changed name of distance command to dist.seqs

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index ae1b0e2ebbb463fefc32a2f8ad3fd1816b01109d..fddb5c9caadb3e2e7fcaf7f940718eacb6c39e30 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -43,7 +43,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                }
                
                //set default value for cutoff
-               if (commandName == "distance") {        cutoff = "1.0";         }
+               if (commandName == "dist.seq") {        cutoff = "1.0";         }
 
                string key, value;              
                //reads in parameters and values
@@ -215,7 +215,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
-               if (commandName == "distance") {
+               if (commandName == "dist.seq") {
                        if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
@@ -290,11 +290,13 @@ string GlobalData::getScale()                     {       return scale;           }
 string GlobalData::getEnds()                   {   return ends;                }
 string GlobalData::getProcessors()             {       return processors;      }
 
-void GlobalData::setListFile(string file)      {       listfile = file;        inputFileName = file;}
-void GlobalData::setRabundFile(string file)    {       rabundfile = file;      inputFileName = file;}
-void GlobalData::setSabundFile(string file)    {       sabundfile = file;      inputFileName = file;}
-void GlobalData::setPhylipFile(string file)    {       phylipfile = file;    inputFileName = file;}
-void GlobalData::setColumnFile(string file)    {       columnfile = file;    inputFileName = file;}
+void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;}
+void GlobalData::setGroupFile(string file)             {       groupfile = file;       }
+void GlobalData::setRabundFile(string file)            {       rabundfile = file;      inputFileName = file;}
+void GlobalData::setSabundFile(string file)            {       sabundfile = file;      inputFileName = file;}
+void GlobalData::setPhylipFile(string file)            {       phylipfile = file;    inputFileName = file;}
+void GlobalData::setColumnFile(string file)            {       columnfile = file;    inputFileName = file;}
+void GlobalData::setSharedFile(string file)            {       sharedfile = file;      inputFileName = file; fileroot = file;}
 void GlobalData::setNameFile(string file)              {       namefile = file;                }
 void GlobalData::setFormat(string Format)              {       format = Format;                }
 void GlobalData::setRandomTree(string Random)  {       randomtree = Random;    }