added check for positive values in pairwise.seqs gap extend, gap open and mismatch...

[mothur.git] / makebiomcommand.cpp

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index 41f2316b3a036840208635d3abbacd89e59f6413..70e3b1ad94698cc6369d64555dd70ed889a9c841 100644 (file)
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -168,7 +168,7 @@ MakeBiomCommand::MakeBiomCommand(string option) {
                        
                        //initialize outputTypes
                        vector<string> tempOutNames;
-                       outputTypes["relabund"] = tempOutNames;
+                       outputTypes["biom"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -328,6 +328,14 @@ int MakeBiomCommand::execute(){
                
         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); }  return 0; }     
                
+        //set sabund file as new current sabundfile
+        string current = "";
+               itTypes = outputTypes.find("biom");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setBiomFile(current); }
+               }
+
+        
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }