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

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index e39d70bee58e1374774453d81d70dcf843c53be2..081f5ef027dc04c30da1eba77647d67288bbfb44 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -48,7 +48,7 @@ SummarySharedCommand::SummarySharedCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"label","calc","groups","all"};
+                       string Array[] =  {"label","calc","groups","all","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -66,6 +66,12 @@ SummarySharedCommand::SummarySharedCommand(string option){
                                 mothurOut("You must read a list and a group, or a shared before you can use the summary.shared 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->getSharedFile()); //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...
                        label = validParameter.validFile(parameters, "label", false);                   
@@ -151,7 +157,7 @@ SummarySharedCommand::SummarySharedCommand(string option){
                                        }
                                }
                                
-                               outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+                               outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "shared.summary";
                                openOutputFile(outputFileName, outputFileHandle);
                                mult = false;
                        }