added a few evenness calculators and fixed a couple of bugs in filter.seqs and pre...

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 2ffb65598a8fc75041190f764742342202e4ed52..b1f40e0a03f65e3dc04153cd554abdb8e8adb5aa 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";                     }
@@ -92,7 +92,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
                        temp = validParameter.validFile(parameters, "shuffle", false);          if (temp == "not found"){       temp = "F";                     }
                        shuffle = isTrue(temp); 
                        
-                       temp = validParameter.validFile(parameters, "neighbor", false);         if (temp == "not found"){       temp = "F";                     }
+                       temp = validParameter.validFile(parameters, "neighbor", false);         if (temp == "not found"){       temp = "T";                     }
                        neighbor = isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "DNA", false);                      if (temp == "not found"){       temp = "F";                     }
@@ -146,7 +146,7 @@ void ClearcutCommand::help(){
                m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");
                m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");
                m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");
-               m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");
+               m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=T. \n");
                
                m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");
                m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");
@@ -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 ";       }