added shhh.seqs command

[mothur.git] / getsharedotucommand.h

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index 3b14b39bb70e8939641dea69c2e53bcb98a82ffa..0e25721b6ca2bcd53967261e7fab18bb0dbead54 100644 (file)
--- a/getsharedotucommand.h
+++ b/getsharedotucommand.h
@@ -22,7 +22,12 @@ class GetSharedOTUCommand : public Command {
        public:
        
                GetSharedOTUCommand(string);    
+               GetSharedOTUCommand();  
                ~GetSharedOTUCommand();
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
@@ -33,14 +38,16 @@ class GetSharedOTUCommand : public Command {
                GroupMap* groupMap;
                
                set<string> labels;
-               string fastafile, label, groups, listfile, groupfile, output;
+               string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
                bool abort, allLines, unique;
                vector<string> Groups;
                map<string, string> groupFinder;
                map<string, string>::iterator it;
                vector<Sequence> seqs;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
                
-               void process(ListVector*);
+               int process(ListVector*);
                
 };
 //**********************************************************************************************************************