adding treeclimber and unifrac pieces

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index f706b5308765cc01db2196c92192f22fb1f86302..bc836e854cb3c4f1b7cc184789b0d49d6e8e3f45 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -114,6 +114,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "freq" )                     { freq = value;                 }
                                if (key == "method" )           { method = value;               }
                                if (key == "fileroot" )         { fileroot = value;             }
+                               if (key == "randomtree" )       { randomtree = value;   }
+                               if (key == "groups" )           { groups = value;       }
                                
                                if (key == "single") {//stores estimators in a vector
                                        singleEstimators.clear(); //clears out old values
@@ -145,20 +147,26 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                        if (value == "default") { value = "sharedobserved"; }
                                        splitAtDash(value, sharedRareEstimators);
                                }
-                               if (key == "line") {//stores lines to be used in a vector
+                               if (key == "line") {//stores lines to be used in a set
                                        lines.clear();
                                        line = value;
                                        label = "";
                                        splitAtDash(value, lines);
                                        allLines = 0;
                                }
-                               if (key == "label") {//stores lines to be used in a vector
+                               if (key == "label") {//stores lines to be used in a set
                                        labels.clear();
                                        label = value;
                                        line = "";
                                        splitAtDash(value, labels);
                                        allLines = 0;
                                }
+                               if (key == "groups") {//stores lines to be used in a vector
+                                       Groups.clear();
+                                       groups = value;
+                                       splitAtDash(value, Groups);
+                               }
+
                        }
                        
                        //saves the last parameter
@@ -181,7 +189,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "freq" )                     { freq = value;                 }
                        if (key == "method" )           { method = value;               }
                        if (key == "fileroot" )         { fileroot = value;             }
-
+                       if (key == "randomtree" )       { randomtree = value;   }
+                       
                        if (key == "single") {//stores estimators in a vector
                                singleEstimators.clear(); //clears out old values
                                if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
@@ -293,14 +302,16 @@ string GlobalData::getFileRoot()          {       return fileroot;        }
 string GlobalData::getIters()                  {       return iters;           }
 string GlobalData::getJumble()                 {       return jumble;          }
 string GlobalData::getFreq()                   {       return freq;            }
+string GlobalData::getRandomTree()             {       return randomtree;      }
 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;}
-//void GlobalData::setGroupFile(string file)   {       groupfile = file;       }
-void GlobalData::setNameFile(string file)      {       namefile = file;        }
-void GlobalData::setFormat(string Format)      {       format = Format;        }
+//void GlobalData::setGroupFile(string file)   {       groupfile = file;               }
+void GlobalData::setNameFile(string file)              {       namefile = file;                }
+void GlobalData::setFormat(string Format)              {       format = Format;                }
+void GlobalData::setRandomTree(string Random)  {       randomtree = Random;    }
 
 
 /*******************************************************/
@@ -334,7 +345,8 @@ void GlobalData::clear() {
        iters                   =       "1000"; 
        line                    =   "";
        label                   =       "";
-       jumble                  =       "1";
+       jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
+       randomtree              =       "0";  //0 means user will enter some user trees, 1 means they just want the random tree distribution.
        freq                    =       "100";
        method                  =       "furthest";
        fileroot                =       "";