added debug statements to trim.seqs

[mothur.git] / removegroupscommand.h

diff --git a/removegroupscommand.h b/removegroupscommand.h
index 955d94d5090b5fc6caf4ba2a937261a173a3eb91..c6db38057f8c206ecbba0806486078eccdcc7278 100644 (file)
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -25,7 +25,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "remove.groups";                       }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
+       string getDescription()         { return "removes sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -33,18 +36,23 @@ public:
        
 private:
        set<string> names;
-       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+       string accnosfile, fastafile, namefile, groupfile, designfile, listfile, taxfile, outputDir, groups, sharedfile;
        bool abort;
        vector<string> outputNames, Groups;
        GroupMap* groupMap;
+       map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
+       //then the other files need to change the unique name in their file to match.
+       //only add the names that need to be changed to keep the map search quick
+       
        
        int readFasta();
+       int readShared();
        int readName();
        int readGroup();
-       void readAccnos();
        int readList();
        int readTax();
        int fillNames();
+    int readDesign();
        
 };