added shen calculator

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 6849b880bd34fc20b74d720b86c299451be71802..8b8f9e39b083d9d4329ff500f335d9f4f04cb786 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 == "dist.seqs") {       cutoff = "1.0";         }
+
                string key, value;              
                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
@@ -80,10 +83,21 @@ 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 == "size" )         { size = value;         }
                                
 
                                
 
+                               if (key == "template")          { templatefile = value; }
+                               if (key == "search")            { search = value;               }
+                               if (key == "ksize")                     { ksize = value;                }
+                               if (key == "align")                 { align = value;            }
+                               if (key == "match")                     { match = value;                }
+                               if (key == "mismatch")          { mismatch = value;         }
+                               if (key == "gapopen")           { gapopen = value;              }
+                               if (key == "gapextend" )        { gapextend = value;    }
                                
                                if (key == "line") {//stores lines to be used in a set
                                        lines.clear();
@@ -144,10 +158,18 @@ 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 == "size" )         { size = value;         }
+
+                       if (key == "template")          { templatefile = value; }
+                       if (key == "search")            { search = value;               }
+                       if (key == "ksize")                     { ksize = value;                }
+                       if (key == "align")                 { align = value;            }
+                       if (key == "match")                     { match = value;                }
+                       if (key == "mismatch")          { mismatch = value;         }
+                       if (key == "gapopen")           { gapopen = value;              }
+                       if (key == "gapextend" )        { gapextend = value;    }
 
                        if (key == "line") {//stores lines to be used in a vector
                                lines.clear();
@@ -181,7 +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-shen"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -197,7 +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-shen"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -211,6 +233,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
+               if (commandName == "dist.seqs") {
+                       if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
+                       Estimators.clear();
+                       splitAtDash(calc, Estimators); 
+               }
                if (commandName == "venn") {
                        if ((calc == "default") || (calc == "")) { 
                                if (format == "list") { calc = "sobs"; }
@@ -278,17 +305,34 @@ 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;      }
+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;           }
+string GlobalData::getAlign()                  {       return align;           }
+string GlobalData::getMatch()                  {       return match;           }
+string GlobalData::getMismatch()               {       return mismatch;        }
+string GlobalData::getGapopen()                        {       return gapopen;         }
+string GlobalData::getGapextend()              {       return gapextend;       }
+
+void GlobalData::setGroupFile(string file)             {       groupfile = 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;                }
 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;                 }
+
 
 /*******************************************************/
 
@@ -318,6 +362,7 @@ void GlobalData::clear() {
        clustalfile             =   "";
        treefile                =       "";
        sharedfile              =       "";
+       templatefile    =       "";
        cutoff                  =       "10.00";
        format                  =       "";
        precision               =       "100";
@@ -338,8 +383,17 @@ void GlobalData::clear() {
        trump           =   "";         
        filter          =   "";         
        soft            =   ""; 
-       scale                   =       "log10";            
-
+       scale                   =       "log10";
+       ends                    =   "T";  //yes
+       processors              =       "1";
+       size            =   "1000";
+       search                  =       "suffix";
+       ksize                   =       "7";
+       align                   =       "blast";
+       match                   =       "1.0";
+       mismatch                =       "-1.0";
+       gapopen                 =       "-5.0";
+       gapextend               =       "-2.0";
 }
 
 //*******************************************************/
@@ -359,6 +413,16 @@ void GlobalData::reset() {
        abund                   =   "10";
        step                    =       "0.01";
        form                    =       "integral";
+       ends                    =   "T";
+       processors              =       "1";
+       size            =   "1000";
+       search                  =       "suffix";
+       ksize                   =       "7";
+       align                   =       "blast";
+       match                   =       "1.0";
+       mismatch                =       "-1.0";
+       gapopen                 =       "-5.0";
+       gapextend               =       "-2.0";
 }
 /*******************************************************/