cleaned up code2

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 434983e8e4c5909be8a083cf8251cee34b0d27ce..474951a9feaee7d497417cf2a03f206367056241 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,20 +17,34 @@ class RemoveSeqsCommand : public Command {
        public:
        
                RemoveSeqsCommand(string);      
-               ~RemoveSeqsCommand(){};
-               int execute();
-               void help();    
-               
+               RemoveSeqsCommand();
+               ~RemoveSeqsCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "remove.seqs";                         }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
+               string getDescription()         { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
-               string accnosfile, fastafile, namefile, groupfile, alignfile;
-               bool abort;
+               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               bool abort, dups;
+               vector<string> outputNames;
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
-               void readAccnos();
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readList();
+               int readTax();
+               int readQual();
                
 };