fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 66a44f25b7246af237194e634eeeeb9514623899..b1ac4e87b986cee6380c997c6c40590b089067f7 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -110,7 +110,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "fileroot" )         { fileroot = value;             }
                                if (key == "abund" )        { abund = value;        }
                                if (key == "random" )           { randomtree = value;   }
-                               if (key == "groups" )           { groups = value;       }
                                if (key == "calc")                      { calc = value;         }
 
                                
@@ -160,7 +159,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "fileroot" )         { fileroot = value;             }
                        if (key == "abund" )        { abund = value;        }
                        if (key == "random" )           { randomtree = value;   }
-                       if (key == "groups" )           { groups = value;       }
                        if (key == "calc")                      { calc = value;         }
 
 
@@ -187,6 +185,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                
                //set format for shared
                if ((listfile != "") && (groupfile != "")) { format = "shared"; }
+               if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
                                
                //input defaults for calculators
                if (commandName == "collect.single") {
@@ -261,6 +260,7 @@ string GlobalData::getJumble()                      {       return jumble;          }
 string GlobalData::getFreq()                   {       return freq;            }
 string GlobalData::getAbund()           {   return abund;       }
 string GlobalData::getRandomTree()             {       return randomtree;      }
+string GlobalData::getGroups()                 {       return groups;          }
 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;}
@@ -269,7 +269,8 @@ void GlobalData::setColumnFile(string file) {       columnfile = file;    inputFileNam
 void GlobalData::setNameFile(string file)              {       namefile = file;                }
 void GlobalData::setFormat(string Format)              {       format = Format;                }
 void GlobalData::setRandomTree(string Random)  {       randomtree = Random;    }
-void GlobalData::setCalc(string Calc)                  {       calc = Calc;    }
+void GlobalData::setGroups(string g)                   {       groups = g;                             }
+void GlobalData::setCalc(string Calc)                  {       calc = Calc;                    }
 
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