removed line option

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index f97d98b311ff46f21d5479c15795eaa3e69fd892..e125e6f3d7032d78d2b1330dece6cf909a6bf320 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -4,14 +4,14 @@
 #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"
 
 
-using namespace std;
-
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
@@ -41,103 +41,53 @@ public:
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
-       string inputFileName, helpRequest, commandName, vertical, argv;
-       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 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 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 setOrderFile(string file);
+       void setFormat(string); //do we need this?
+       
        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, 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;
-
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
 
        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&);
-       
        
        
 };