X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.h;h=30a578221f09042817534b51f91d8e33f3125c6c;hb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;hp=0322daf423ab716022e2146b6d4f352911fed693;hpb=7a2154809d332281cf4006943a9bd94b8208c837;p=mothur.git diff --git a/phylotypecommand.h b/phylotypecommand.h index 0322daf..30a5782 100644 --- a/phylotypecommand.h +++ b/phylotypecommand.h @@ -20,19 +20,31 @@ class PhylotypeCommand : public Command { public: PhylotypeCommand(string); - ~PhylotypeCommand(); - int execute(); - void help(); + PhylotypeCommand(); + ~PhylotypeCommand(){} + + vector setParameters(); + string getCommandName() { return "phylotype"; } + string getCommandCategory() { return "Clustering"; } + string getHelpString(); + + int execute(); + void help() { m->mothurOut(getHelpString()); } private: bool abort, allLines; - string taxonomyFileName, label; + string taxonomyFileName, label, outputDir, namefile; set labels; //holds labels to be used int cutoff; + map namemap; + vector outputNames; + map > outputTypes; map currentNodes; map parentNodes; map::iterator itCurrent; + + int readNamesFile(); };