adding current file class

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index b9b5deeb5e670ef2f119eb09bded37ab870efe4d..74fbda7ff6164128551bead9cfb4c8bfabb7ba0e 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -115,12 +115,12 @@ AmovaCommand::AmovaCommand(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 +128,10 @@ AmovaCommand::AmovaCommand(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->getPhylipFile(); m->mothurOut("Using " + designFileName + " as phylip file."); m->mothurOutEndLine();
+                               }else { m->mothurOut("You must provide an design file."); m->mothurOutEndLine(); abort = true;  }
                        }       
 
                        string temp = validParameter.validFile(parameters, "iters", false);