X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.h;fp=corraxescommand.h;h=2aa7ae0d345cff024b7485ad856013f88895edd9;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/corraxescommand.h b/corraxescommand.h new file mode 100644 index 0000000..2aa7ae0 --- /dev/null +++ b/corraxescommand.h @@ -0,0 +1,57 @@ +#ifndef CORRAXESCOMMAND_H +#define CORRAXESCOMMAND_H + +/* + * corraxescommand.h + * Mothur + * + * Created by westcott on 12/22/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "command.hpp" +#include "sharedrabundfloatvector.h" +#include "inputdata.h" + + +class CorrAxesCommand : public Command { +public: + CorrAxesCommand(string); + CorrAxesCommand(); + ~CorrAxesCommand(){} + + vector setParameters(); + string getCommandName() { return "corr.axes"; } + string getCommandCategory() { return "Hypothesis Testing"; } + string getHelpString(); + string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Corr.axes"; } + string getDescription() { return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; } + + int execute(); + void help() { m->mothurOut(getHelpString()); } +private: + + string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method; + bool abort, pickedGroups; + int numaxes; + set names; + + vector outputNames, Groups; + vector lookupFloat; + vector metadataLabels; + + int getSharedFloat(InputData*); + int getMetadata(); + int eliminateZeroOTUS(vector&); + map > readAxes(); + int calcPearson(map >&, ofstream&); + int calcSpearman(map >&, ofstream&); + int calcKendall(map >&, ofstream&); + +}; + + +#endif + +