major change to the tree class to use the count table class instead of tree map....

[mothur.git] / sensspeccommand.cpp

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index cfa1f5b6dc0649925ff4762abdef070e93fd7688..b62bb00548f3e1ee66f0c1cf2b4bee117c5416cf 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -14,7 +14,6 @@ vector<string> SensSpecCommand::setParameters(){
        try {
                CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
                CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
-               //CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
                CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
@@ -136,16 +135,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                                        path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["column"] = inputDir + it->second;           }
-                               }
-                               
-                               //it = parameters.find("name");
-                               //user has given a template file
-                               //if(it != parameters.end()){ 
-                                       //path = m->hasPath(it->second);
-                                       //if the user has not given a path then, add inputdir. else leave path alone.
-                                       //if (path == "") {     parameters["name"] = inputDir + it->second;             }
-                               //}
-                               
+                               }                               
                        }
                        //check for required parameters
                        listFile = validParameter.validFile(parameters, "list", true);
@@ -196,12 +186,6 @@ SensSpecCommand::SensSpecCommand(string option)  {
                        else if(!m->isTrue(temp))       {       hard = 0;       }
                        else if(m->isTrue(temp))        {       hard = 1;       }
                        
-//                     temp = validParameter.validFile(parameters, "name", true);
-//                     if (temp == "not found")        {       nameFile = "";          }
-//                     else if(temp == "not open")     {       abort = true;           }
-//                     else                                            {       nameFile = temp;        }
-//                     cout << "name:\t" << nameFile << endl;
-
                        temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found") { temp = "-1.00"; }
                        m->mothurConvert(temp, cutoff);  
 //                     cout << cutoff << endl;