working on libshuff

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 17b4908515179211b792a6d06801d2dc878a7bca..a0ccdcb690eda34efb4fe9964b375b47b0e71d2f 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -39,6 +39,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        helpRequest = optionText;
                }
                
+               if (commandName == "libshuff") {
+                       iters = "10000";
+                       cutoff = "1.0";
+               }
+               
                string key, value;              
                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
@@ -66,7 +71,10 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "fileroot" )         { fileroot = value;             }
                                if (key == "abund" )        { abund = value;        }
                                if (key == "random" )           { randomtree = value;   }
-                               if (key == "calc")                      { calc = value;         }
+                               if (key == "calc")                      { calc = value;                 }
+                               if (key == "step")                      { step = value;                 }
+                               if (key == "form")                      { form = value;                 }
+                               
 
                                
                                if (key == "line") {//stores lines to be used in a set
@@ -116,7 +124,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "abund" )        { abund = value;        }
                        if (key == "random" )           { randomtree = value;   }
                        if (key == "calc")                      { calc = value;         }
-
+                       if (key == "step")                      { step = value;                 }
+                       if (key == "form")                      { form = value;                 }
 
                        if (key == "line") {//stores lines to be used in a vector
                                lines.clear();
@@ -218,6 +227,8 @@ string GlobalData::getFreq()                        {       return freq;            }
 string GlobalData::getAbund()           {   return abund;       }
 string GlobalData::getRandomTree()             {       return randomtree;      }
 string GlobalData::getGroups()                 {       return groups;          }
+string GlobalData::getStep()                   {       return step;            }
+string GlobalData::getForm()                   {       return form;            }
 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;}
@@ -266,6 +277,8 @@ void GlobalData::clear() {
        method                  =       "furthest";
        fileroot                =       "";
        abund           =   "10";
+       step                    =       "0.01";
+       form                    =       "integral";
 }
 
 //*******************************************************/
@@ -281,7 +294,9 @@ void GlobalData::reset() {
        freq                    =       "100";
        method                  =       "furthest";
        calc                    =       "";
-       abund = "10";
+       abund                   =   "10";
+       step                    =       "0.01";
+       form                    =       "integral";
 }
 /*******************************************************/