removed parse.sff command and made its functionality part of sffinfo command. fixed...

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 547b567c62e67c01d2dcce2b4cd573c5ad1c08bc..2a7908167ac1ede1d402fa26c2f9c30978b31469 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -15,8 +15,10 @@
 #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.
+       The user can select the 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;
@@ -24,13 +26,19 @@ class GlobalData;
 class MatrixOutputCommand : public Command {
        
 public:
+       MatrixOutputCommand(string);
        MatrixOutputCommand();  
        ~MatrixOutputCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
+       void help();
        
 private:
        void printSims(ostream&);
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);
        
        GlobalData* globaldata;
        ReadOTUFile* read;
@@ -39,9 +47,15 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
-       string exportFileName;
+       string exportFileName, output;
        int numGroups;
        ofstream out;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string outputFile, calc, groups, label, outputDir;
+       vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
+       map<string, vector<string> > outputTypes;
        
 
 };