added list.seqs command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index cb9aff67dfb4c07918891630c8729b61960451b5..759bcae6fd7631988bf15407e7234330c2c9f659 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;
@@ -41,100 +41,54 @@ 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?
+       
        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;
 
        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&);
-       
        
        
 };