changes while setting up test files

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index f97d98b311ff46f21d5479c15795eaa3e69fd892..59bbac5dc3c0bf0a4d99d6e671b083f9ed2dd954 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,17 +1,18 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
-
+/*
 #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;
@@ -28,8 +29,8 @@ class SequenceDB;
 class GlobalData {
 public:
        static GlobalData* getInstance();
-       ListVector* gListVector;
-       SparseMatrix* gSparseMatrix;
+       /*ListVector* gListVector;
+       //SparseMatrix* gSparseMatrix;
        InputData* ginput;
        OrderVector* gorder;
        ListVector* glist;
@@ -37,109 +38,68 @@ public:
        SharedListVector* gSharedList;
        SAbundVector* sabund;
        RAbundVector* rabund;
-       GroupMap* gGroupmap;
+       //GroupMap* gGroupmap;
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
-       string inputFileName, helpRequest, commandName, vertical, argv;
-       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
+       NameAssignment* nameMap;
+       string argv; //inputFileName,
+       bool runParse, jumble, sim; //allLines, 
+       vector<string>  Estimators;//, Groups; //holds estimators to be used
+       //set<string> labels; //holds labels to be used
        vector<string> Treenames;
+       map<string, string> names;
+       string saveNextLabel;
        
-       string getPhylipFile();
+       
+       /*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 getOrderGroupFile();
        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 getCountEnds();
-       string getProcessors();
-       string getSize();
-       string getCandidateFile();
-       string getSearch();
-       string getKSize();
-       string getAlign();
-       string getMatch();
-       string getMismatch();
-       string getGapopen();
-       string getGapextend();
-       string getVertical();
-       string getTrump();
-       string getSoft();
-       string getHard();
-       string getScale();
-       string getStartPos();
-       string getEndPos();
-       string getMaxAmbig();
-       string getMaxHomoPolymer();
-       string getMinLength();
-       string getMaxLength();
+       string getRelAbundFile();
+       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 setCountEnds(string);
-       void setProcessors(string);
-
-       void clear(); 
-       void clearLabels();
-       void clearAbund();
+       void setRelAbundFile(string);
+       void setOrderFile(string file);
+       void setOrderGroupFile(string file);
+       void setFormat(string); //do we need this?*/
        
-       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.
-
-               
+       
+       //void clear(); 
+       //void clearLabels();
+       //void clearAbund();
+       
+       //void newRead();
+       /*
 private:
-
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups, cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer;
-
+       MothurOut* m;
+       //string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup, relAbundfile;
 
        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&);
-       
        
        
-};
+};*/
 
 #endif