added shared file to catchall command

[mothur.git] / catchallcommand.h

diff --git a/catchallcommand.h b/catchallcommand.h
index 4406361a37230aced27bbaa4ca62c3f42bcd4db3..49e0d542374eea94228ca7fa7fb2932d511989e0 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -38,17 +38,18 @@ public:
 private:
 
        GlobalData* globaldata;
-       ReadOTUFile* read;
-       InputData* input;
        
-       string outputDir, sabundfile, rabundfile, listfile, format, path;
+       string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
        bool abort, allLines;
        set<string> labels;
        vector<string> outputNames;
        map< string, vector<string> > outputTypes;
+       vector<string> groups;
        
-       string process(SAbundVector*);
+       string process(SAbundVector*, string);
        int createSummaryFile(string, string, ofstream&); 
+       vector<string> parseSharedFile(string);
+       string combineSummmary(vector<string>&);
 };
 
 /****************************************************************************/