added distance search method to classify.seqs

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 80a44297b48bfde50c633edfe7354e2f3e0cb115..10b998e73d78a3af0d41c3106743c52e6235359b 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -23,7 +23,7 @@ GetSAbundCommand::GetSAbundCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"label"};
+                       string Array[] =  {"label","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -36,6 +36,12 @@ GetSAbundCommand::GetSAbundCommand(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 
+                       string 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->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; }
                        
@@ -55,7 +61,7 @@ GetSAbundCommand::GetSAbundCommand(string option){
                        }
                                
                        if (abort == false) {
-                               filename = getRootName(globaldata->inputFileName) + "sabund";
+                               filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund";
                                openOutputFile(filename, out);
                        }
                }
@@ -123,6 +129,8 @@ int GetSAbundCommand::execute(){
                        }
                        
                        if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       string saveLabel = order->getLabel();
+                                       
                                        delete order;           
                                        order = (input->getOrderVector(lastLabel));
                                        
@@ -134,6 +142,9 @@ int GetSAbundCommand::execute(){
 
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
+                                       
+                                       //restore real lastlabel to save below
+                                       order->setLabel(saveLabel);
                        }