deconvolute command

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index aba99444049cbad7c94576314e6c1347469e0d2f..6d67d0da0fd41c2978a073a5f377746331b0d9a6 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -79,8 +79,10 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                allLines = 1;
                commandName = commandString; //save command name to be used by other classes
                
-               //clears out data from previous read and sets format
-               setReadFormat(commandName);
+               //clears out data from previous read
+               if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.list")) { 
+                       clear();
+               }
                
                //saves help request
                if (commandName =="help") {
@@ -99,6 +101,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
                                if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
                                if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } 
+                               if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } 
                                if (key == "namefile" )         { namefile = value; }
                                if (key == "orderfile" )        { orderfile = value; }
                                if (key == "groupfile" )        { groupfile = value; }
@@ -162,6 +165,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
                        if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
                        if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
+                       if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } 
                        if (key == "namefile" )         { namefile = value; }
                        if (key == "orderfile" )        { orderfile = value; }
                        if (key == "groupfile" )        { groupfile = value; }
@@ -253,30 +257,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 }
 /*******************************************************/
 
-/******************************************************/
-void GlobalData::setReadFormat(string command){
-       try {
-               if (command == "read.dist") { 
-                       clear();
-               }else if (command == "read.otu") { 
-                       clear();
-               }else if (command == "read.shared") { 
-                       clear();
-                       format = "shared";
-               }else if (command == "parselist") { format = "list"; }
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setReadFormat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the GlobalData class function setReadFormat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-
-/*******************************************************/
-
 /******************************************************/
 // These functions give you the option parameters of the commands
 string GlobalData::getPhylipFile()             {       return phylipfile;      }
@@ -287,6 +267,7 @@ string GlobalData::getSabundFile()          {       return sabundfile;      }
 string GlobalData::getNameFile()               {       return namefile;        }
 string GlobalData::getGroupFile()              {       return groupfile;       }
 string GlobalData::getOrderFile()              {       return orderfile;       }
+string GlobalData::getFastaFile()              {       return fastafile;       }
 string GlobalData::getCutOff()                 {       return cutoff;          }
 string GlobalData::getFormat()                 {       return format;          }
 string GlobalData::getPrecision()              {       return precision;       }
@@ -328,6 +309,7 @@ void GlobalData::clear() {
        namefile                =       "";
        groupfile               =       ""; 
        orderfile               =       "";
+       fastafile               =   "";
        cutoff                  =       "10.00";
        format                  =       "";
        precision               =       "100";