removed readseqs, readfasta, readnexus, readclustal, readseqsphylip and updated seque...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index d7afc40b352229484d2f350f1ad190631a5ab7ed..b446d676fdb702aa0cb4a836dcb757a0e541fd0c 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -60,8 +60,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                                if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       } 
                                if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
-                               if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         } 
-                               if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
                                if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
                                if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
                                if (key == "name" )             { namefile = value;             }
@@ -138,8 +136,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                        if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
                        if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
-                       if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
-                       if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; } 
                        if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           } 
                        if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
                        if (key == "name" )             { namefile = value;             }
@@ -303,8 +299,6 @@ string GlobalData::getOrderFile()           {       return orderfile;       }
 string GlobalData::getTreeFile()               {       return treefile;        }
 string GlobalData::getSharedFile()             {       return sharedfile;      }
 string GlobalData::getFastaFile()              {       return fastafile;       }
-string GlobalData::getNexusFile()              {       return nexusfile;       }
-string GlobalData::getClustalFile()     {   return clustalfile; }
 string GlobalData::getCutOff()                 {       return cutoff;          }
 string GlobalData::getFormat()                 {       return format;          }
 string GlobalData::getPrecision()              {       return precision;       }
@@ -383,8 +377,6 @@ void GlobalData::clear() {
        groupfile               =       ""; 
        orderfile               =       "";
        fastafile               =   "";
-       nexusfile               =   "";
-       clustalfile             =   "";
        treefile                =       "";
        sharedfile              =       "";
        candidatefile   =       "";