adding current file class

[mothur.git] / anosimcommand.cpp

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index bb0f495a0ac81d6ce72c358b0c02d13592f8dbb2..443cf8aae28e423b703085c4b2f14ce65ef86cfa 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -115,12 +115,12 @@ AnosimCommand::AnosimCommand(string option) {
                        
                        phylipFileName = validParameter.validFile(parameters, "phylip", true);
                        if (phylipFileName == "not open") { phylipFileName = ""; abort = true; }
-                       else if (phylipFileName == "not found") { phylipFileName = ""; }        
-                       else if (designFileName == "not found") {
-                               designFileName = "";
-                               m->mothurOut("You must provide an phylip file.");
-                               m->mothurOutEndLine();
-                               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
@@ -128,9 +128,11 @@ AnosimCommand::AnosimCommand(string option) {
                        if (designFileName == "not open") { abort = true; }
                        else if (designFileName == "not found") {
                                designFileName = "";
-                               m->mothurOut("You must provide an design file.");
-                               m->mothurOutEndLine();
-                               abort = true;
+                               
+                               //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);