#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;
FullMatrix* gMatrix;
TreeMap* gTreemap;
SequenceDB* gSequenceDB;
- string inputFileName, helpRequest, commandName, vertical;
- bool allLines;
+ string inputFileName, argv;
+ 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 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 getSize();
- 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, size;
- string mismatch, gapopen, gapextend;
-
+ MothurOut* m;
+ 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&);
-
};