modified reverse.seqs and qualscores.cpp

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 5155cbd7982eada5dc20480067a5c34e051d30dc..3240860fc329bed3b9551359a6ff1b23a16b8019 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -20,8 +20,13 @@ class GlobalData;
 class LibShuffCommand : public Command {
        
 public:
-       LibShuffCommand(string);        
+       LibShuffCommand(string);
+       LibShuffCommand();      
        ~LibShuffCommand(){};
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
 
@@ -29,8 +34,8 @@ private:
        vector<string> groupNames;
        
        void setGroups();
-       void printCoverageFile();
-       void printSummaryFile();
+       int printCoverageFile();
+       int printSummaryFile();
 
        GlobalData* globaldata;
        FullMatrix* matrix;
@@ -45,6 +50,7 @@ private:
        bool abort;
        string outputFile, groups, userform, savegroups, outputDir;
        vector<string> Groups, outputNames; //holds groups to be used
+       map<string, vector<string> > outputTypes;
 };
 
 #endif