X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=cc13bae137577dc28e554c39d9088725114740f3;hb=d59f91eb1230d2c7867a92cb86138b7003100ab4;hp=16bc8d32b6bc75c2b4cbabfdb4ef6dfb78890d4c;hpb=2d2fbc80f9359b19873ba3e63970b58f4f8f49f3;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 16bc8d3..cc13bae 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -5,6 +5,11 @@
 #include "groupmap.h"
 #include "treemap.h"
 
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
+
+
 using namespace std;
 
 class ListVector;
@@ -17,6 +22,7 @@ class InputData;
 class GroupMap;
 class TreeMap;
 class SAbundVector;
+class RAbundVector;
 
 class GlobalData {
 public:
@@ -29,6 +35,7 @@ public:
 	vector<Tree*> gTree;
 	SharedListVector* gSharedList;
 	SAbundVector* sabund;
+	RAbundVector* rabund;
 	GroupMap* gGroupmap;
 	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
@@ -37,6 +44,7 @@ public:
 	vector<string>  Estimators, Groups; //holds estimators to be used
 	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
+	vector<string> Treenames;
 	
 	string getPhylipFile();
 	string getColumnFile();
@@ -62,6 +70,8 @@ public:
 	string getGroups();
 	string getStep();
 	string getForm();
+	string getSorted();
+	string getScale();
 
 	void setListFile(string);
 	void setPhylipFile(string);
@@ -79,10 +89,16 @@ public:
 	void clearAbund();
 	
 	void parseGlobalData(string, string);
+	
+	void parseTreeFile();		//parses through tree file to find names of nodes and number of them
+							//this is required in case user has sequences in the names file that are
+							//not included in the tree. 
+							//only takes names from the first tree in the tree file and assumes that all trees use the same names.
+
 		
 private:
 	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
-	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form;
+	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, scale;
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor
@@ -90,6 +106,7 @@ private:
 	GlobalData();
 	~GlobalData();
 	void reset();	//clears all non filename parameters
+	void readTreeString(ifstream&);