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

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index e26dbcc5f6e926be9531dd7c719fcf79abfd13a3..437f044e841783059421a121a2d89bc079207c54 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -31,7 +31,7 @@ VennCommand::VennCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"groups","label","calc", "abund"};
+                       string AlignArray[] =  {"groups","label","calc", "abund","outputdir","inputdir"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -48,6 +48,12 @@ VennCommand::VennCommand(string option){
                        if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
                                mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); mothurOutEndLine(); 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  
+                       }
 
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -122,7 +128,7 @@ VennCommand::VennCommand(string option){
                                        }
                                }
                                
-                               venn = new Venn();
+                               venn = new Venn(outputDir);
                        }
                }