changes while testing

[mothur.git] / setdircommand.cpp

diff --git a/setdircommand.cpp b/setdircommand.cpp
index b0d12b87bc49f4d3b6e9cae63558ba622b199701..3e50f4a508d2608ef1b51b9445fd3a388d1f4dec 100644 (file)
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -12,12 +12,13 @@
 //**********************************************************************************************************************
 vector<string> SetDirectoryCommand::setParameters(){   
        try {
-               CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
-        CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug);
-               CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
-               CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
+        CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
+        CommandParameter pmodnames("modifynames", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmodnames);
+               CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput);
+               CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); parameters.push_back(poutput);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -36,6 +37,7 @@ string SetDirectoryCommand::getHelpString(){
                helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
                helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
         helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
+        helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees.  modifynames=F will leave sequence names as they are.\n";
                helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
         helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n";
                helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
@@ -92,9 +94,18 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
                        if (temp == "not found") {  debug = false;  nodebug=true; }
             else {  debug = m->isTrue(temp); }
             m->debug = debug;
+            
+            bool nomod = false;
+            temp = validParameter.validFile(parameters, "modifynames", false);
+                       if (temp == "not found") {  modifyNames = true;  nomod=true; }
+            else {  modifyNames = m->isTrue(temp); }
+            m->modifyNames = modifyNames;
+            
+            if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
+            
                                
-                       if ((input == "") && (output == "") && (tempdefault == "") && nodebug) {        
-                               m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true;
+                       if ((input == "") && (output == "") && (tempdefault == "") && nodebug && nomod) {
+                               m->mothurOut("You must provide either an input, output, tempdefault, debug or modifynames for the set.outdir command."); m->mothurOutEndLine(); abort = true;
                        }else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; }
                }
        }