); abort = true; }
                        
@@ -127,7 +133,7 @@ int RareFactCommand::execute(){
                
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
-                       string fileNameRoot = getRootName(inputFileNames[p]);
+                       string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
                        globaldata->inputFileName = inputFileNames[p];
                        
                        if (inputFileNames.size() > 1) {