changes to chop.seqs

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 1e4e42fa6f4e3e4a3eb4fab97bcf35472bfe5d67..ab8bdcfdfa6ea950745c857efe482352bbc19d4c 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -27,7 +27,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","splitcutoff","outputdir","inputdir"};
+                       string Array[] =  {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -121,11 +121,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        convert(temp, cutoff); 
                        if (!hard) {    cutoff += (5 / (precision * 10.0));  }
                        
-                       temp = validParameter.validFile(parameters, "splitcutoff", false);
-                       if (temp == "not found") { temp = "0.10"; }
-                       convert(temp, splitcutoff); 
-                       if (!hard) {    splitcutoff += (5 / (precision * 10.0));  }
-                       
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
                        
@@ -208,7 +203,7 @@ int ClusterSplitCommand::execute(){
                time_t estart = time(NULL);
                
                //split matrix into non-overlapping groups
-               SplitMatrix* split = new SplitMatrix(distfile, namefile, splitcutoff);
+               SplitMatrix* split = new SplitMatrix(distfile, namefile, cutoff);
                split->split();
                
                if (m->control_pressed) { delete split; return 0; }