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

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 7f60d712861f34a79b798e0ef8d1a3cbcbe714a5..414f33087738ba355ad5ff51c2e89349d41b21f9 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -22,7 +22,7 @@ ReadDistCommand::ReadDistCommand(string option) {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
+                       string Array[] =  {"phylip", "column", "name", "cutoff","hard", "precision", "group","outputdir","inputdir","sim"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -126,9 +126,12 @@ ReadDistCommand::ReadDistCommand(string option) {
                        sim = isTrue(temp); 
                        globaldata->sim = sim;
                        
+                       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));  }
                        
                        if (abort == false) {
                                distFileName = globaldata->inputFileName;