added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 5bc7f5857b686742d42afff89025f5f0096796df..714b5ad2e447a579872f9f5b8d8c7886303a8391 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -73,7 +73,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "step")                      { step = value;                 }
                                if (key == "form")                      { form = value;                 }
                                if (key == "sorted")            { sorted = value;               }
-                               if (key == "scaler")            { scaler = value;               }
+                               if (key == "scale")                     { scale = value;                }
                                
 
                                
@@ -129,7 +129,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "step")                      { step = value;                 }
                        if (key == "form")                      { form = value;                 }
                        if (key == "sorted")            { sorted = value;               }
-                       if (key == "scaler")            { scaler = value;               }
+                       if (key == "scale")                     { scale = value;                }
                        
 
                        if (key == "line") {//stores lines to be used in a vector
@@ -200,7 +200,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
-               if (commandName == "tree.groups") {
+               if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
                        if (calc != "") { 
                                Estimators.clear();
                                splitAtDash(calc, Estimators);                  
@@ -253,7 +253,7 @@ string GlobalData::getGroups()                      {       return groups;          }
 string GlobalData::getStep()                   {       return step;            }
 string GlobalData::getForm()                   {       return form;            }
 string GlobalData::getSorted()                 {       return sorted;          }
-string GlobalData::getScaler()                 {       return scaler;          }
+string GlobalData::getScale()                  {       return scale;           }
 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;}
@@ -304,8 +304,8 @@ void GlobalData::clear() {
        abund           =   "10";
        step                    =       "0.01";
        form                    =       "integral";
-       sorted                  =       "1";  //0 means don't sort, 1 means sort.
-       scaler                  =       "log10";
+       sorted                  =       "T";  //F means don't sort, T means sort.
+       scale                   =       "log10";
 }
 
 //*******************************************************/
@@ -317,7 +317,7 @@ 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.
+       sorted                  =       "T";  //F means don't sort, T 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";
@@ -392,7 +392,7 @@ void GlobalData::parseTreeFile() {
                        
                        //use nexus translation rather than parsing tree to save time
                        if ((holder == "translate") || (holder == "Translate")) {
-cout << "there is a translate " << endl;
+
                                string number, name, h;
                                h = ""; // so it enters the loop the first time
                                while((h != ";") && (number != ";")) {