working on pam

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 647cb765f0e75781862d0fa74305d55573c85872..7aaff172800c43b160fe62b2b49c2035e08502f8 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,21 +17,38 @@ 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 getHelpString(); 
+    string getOutputPattern(string);   
+               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, listfile, outputDir;
+               string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
+               vector<string> outputNames;
+        map<string, string> uniqueMap;
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
-               void readAccnos();
-               void readList();
+               int readFasta();
+        int readFastq();
+               int readName();
+               int readGroup();
+        int readCount();
+               int readAlign();
+               int readList();
+               int readTax();
+               int readQual();
                
 };