took out couts

[mothur.git] / splitabundcommand.h

diff --git a/splitabundcommand.h b/splitabundcommand.h
index 8d2ab2e0503416a9e9e48fb49162a63e794c0191..2e409b2aedd7606b6c689f48cb9e0e58f7a0bcfe 100644 (file)
--- a/splitabundcommand.h
+++ b/splitabundcommand.h
@@ -28,24 +28,40 @@ class SplitAbundCommand : public Command {
        
 public:
        SplitAbundCommand(string);      
+       SplitAbundCommand();
        ~SplitAbundCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
 
        
 private:
-       int split(ListVector*);
-       int split(); //namefile
+       int splitList(ListVector*);
+       int splitNames(); //namefile
+       int writeNames(); 
+       int writeList(ListVector*, string); 
+       int writeAccnos(string); 
+       int parseGroup(string); 
+       int parseFasta(string); 
+       int readNamesFile(); //namefile
+       int createNameMap(ListVector*);
        
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        ListVector* list;
        GroupMap* groupMap;
        InputData* input;
        
-       string outputDir, listfile, namefile, groupfile, label;
-       set<string> labels;
-       bool abort, allLines, accnos, wroteRareList, wroteAbundList;
+       string outputDir, listfile, namefile, groupfile, label, groups, fastafile, inputFile;
+       set<string> labels, rareNames, abundNames;
+       vector<string> Groups;
+       bool abort, allLines, accnos;
        int cutoff;
+       //map<string, bool> wroteListFile;
+       map<string, string> nameMap;