X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapsimcommand.h;h=f421fdc5bf2c3ff8aed22a197afc3309a86b4e34;hp=33696a33ac87b34bedea636810b32e4daa09be8c;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=f15f7092c97277337d4fdd9ef674015c15a13220 diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h index 33696a3..f421fdc 100644 --- a/heatmapsimcommand.h +++ b/heatmapsimcommand.h @@ -12,27 +12,45 @@ #include "command.hpp" #include "inputdata.h" -#include "readotu.h" #include "validcalculator.h" #include "heatmapsim.h" - -class GlobalData; +#include "nameassignment.hpp" class HeatMapSimCommand : public Command { public: + HeatMapSimCommand(string); HeatMapSimCommand(); - ~HeatMapSimCommand(); - int execute(); + ~HeatMapSimCommand(){} + + vector setParameters(); + string getCommandName() { return "heatmap.sim"; } + string getCommandCategory() { return "OTU-Based Approaches"; } + + string getHelpString(); + string getOutputPattern(string); + string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; } + string getDescription() { return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; } + + int execute(); + void help() { m->mothurOut(getHelpString()); } + private: - GlobalData* globaldata; - ReadOTUFile* read; InputData* input; vector lookup; vector heatCalculators; - ValidCalculators* validCalculator; HeatMapSim* heatmap; + OptionParser* parser; + bool abort, allLines; + set labels; //holds labels to be used + string format, groups, label, calc, sharedfile, phylipfile, columnfile, countfile, namefile, outputDir, inputfile; + vector Estimators, Groups, outputNames; + int fontsize; + + int runCommandShared(); + int runCommandDist(); + };