1.12.0

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index d9a14d9b5979636dba434733a132d35c25de8568..b4d601751630af81741d64ab605c95d5650838a5 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -21,7 +21,7 @@ HClusterCommand::HClusterCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
+                       string Array[] =  {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -104,10 +104,13 @@ HClusterCommand::HClusterCommand(string option)  {
                        length = temp.length();
                        convert(temp, precision); 
                        
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       hard = isTrue(temp);
+                       
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
-                       cutoff += (5 / (precision * 10.0));
+                       cutoff += (5 / (precision * 10.0)); 
                        
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
@@ -160,7 +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");
@@ -189,7 +192,7 @@ int HClusterCommand::execute(){
                time_t estart = time(NULL);
                
                if (!sorted) {
-                       read = new ReadCluster(distfile, cutoff);       
+                       read = new ReadCluster(distfile, cutoff, outputDir, true);      
                        read->setFormat(format);
                        read->read(globaldata->nameMap);
                        
@@ -276,8 +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");