modified calculators to use doubles, added numotu and fontsize parameters to heatmap...

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 7bea292ee6b1dfd7afe9a2ce1300e6b71f2b1324..b1f40e0a03f65e3dc04153cd554abdb8e8adb5aa 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -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");