started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 67c49bd28c942d5c432538b6f965406c0b592ae6..2c02ca9ad560f73ecea8277420fb569b04844d82 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,9 +1,6 @@
 #include "globaldata.hpp"
-#include "sparsematrix.hpp"
 #include "tree.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
+#include "sparsematrix.hpp"
 
 /*******************************************************/
 
@@ -76,6 +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;               }
                                
 
                                
@@ -131,6 +129,8 @@ 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 == "line") {//stores lines to be used in a vector
                                lines.clear();
@@ -140,6 +140,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
+                       
                        if (key == "label") {//stores lines to be used in a vector
                                labels.clear();
                                lines.clear();
@@ -199,6 +200,13 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
+               if (commandName == "tree.groups") {
+                       if (calc != "") { 
+                               Estimators.clear();
+                               splitAtDash(calc, Estimators);                  
+                       }else { cout << "You have not specified any calculators." << endl; }
+               }
+
 
                //if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
                if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
@@ -245,6 +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;          }
 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;}
@@ -296,6 +305,7 @@ void GlobalData::clear() {
        step                    =       "0.01";
        form                    =       "integral";
        sorted                  =       "1";  //0 means don't sort, 1 means sort.
+       scaler                  =       "log2";
 }
 
 //*******************************************************/