modified the engine to extract the path of mothur executable if argv does not contain...

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 2ffb65598a8fc75041190f764742342202e4ed52..7bea292ee6b1dfd7afe9a2ce1300e6b71f2b1324 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -72,7 +72,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
 
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
-                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = hasPath(inputFile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "version", false);          if (temp == "not found"){       temp = "F";                     }
@@ -182,13 +182,8 @@ int ClearcutCommand::execute() {
                string path = globaldata->argv;
                path = path.substr(0, (path.find_last_of('m')));
                
-               string clearcutCommand = "";
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       clearcutCommand = path + "clearcut/clearcut ";
-               #else
-                       clearcutCommand = path + "clearcut\\clearcut ";
-               #endif
-               
+               string clearcutCommand = path + "clearcut ";
+                               
                //you gave us a distance matrix
                if (phylipfile != "") { clearcutCommand += "--distance ";       }