X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=07d13d6703426e1990fab1a1bc9afdb82124c801;hb=0571957d68cbbc0e425af1db8e808f826010b9e2;hp=809109c486de9f00b39091b863da8a23dfc95a96;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git diff --git a/getseqscommand.h b/getseqscommand.h index 809109c..07d13d6 100644 --- a/getseqscommand.h +++ b/getseqscommand.h @@ -17,22 +17,33 @@ class GetSeqsCommand : public Command { public: GetSeqsCommand(string); - ~GetSeqsCommand(){}; - int execute(); - void help(); - + GetSeqsCommand(); + ~GetSeqsCommand(){} + + vector setParameters(); + string getCommandName() { return "get.seqs"; } + string getCommandCategory() { return "Sequence Processing"; } + string getHelpString(); + + int execute(); + void help() { m->mothurOut(getHelpString()); } + + private: set names; vector 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; - 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(); };