added chimera.uchime

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 8b38a76f4a3c2bdcfbd0855d6a8be0ff3bad1714..4fef8e795be355d23d1348f2ed323e225092b0f9 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -16,22 +16,35 @@ class GetSeqsCommand : public Command {
        
        public:
        
-               GetSeqsCommand(string); 
-               ~GetSeqsCommand(){};
-               int execute();
-               void help();    
-               
+               GetSeqsCommand(string);
+               GetSeqsCommand();
+               ~GetSeqsCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.seqs";                            }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile;
-               bool abort;
+               vector<string> outputNames;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               bool abort, dups;
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
-               void readAccnos();
-               void readList();
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readAccnos();
+               int readList();
+               int readTax();
+               int readQual();
+               int compareAccnos();
                
 };