merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 68f7fc389bb70948c1a22255af0cec275ba0ca5a..fe3c11b87dba7519ebec6c1e39168b764563233e 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,6 +1,6 @@
+
+
 #include "globaldata.hpp"
-#include "tree.h"
-#include "sparsematrix.hpp"
 
 /*******************************************************/
 
@@ -25,15 +25,12 @@ string GlobalData::getGroupFile()           {       return groupfile;               }
 string GlobalData::getOrderFile()              {       return orderfile;               }
 string GlobalData::getTreeFile()               {       return treefile;                }
 string GlobalData::getSharedFile()             {       return sharedfile;              }
-string GlobalData::getFastaFile()              {       return fastafile;               }       
+//string GlobalData::getFastaFile()            {       return fastafile;               }       
 string GlobalData::getFormat()                 {       return format;                  }
-string GlobalData::getCandidateFile()  {       return candidatefile;   }
-
 
 void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;                                   }
-void GlobalData::setFastaFile(string file)             {       fastafile = file;       inputFileName = file;                                   }
+//void GlobalData::setFastaFile(string file)           {       fastafile = file;       inputFileName = file;                                   }
 void GlobalData::setTreeFile(string file)              {       treefile = file;        inputFileName = file;                                   }
-void GlobalData::setCandidateFile(string file) {       candidatefile = 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;                                     }
@@ -59,19 +56,20 @@ GlobalData::GlobalData() {
 /******************************************************/
 void GlobalData::clear() {
        //option definitions should go here...
-       phylipfile              =       "";
-       columnfile              =       "";
+       phylipfile              =       ""; //do we need this?
+       columnfile              =       ""; //do we need this?
        listfile                =       "";
        rabundfile              =       "";
        sabundfile              =       "";
-       namefile                =       "";
-       groupfile               =       ""; 
+       namefile                =       ""; //do we need this?
+       groupfile               =       ""; //do we need this?
        orderfile               =       "";
-       fastafile               =   "";
+//     fastafile               =   ""; //do we need this?
        treefile                =       "";
        sharedfile              =       "";
-       candidatefile   =       "";
 }
+
+
 /*******************************************************/
 
 /******************************************************/