added boneh, efron, and solow calculators

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index b4239f36bebb2fce5544cb171d6493c0d4a86aaf..88c5a13aa364239131f0d86ecb2b99dfe25d5930 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -85,6 +85,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "scale")                     { scale = value;                }
                                if (key == "ends" )                     { ends = value;                 }
                                if (key == "processors" )       { processors = value;   }
+                               if (key == "size" )         { size = value;         }
+                               
+
+                               
+
                                if (key == "template")          { templatefile = value; }
                                if (key == "search")            { search = value;               }
                                if (key == "ksize")                     { ksize = value;                }
@@ -155,6 +160,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "scale")                     { scale = value;                }
                        if (key == "ends" )                     { ends = value;                 }
                        if (key == "processors" )       { processors = value;   }
+                       if (key == "size" )         { size = value;         }
+
                        if (key == "template")          { templatefile = value; }
                        if (key == "search")            { search = value;               }
                        if (key == "ksize")                     { ksize = value;                }
@@ -196,7 +203,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                //input defaults for calculators
                if (commandName == "collect.single") {
 
-                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -212,7 +219,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "summary.single") {
-                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -300,6 +307,13 @@ string GlobalData::getFilter()                     {   return filter;              }
 string GlobalData::getScale()                  {       return scale;           }
 string GlobalData::getEnds()                   {   return ends;                }
 string GlobalData::getProcessors()             {       return processors;      }
+string GlobalData::getSize()            {   return size;        }
+
+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;}
+void GlobalData::setPhylipFile(string file)    {       phylipfile = file;    inputFileName = file;}
+void GlobalData::setColumnFile(string file)    {       columnfile = file;    inputFileName = file;}
 string GlobalData::getTemplateFile()   {       return templatefile;}
 string GlobalData::getSearch()                 {       return search;          }
 string GlobalData::getKSize()                  {       return ksize;           }
@@ -309,12 +323,7 @@ string GlobalData::getMismatch()           {       return mismatch;        }
 string GlobalData::getGapopen()                        {       return gapopen;         }
 string GlobalData::getGapextend()              {       return gapextend;       }
 
-void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;}
 void GlobalData::setGroupFile(string file)             {       groupfile = file;       }
-void GlobalData::setRabundFile(string file)            {       rabundfile = file;      inputFileName = file;}
-void GlobalData::setSabundFile(string file)            {       sabundfile = file;      inputFileName = file;}
-void GlobalData::setPhylipFile(string file)            {       phylipfile = file;    inputFileName = file;}
-void GlobalData::setColumnFile(string file)            {       columnfile = file;    inputFileName = file;}
 void GlobalData::setSharedFile(string file)            {       sharedfile = file;      inputFileName = file; fileroot = file;}
 void GlobalData::setNameFile(string file)              {       namefile = file;                }
 void GlobalData::setFormat(string Format)              {       format = Format;                }
@@ -377,6 +386,7 @@ void GlobalData::clear() {
        scale                   =       "log10";
        ends                    =   "T";  //yes
        processors              =       "1";
+       size            =   "1000";
        search                  =       "suffix";
        ksize                   =       "7";
        align                   =       "blast";
@@ -384,8 +394,6 @@ void GlobalData::clear() {
        mismatch                =       "-1.0";
        gapopen                 =       "-5.0";
        gapextend               =       "-2.0";
-       
-
 }
 
 //*******************************************************/
@@ -407,6 +415,7 @@ void GlobalData::reset() {
        form                    =       "integral";
        ends                    =   "T";
        processors              =       "1";
+       size            =   "1000";
        search                  =       "suffix";
        ksize                   =       "7";
        align                   =       "blast";