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

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index e68890cec67c253ae78e9400f865b4b66739a07b..a8d5069d7d123277b58df1cfdf1d0ff8b773c4e6 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -50,7 +50,7 @@ CollectSharedCommand::CollectSharedCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"freq","label","calc","groups","all"};
+                       string Array[] =  {"freq","label","calc","groups","all","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -63,6 +63,10 @@ CollectSharedCommand::CollectSharedCommand(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 = "";         }
+                       
+                                               
                        //make sure the user has already run the read.otu command
                        if (globaldata->getSharedFile() == "") {
                                if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
@@ -107,8 +111,9 @@ CollectSharedCommand::CollectSharedCommand(string option){
                        all = isTrue(temp);
                                                
                        if (abort == false) {
-                       
-                               string fileNameRoot = getRootName(globaldata->inputFileName);
+                               
+                               if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
+                               string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
                                format = globaldata->getFormat();
                                int i;