1.18.0

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 221646700817bdddf61c1f2b968328a1af590ac1..cdcc6ca9745d8bdf3509c3505ef5c15dc61fd991 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -20,11 +20,11 @@ vector<string> ClusterCommand::setParameters(){
                CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);              
                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 pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
                CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
                CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
                CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -44,7 +44,7 @@ string ClusterCommand::getHelpString(){
                helpString += "The cluster command parameter options are phylip, column, name, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
                helpString += "The cluster command should be in the following format: \n";
                helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
-               helpString += "The acceptable cluster methods are furthest, nearest, average and weighted.  If no method is provided then furthest is assumed.\n";      
+               helpString += "The acceptable cluster methods are furthest, nearest, average and weighted.  If no method is provided then average is assumed.\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -182,7 +182,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        length = temp.length();
                        convert(temp, precision); 
                        
-                       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"; }
@@ -194,7 +194,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        cutoff += (5 / (precision * 10.0));  
                        
                        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")) { }
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; }