# Namespace for ff
# (c) 2007 Jens Oehlschägel
# Licence: GPL2
# Created: 2007-08-24
# Last changed: 2017-11-19

useDynLib(ff, .registration = TRUE, .fixes = "C_")

importFrom(utils, packageDescription, read.fwf, read.table, str, write.table)
importFrom(stats, median, quantile, runif)
import(bit)

export(

# 'clone' and 'clone.default' are defined in package 'bit'
# ff wants to add methods 'clone.ff' and 'clone.ffdf'
# however but then clone(ff) dispatches to clone.default
# probably because 'clone' in bit does not find 'clone.ff' in ff
# hence it seems to be necessary to redefine 'clone' and 'clone.default' in ff 
# hence it seems to be necessary to export 'clone' in ff again
# hence it seems to be necessary to export 'clone.default' and/or register S3method(clone, default) in ff
# for now I only S3method(clone, default) in ff
# clone
#,clone.default
 clone.ff
,clone.ffdf

# -- generics.R - all new generics --
,as.hi
#,physical
#,"physical<-"
#,virtual
#,"virtual<-"
#,maxwidth
,pattern
,"pattern<-"
,filename
,"filename<-"
, pagesize
,is.open
,is.readonly
,vmode
,as.vmode
,"vmode<-"
,finalizer
,"finalizer<-"
,finalize
,delete
,deleteIfOpen
,as.ff
,as.ram
,dimorder
,"dimorder<-"
,vw
,"vw<-"
,is.factor
,is.ordered
,ramclass
,ramattribs
,recodeLevels
,sortLevels
,add
,swap
,symmetric
,fixdiag
,"fixdiag<-"
,bigsample
,vt
,"nrow<-"
,"ncol<-"

# -- array.R - array related tools --
,vector2array
,array2vector
,arrayIndex2vectorIndex
,vectorIndex2arrayIndex
,symmIndex2vectorIndex
,dummy.dimnames
,matcomb
,matprint
,vecprint


# -- CFUN.R - some collapse functions useful with ffapply and friends - xx TODO yet incomplete --
,ccbind
,crbind
,cfun
,cmedian
,csummary
,cquantile
,clength
,csum
,cmean
 
# -- ff.R - creating and manipulating ff objects: the core of package ff --
#,ramphysical_includes
#,ramvirtual_includes
,ffxtensions
,ffsymmxtensions
,geterror.ff
,geterrstr.ff
,is.ff
#,ffdir
,maxlength
# xx todo print.ff_array via arrprint and print.arrprint
,ff
,getset.ff	# ,add=TRUE
,get.ff
,set.ff		# ,add=TRUE
,readwrite.ff	# ,add=TRUE
,read.ff
,write.ff	# ,add=TRUE

# -- ffapply.R - applying expressions (not functions) to large ff (or ram) objects (R.ff foundation) --
,ffvecapply
,ffrowapply
,ffcolapply
,ffapply

# -- ffreturn.R - basic infrastructure for checking/creating FF_RETURN values (R.ff foundation) --
,mismatch
,ymismatch
#,ffchecknonulldiff # not used
,dimorderStandard
,dimorderCompatible
,vectorStandard
,vectorCompatible
,ffconform
#,ffsuitableattribs
,ffsuitable
,ffreturn

