added phylo.diversity command. added hard parameter to cluster, hcluster and read...

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 6f6e309331df3caf27dc5d2d0c6d4e19ab246590..9ed67e04433edecd93262c1824732edbb3cd186c 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -22,7 +22,7 @@ ClusterCommand::ClusterCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"cutoff","precision","method","showabund","timing","outputdir","inputdir"};
+                       string Array[] =  {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -56,10 +56,13 @@ ClusterCommand::ClusterCommand(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));
+                       if (!hard) {    cutoff += (5 / (precision * 10.0));  }
                        
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
@@ -114,7 +117,7 @@ ClusterCommand::ClusterCommand(string option)  {
 void ClusterCommand::help(){
        try {
                m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
-               m->mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
+               m->mothurOut("The cluster command parameter options are method, cuttoff, hard, precision, showabund and timing. No parameters are required.\n");
                m->mothurOut("The cluster command should be in the following format: \n");
                m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
                m->mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n");