X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.h;h=487c4601780a209418be72b8eb8c04edd0a55442;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=88b7a382d4c175a14c243d21e97a7580cba9c32d;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git diff --git a/deconvolutecommand.h b/deconvolutecommand.h index 88b7a38..487c460 100644 --- a/deconvolutecommand.h +++ b/deconvolutecommand.h @@ -22,17 +22,22 @@ public: DeconvoluteCommand(string); DeconvoluteCommand(); ~DeconvoluteCommand() {} - vector getRequiredParameters(); - vector getValidParameters(); - vector getRequiredFiles(); - map > getOutputFiles() { return outputTypes; } - int execute(); - void help(); + + vector setParameters(); + string getCommandName() { return "unique.seqs"; } + string getCommandCategory() { return "Sequence Processing"; } + string getHelpString(); + string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; } + string getDescription() { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; } + + + int execute(); + void help() { m->mothurOut(getHelpString()); } + private: string inFastaName, oldNameMapFName, outputDir; vector outputNames; - map > outputTypes; bool abort; };