added logfile feature

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 547b567c62e67c01d2dcce2b4cd573c5ad1c08bc..07743e5b4df6d867323c89c2acd78b241486bd00 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. */
@@ -24,9 +26,10 @@ class GlobalData;
 class MatrixOutputCommand : public Command {
        
 public:
-       MatrixOutputCommand();  
+       MatrixOutputCommand(string);    
        ~MatrixOutputCommand();
        int execute();  
+       void help();
        
 private:
        void printSims(ostream&);
@@ -42,6 +45,12 @@ private:
        string exportFileName;
        int numGroups;
        ofstream out;
+
+       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
        
 
 };