working on current change

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 3f145e92b4780fa4f40a45ed1849150dafffc800..a52d3b189354f910c3b92cf65a24aeac4a137c68 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -13,7 +13,6 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
@@ -27,25 +26,31 @@
        The user can select the lines or labels they wish to use as well as the groups they would like included.
        They can also use as many or as few calculators as they wish. */
        
-class GlobalData;
 
 typedef list<PCell>::iterator MatData;
 
 class TreeGroupCommand : public Command {
        
 public:
-       TreeGroupCommand();     
+       TreeGroupCommand(string);       
+       TreeGroupCommand();
        ~TreeGroupCommand();
-       int execute();  
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "tree.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void createTree();
+       int createTree();
        void printSims(ostream&);
-       void makeSimsShared();
-       void makeSimsDist();
+       int makeSimsShared();
+       int makeSimsDist();
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        ReadMatrix* readMatrix;
        SparseMatrix* matrix;
        NameAssignment* nameMap;
@@ -56,13 +61,23 @@ private:
        vector< vector<float> > simMatrix;
        map<int, int> index;  //maps row in simMatrix to vector index in the tree       
        InputData* input;
-       ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
-       string format, outputFile, groupNames, filename;
+       string lastLabel;
+       string format, outputFile, groupNames, filename, sharedfile, inputfile;
        int numGroups;
        ofstream out;
        float precision, cutoff;
 
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string phylipfile, columnfile, namefile, calc, groups, label, outputDir;
+       vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
+       
+       //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+       int process(vector<SharedRAbundVector*>);
+       
+       
+
 };