sped up the remove.seqs and remove.lineage and get.seqs and get.lineage. fixed bug...

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 04d0ccbf8e46145591acca443d37039809da88d0..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;
@@ -24,12 +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&);
+       int process(vector<SharedRAbundVector*>);
        
        GlobalData* globaldata;
        ReadOTUFile* read;
@@ -38,10 +47,17 @@ 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;
+       
+
 };