made sorting optional but sort by default, in case the user wants to see the heatmap...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 2848860d41c35db65029a26409b8b9d3f5201685..64a7c93ac0a7c5067cf102250d3efd9cf8ab7380 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -74,6 +74,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "calc")                      { calc = value;                 }
                                if (key == "step")                      { step = value;                 }
                                if (key == "form")                      { form = value;                 }
+                               if (key == "sorted")            { sorted = value;               }
                                
 
                                
@@ -125,9 +126,10 @@ 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 == "sorted")            { sorted = value;               }
 
                        if (key == "line") {//stores lines to be used in a vector
                                lines.clear();
@@ -233,6 +235,7 @@ string GlobalData::getRandomTree()          {       return randomtree;      }
 string GlobalData::getGroups()                 {       return groups;          }
 string GlobalData::getStep()                   {       return step;            }
 string GlobalData::getForm()                   {       return form;            }
+string GlobalData::getSorted()                 {       return sorted;          }
 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;}
@@ -283,6 +286,7 @@ void GlobalData::clear() {
        abund           =   "10";
        step                    =       "0.01";
        form                    =       "integral";
+       sorted                  =       "1";  //0 means don't sort, 1 means sort.
 }
 
 //*******************************************************/
@@ -294,6 +298,7 @@ void GlobalData::reset() {
        iters                   =       "1000"; 
        groups                  =       "";
        jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
+       sorted                  =       "1";  //0 means don't sort, 1 means sort.
        randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
        freq                    =       "100";
        method                  =       "furthest";