X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=0238a0aaeffa7a7e710182af82010ea058edf1df;hb=72ebb6fa35b45b149812d47c2b1cb8acaca64659;hp=cb9aff67dfb4c07918891630c8729b61960451b5;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index cb9aff6..0238a0a 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -4,14 +4,15 @@
 #include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
-
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
+#include "tree.h"
+#include "sparsematrix.hpp"
+#include "sequencedb.h"
+#include "nameassignment.hpp"
 
 
-using namespace std;
-
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
@@ -41,100 +42,55 @@ public:
 	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
 	SequenceDB* gSequenceDB;
-	string inputFileName, helpRequest, commandName, vertical;
-	bool allLines;
+	string inputFileName, argv;
+	bool allLines, runParse, jumble;
 	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();
 	string getListFile();
 	string getRabundFile();
 	string getSabundFile();
-	string getNameFile();
-	string getGroupFile();
+	string getNameFile();	//do we need this?
+	string getGroupFile();	//do we need this?
 	string getOrderFile();
-	string getFastaFile();
-	string getNexusFile();
-	string getClustalFile();
 	string getTreeFile();
 	string getSharedFile();
-	string getCutOff();
-	string getFormat();
-	string getPrecision();
-	string getMethod();
-	string getFileRoot();
-	string getIters();
-	string getJumble();
-	string getFreq();
-	string getAbund();
-	string getRandomTree();
-	string getGroups();
-	string getStep();
-	string getForm();
-	string getSorted();
-	string getEnds();
-	string getProcessors();
-	string getTemplateFile();
-	string getSearch();
-	string getKSize();
-	string getAlign();
-	string getMatch();
-	string getMismatch();
-	string getGapopen();
-	string getGapextend();
-	string getTrump();
-	string getSoft();
-	string getFilter();
-	
-
-	string getScale();
+	string getFormat();	//do we need this?
 
 
 	void setListFile(string);
-	void setGroupFile(string file);	
+	void setTreeFile(string);
+	void setGroupFile(string);		//do we need this?
 	void setPhylipFile(string);
 	void setColumnFile(string);
-	void setNameFile(string);
+	void setNameFile(string);	//do we need this?
 	void setRabundFile(string);
 	void setSabundFile(string);
 	void setSharedFile(string);
-	void setFormat(string);
-	void setRandomTree(string);
-	void setGroups(string);
-	void setCalc(string);
-	void setEnds(string);
-	void setProcessors(string);
-
+	void setOrderFile(string file);
+	void setFormat(string);	//do we need this?
+	
+	NameAssignment* nameMap;
+	
 	void clear(); 
 	void clearLabels();
 	void clearAbund();
 	
-	void parseGlobalData(string, string);
+	void newRead();
 	
-	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, 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, ends, processors, templatefile, search, ksize, align, match;
-	string mismatch, gapopen, gapextend;
-
+	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor
 	void operator=( const GlobalData& ); // Disable assignment operator
 	GlobalData();
 	~GlobalData();
-	void reset();	//clears all non filename parameters
-	void readTreeString(ifstream&);
-	
 	
 	
 };