X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=df96e4514bc84787ad901e137bbc794588681705;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=8321212fff48bb240c54f1a1df4516b393f7216f;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git diff --git a/removeseqscommand.h b/removeseqscommand.h index 8321212..df96e45 100644 --- a/removeseqscommand.h +++ b/removeseqscommand.h @@ -19,19 +19,23 @@ class RemoveSeqsCommand : public Command { RemoveSeqsCommand(string); RemoveSeqsCommand(); ~RemoveSeqsCommand(){} - vector getRequiredParameters(); - vector getValidParameters(); - vector getRequiredFiles(); - map > getOutputFiles() { return outputTypes; } - int execute(); - void help(); - + + vector setParameters(); + string getCommandName() { return "remove.seqs"; } + string getCommandCategory() { return "Sequence Processing"; } + string getHelpString(); + 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 names; - string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir; + string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir; bool abort, dups; vector outputNames; - map > outputTypes; int readFasta(); int readName(); @@ -40,6 +44,7 @@ class RemoveSeqsCommand : public Command { void readAccnos(); int readList(); int readTax(); + int readQual(); };