removing chime source files from mother project.

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index b574afe38734a789fa39985090012cff358d2e95..4561d28614c62686c42e29a9747b84d853537fd0 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,15 +17,25 @@ class GetSeqsCommand : public Command {
        public:
        
                GetSeqsCommand(string);
-               ~GetSeqsCommand(){};
-               int execute();
-               void help();    
-               
+               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"; }
+               string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
-               bool abort;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               bool abort, dups;
                
                int readFasta();
                int readName();
@@ -33,6 +43,9 @@ class GetSeqsCommand : public Command {
                int readAlign();
                int readAccnos();
                int readList();
+               int readTax();
+               int readQual();
+               int compareAccnos();
                
 };