#include "tree.h"
#include "sparsematrix.hpp"
#include "sequencedb.h"
+#include "nameassignment.hpp"
class ListVector;
TreeMap* gTreemap;
SequenceDB* gSequenceDB;
string inputFileName, argv;
- bool allLines, runParse;
+ bool allLines, runParse, jumble, sim;
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;
+ map<string, string> names;
+
string getPhylipFile();
string getColumnFile();
string getNameFile(); //do we need this?
string getGroupFile(); //do we need this?
string getOrderFile();
-// string getFastaFile();
+ string getOrderGroupFile();
string getTreeFile();
string getSharedFile();
string getFormat(); //do we need this?
-// string getCandidateFile();
-// string getTemplateFile();
+
void setListFile(string);
-// void setFastaFile(string);
void setTreeFile(string);
-// void setCandidateFile(string);
-// void setTemplateFile(string);
void setGroupFile(string); //do we need this?
void setPhylipFile(string);
void setColumnFile(string);
void setSabundFile(string);
void setSharedFile(string);
void setOrderFile(string file);
+ void setOrderGroupFile(string file);
void setFormat(string); //do we need this?
+ NameAssignment* nameMap;
+
void clear();
void clearLabels();
void clearAbund();
void newRead();
private:
-
- string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
+ MothurOut* m;
+ string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup;
static GlobalData* _uniqueInstance;
GlobalData( const GlobalData& ); // Disable copy constructor