added set.current and get.current commands and modified existing commands to update...

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index 13c8b2636680ee247cf05750cd57b6d5916b7d9c..8ab08553c4969268be12230b68f0f80303da2989 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -117,10 +117,6 @@ AmovaCommand::AmovaCommand(string option) {
                        if (phylipFileName == "not open") { phylipFileName = ""; abort = true; }
                        else if (phylipFileName == "not found") { 
                                phylipFileName = ""; 
-                               
-                               //check currentFiles for a phylip file
-                               //if (currentFiles->getPhylipFile() != "") {  phylipFileName = currentFiles->getPhylipFile(); m->mothurOut("Using " + phylipFileName + " as phylip file."); m->mothurOutEndLine();
-                               //}else { m->mothurOut("You must provide an phylip file."); m->mothurOutEndLine(); abort = true;  }
                        }       
                        
                        //check for required parameters
@@ -128,10 +124,6 @@ AmovaCommand::AmovaCommand(string option) {
                        if (designFileName == "not open") { abort = true; }
                        else if (designFileName == "not found") {
                                designFileName = "";
-                               
-                               //check currentFiles for a design file
-                               //if (currentFiles->getDesignFile() != "") {  designFileName = currentFiles->getDesignFile(); m->mothurOut("Using " + designFileName + " as design file."); m->mothurOutEndLine();
-                               //}else { m->mothurOut("You must provide an design file."); m->mothurOutEndLine(); abort = true;  }
                        }       
 
                        string temp = validParameter.validFile(parameters, "iters", false);