changed hard parameter in cluster commands

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index dc14e1670c5221599dd14929dd6d08fde6c6b766..b4d601751630af81741d64ab605c95d5650838a5 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -110,7 +110,7 @@ HClusterCommand::HClusterCommand(string option)  {
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
-                       if (!hard) {  cutoff += (5 / (precision * 10.0));  }
+                       cutoff += (5 / (precision * 10.0)); 
                        
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
@@ -163,7 +163,7 @@ void HClusterCommand::help(){
                m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
                m->mothurOut("The hcluster command should be in the following format: \n");
                m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
-               m->mothurOut("The acceptable hcluster methods are furthest and nearest, but we hope to add average in the future.\n\n");        
+               m->mothurOut("The acceptable hcluster methods are furthest, nearest and average.\n\n"); 
        }
        catch(exception& e) {
                m->errorOut(e, "HClusterCommand", "help");
@@ -279,8 +279,14 @@ int HClusterCommand::execute(){
                                                return 0;  
                                        }
 
-                                       
-                                       float rndDist = roundDist(seqs[i].dist, precision);
+                       
+                                       float rndDist;
+                                       if (hard) {
+                                               rndDist = ceilDist(seqs[i].dist, precision); 
+                                       }else{
+                                               rndDist = roundDist(seqs[i].dist, precision); 
+                                       }
+
                                        
                                        if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
                                                printData("unique");