altered venn command to make use of sharedchao for any number of groups, fixed window...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 6849b880bd34fc20b74d720b86c299451be71802..ae1b0e2ebbb463fefc32a2f8ad3fd1816b01109d 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -42,6 +42,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        cutoff = "1.0";
                }
                
+               //set default value for cutoff
+               if (commandName == "distance") {        cutoff = "1.0";         }
+
                string key, value;              
                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
@@ -80,6 +83,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "filter")            { filter = value;               }
                                if (key == "soft")                  { soft = value;                 }
                                if (key == "scale")                     { scale = value;                }
+                               if (key == "ends" )                     { ends = value;                 }
+                               if (key == "processors" )       { processors = value;   }
                                
 
                                
@@ -144,9 +149,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "filter")            { filter = value;               }
                        if (key == "soft")                  { soft = value;                 }
                        if (key == "scale")                     { scale = value;                }
-
-                       
-                       
+                       if (key == "ends" )                     { ends = value;                 }
+                       if (key == "processors" )       { processors = value;   }
 
 
                        if (key == "line") {//stores lines to be used in a vector
@@ -211,6 +215,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
+               if (commandName == "distance") {
+                       if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
+                       Estimators.clear();
+                       splitAtDash(calc, Estimators); 
+               }
                if (commandName == "venn") {
                        if ((calc == "default") || (calc == "")) { 
                                if (format == "list") { calc = "sobs"; }
@@ -278,6 +287,8 @@ string GlobalData::getTrump()                       {   return trump;       }
 string GlobalData::getSoft()                   {   return soft;                }
 string GlobalData::getFilter()                 {   return filter;              }
 string GlobalData::getScale()                  {       return scale;           }
+string GlobalData::getEnds()                   {   return ends;                }
+string GlobalData::getProcessors()             {       return processors;      }
 
 void GlobalData::setListFile(string file)      {       listfile = file;        inputFileName = file;}
 void GlobalData::setRabundFile(string file)    {       rabundfile = file;      inputFileName = file;}
@@ -289,6 +300,9 @@ void GlobalData::setFormat(string Format)           {       format = Format;                }
 void GlobalData::setRandomTree(string Random)  {       randomtree = Random;    }
 void GlobalData::setGroups(string g)                   {       groups = g;                             }
 void GlobalData::setCalc(string Calc)                  {       calc = Calc;                    }
+void GlobalData::setEnds(string e)                             {   ends = e;                           }
+void GlobalData::setProcessors(string p)               {       processors = p;                 }
+
 
 /*******************************************************/
 
@@ -338,7 +352,9 @@ void GlobalData::clear() {
        trump           =   "";         
        filter          =   "";         
        soft            =   ""; 
-       scale                   =       "log10";            
+       scale                   =       "log10";
+       ends                    =   "T";  //yes
+       processors              =       "1";
 
 }
 
@@ -359,6 +375,8 @@ void GlobalData::reset() {
        abund                   =   "10";
        step                    =       "0.01";
        form                    =       "integral";
+       ends                    =   "T";
+       processors              =       "1";
 }
 /*******************************************************/