broke up globaldata and moved error checking and help into commands

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 04d0ccbf8e46145591acca443d37039809da88d0..d6099326a69ac5ef1daf95ce192bc3cad1fd712f 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -15,6 +15,8 @@
 #include "readotu.h"
 #include "validcalculator.h"
 
+// aka. dist.shared()
+
 /* This command create a tree file for each similarity calculator at distance level, using various calculators to find the similiarity between groups. 
        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. */
@@ -24,12 +26,14 @@ class GlobalData;
 class MatrixOutputCommand : public Command {
        
 public:
-       MatrixOutputCommand();  
+       MatrixOutputCommand(string);    
        ~MatrixOutputCommand();
        int execute();  
+       void help();
        
 private:
        void printSims(ostream&);
+       void process(vector<SharedRAbundVector*>);
        
        GlobalData* globaldata;
        ReadOTUFile* read;
@@ -41,6 +45,15 @@ private:
        string exportFileName;
        int numGroups;
        ofstream out;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string outputFile, calc, groups, line, label;
+       vector<string>  Estimators, Groups; //holds estimators to be used
+       
 
 };