fixed some bugs found while testing 1.8

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index a31883cf3c65aabf3955d12191b91b9ad9fe050c..473d2db8b473bbef240793c419e6c8beece29ddf 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -136,17 +136,17 @@ int CollectCommand::execute(){
                
                if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
                else {  inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
-               
+       
                for (int p = 0; p < inputFileNames.size(); p++) {
-                       
+               
                        if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
                        string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
                        globaldata->inputFileName = inputFileNames[p];
-                       
+               
                        if (inputFileNames.size() > 1) {
                                mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
                        }
-                       
+               
                        validCalculator = new ValidCalculators();
                        
                        for (int i=0; i<Estimators.size(); i++) {
@@ -195,13 +195,12 @@ int CollectCommand::execute(){
                                }
                        }
                
-                       
                        //if the users entered no valid calculators don't execute command
                        if (cDisplays.size() == 0) { return 0; }
                        
                        read = new ReadOTUFile(inputFileNames[p]);      
                        read->read(&*globaldata); 
-                               
+               
                        order = globaldata->gorder;
                        string lastLabel = order->getLabel();
                        input = globaldata->ginput;