fixed sub.sample so that it will eliminate samples with abundances that are less...

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 899716c6055b0dc12cbe493fc1ff3e5b8170d769..6bb35f26056ea14873b3b8d76773c207ab83243b 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"
@@ -27,7 +26,6 @@
        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;
 
@@ -35,18 +33,23 @@ class TreeGroupCommand : public Command {
        
 public:
        TreeGroupCommand(string);       
+       TreeGroupCommand();
        ~TreeGroupCommand();
-       int execute();  
-       void help();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "tree.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       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;
@@ -57,10 +60,9 @@ 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 lastLabel;
-       string format, outputFile, groupNames, filename;
+       string format, outputFile, groupNames, filename, sharedfile, inputfile;
        int numGroups;
        ofstream out;
        float precision, cutoff;
@@ -71,7 +73,7 @@ private:
        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.
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);