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

[mothur.git] / anosimcommand.cpp

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index 443cf8aae28e423b703085c4b2f14ce65ef86cfa..79064a4bf6731cfcd1604f2a2c8d28f42e501b13 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -117,10 +117,6 @@ AnosimCommand::AnosimCommand(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
@@ -128,11 +124,6 @@ AnosimCommand::AnosimCommand(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);