modified trim.seqs command

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index bf28cc62ac9e7c232a03670f2a17654776459140..c42969e5ff5b8450a5ae63e9876e0f5bde8d29ad 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -102,9 +102,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if(key == "maxlength")          {       maxLength = value;              }
                                if(key == "flip"        )               {       flip = value;                   }
                                if(key == "oligos"      )               {       oligoFile = value;              }
-                               if(key == "forward"     )               {       forMismatch = value;    }
-                               if(key == "reverse"     )               {       revMismatch = value;    }
-                               if(key == "barcode"     )               {       barMismatch = value;    }
                                        
                                if(key == "line") {//stores lines to be used in a vector
                                        lines.clear();
@@ -183,9 +180,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if(key == "maxlength")  {       maxLength = value;              }
                        if(key == "flip"        )       {       flip = value;                   }
                        if(key == "oligos"      )       {       oligoFile = value;              }
-                       if(key == "forward"     )       {       forMismatch = value;    }
-                       if(key == "reverse"     )       {       revMismatch = value;    }
-                       if(key == "barcode"     )       {       barMismatch = value;    }
                        
 
                        if(key == "line") {//stores lines to be used in a vector
@@ -347,9 +341,6 @@ string GlobalData::getMinLength()           {       return minLength;               }
 string GlobalData::getMaxLength()              {       return maxLength;               }
 string GlobalData::getFlip()                   {       return flip;                    }
 string GlobalData::getOligosFile()             {       return oligoFile;               }
-string GlobalData::getForwardMismatch()        {       return forMismatch;             }
-string GlobalData::getReverseMismatch()        {       return revMismatch;             }
-string GlobalData::getBarcodeMismatch()        {       return barMismatch;             }
 
 
 void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;                                   }
@@ -433,9 +424,6 @@ void GlobalData::clear() {
        minLength               =       "-1";
        maxLength               =       "-1";
        flip                    =       "0";
-       forMismatch             =       "0";
-       revMismatch             =       "0";
-       barMismatch             =       "0";
        oligoFile               =       "";
 }
 
@@ -479,9 +467,6 @@ void GlobalData::reset() {
        minLength               =       "-1";
        maxLength               =       "-1";
        flip                    =       "0";
-       forMismatch             =       "0";
-       revMismatch             =       "0";
-       barMismatch             =       "0";
        oligoFile               =       "";
        
 }