1.18.0

[mothur.git] / clusterdoturcommand.cpp

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 4471b357d268490a2c22ff7d44e9172be392512b..2b7b02b63a3a97d683d16a01b4514c5aa2671626 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -17,8 +17,8 @@ vector<string> ClusterDoturCommand::setParameters(){
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
                CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -40,7 +40,7 @@ string ClusterDoturCommand::getHelpString(){
                helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
                helpString += "The cluster.classic command should be in the following format: \n";
                helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
-               helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then furthest is assumed.\n";      
+               helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then average is assumed.\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -151,14 +151,14 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
-                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
                        sim = m->isTrue(temp); 
                        
                        method = validParameter.validFile(parameters, "method", false);
-                       if (method == "not found") { method = "furthest"; }
+                       if (method == "not found") { method = "average"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { 
                                if (method == "furthest") { tag = "fn"; }