X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=40b87583aaa2e472f788b2102f5daea0628c2f9e;hb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;hp=f74619e29c792d28486447c919281f88b5d03ba0;hpb=69180c6a4fd3c9ad48974b402d398efe61a58fa7;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index f74619e..40b8758 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:
@@ -29,14 +35,16 @@ public:
 	vector<Tree*> gTree;
 	SharedListVector* gSharedList;
 	SAbundVector* sabund;
+	RAbundVector* rabund;
 	GroupMap* gGroupmap;
 	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
-	string inputFileName, helpRequest, commandName;
+	string inputFileName, helpRequest, commandName, vertical;
 	bool allLines;
 	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();
@@ -47,6 +55,8 @@ public:
 	string getGroupFile();
 	string getOrderFile();
 	string getFastaFile();
+	string getNexusFile();
+	string getClustalFile();
 	string getTreeFile();
 	string getSharedFile();
 	string getCutOff();
@@ -64,6 +74,14 @@ public:
 	string getForm();
 	string getSorted();
 
+	string getTrump();
+	string getSoft();
+	string getFilter();
+	
+
+	string getScale();
+
+
 	void setListFile(string);
 	void setPhylipFile(string);
 	void setColumnFile(string);
@@ -80,10 +98,18 @@ 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, sorted;
+
+	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
+	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale;
+
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor
@@ -91,6 +117,7 @@ private:
 	GlobalData();
 	~GlobalData();
 	void reset();	//clears all non filename parameters
+	void readTreeString(ifstream&);