# -- getpagesize.R - utility for getting default pagesize --
,getpagesize
,getdefaultpagesize
,getalignedpagesize

# -- regtest.R --  # xx TODO just draft fragments yet
#,regtest.ff 	   # xx TODO not up to date

# -- hi.R - class for Hybrid Index Preprocessing (HIP) --
,hi
,hiparse  #must not be exported
,subscript2integer
,unsort

# -- fileutil.R - filename utitlities --
,standardPathFile
,splitPathFile
,unsplitPathFile
,tempPathFile
,fftempfile


# -- util.R - some utitlities --
,"unclass<-"
,undim
#,asCharNA
,repnam

# -- vmode.R - metadata and functions for virtual storage modes --
,".vimplemented"
,".vmode"
,".vunsigned"
,".vvalues"
,".rammode"
,".ffmode"
,".vmin"
,".vmax"
,".vNA"
,".rambytes"
,".ffbytes"
,".vcoerceable"
,boolean
,as.boolean
,quad
,as.quad
,nibble
,as.nibble
,byte
,as.byte
,ubyte
,as.ubyte
,short
,as.short
,ushort
,as.ushort
,vector.vmode
,ram2ramcode
,ram2ffcode
,maxffmode
#,charmode   # experimental, not used
,regtest.vmode

# --- fffactor.R - utilities for factors ---
,appendLevels

# -- ffdf.R - dataframe class on top of ff --
,ffdf
,is.ffdf
,as.ffdf

# -- ffcsv.R - reading/writing csv into/from ff --
,read.table.ffdf
,write.table.ffdf
,read.csv.ffdf
,read.csv2.ffdf
,read.delim.ffdf
,read.delim2.ffdf
,write.csv
,write.csv2
,write.csv.ffdf
,write.csv2.ffdf


# -- ffsave.R - saving / loading many ff objects WITH ff files --
,ffsave
,ffsave.image
,ffinfo
,ffload
,ffdrop


# -- x_ff_symm.R - ff extension (dual licensing, no GPL): symmetric  ff matrices with free and fixed diagonal --

#,swapdiag
#,diag
#,"diag<-"
#,diag.default   # turned R function to default method
#,"diag<-.default" # turned R function to default method
#,swapset
#,"subset<-"
#,"fixdiag<-.ff_symm"
#,"dim<-.ff_symm"
#,dimnames.ff_symm
#,"dimnames<-.ff_symm"
#,"na.count<-.ff_symm"
#,print.ff_symm
#,swap.ff_symm
#,"[.ff_symm"
#,"[<-.ff_symm"
#,swapset.ff_symm
#,subset.ff_symm
#,"subset<-.ff_symm"
#,swapdiag.ff_symm
#,diag.ff_symm
#,"diag<-.ff_symm"

# -- x_symm.R    - ff extension (dual licensing, no GPL): symmetric ram matrices with free and fixed diagonal --

#,symm
#,as.symm
#,as.symm.dist
#,as.symm.matrix
#,as.matrix.symm
#,dim.symm
#,"dim<-.symm"
#,dimnames.symm
#,"dimnames<-.symm"
#,symmetric.symm
#,fixdiag.symm
#,"fixdiag<-.symm"
#,diag.symm
#,"diag<-.symm"
#,"na.count<-.symm"
#,print.symm
#,"[.symm"
#,"[<-.symm"
#,subset.symm
#,"subset<-.symm"

# -- fileresize.R (by Daniel Adler, ISC license) --
,file.resize
,file.move


# -- ordermerge.R  --
, regtest.fforder
, ffsort
, fforder
, ffindexordersize
, ffindexorder
, ffindexget
, ffindexset
, ffdfindexget
, ffdfindexset
, dfsort
, dforder
, ramdfsort
, ramdforder
, ffdfsort
, ffdforder

#,.Last.lib

)

# -- generics.R - all new generics --
S3method(is.factor, default)
S3method(is.ordered, default)
# -- array.R - array related tools --
S3method(print,matprint)
S3method(print,vecprint)
# -- as.ff.R - coercion from ram to ff and vice versa (cache-in/cache-out of complete ff objects) --
S3method("as.ff",default)
S3method("as.ff",ff)
S3method("as.ram",default)
S3method("as.ram",ff)
# -- bigsample.R - sampling from big objects --
S3method(bigsample, default)
S3method(bigsample, ff)
# -- CFUN.R - some collapse functions useful with ffapply and friends - xx TODO yet incomplete --
# -- compatibility.R - methods that help to write similar code for ram and ff objects --
# -- ff.R - creating and manipulating ff objects: the core of package ff --
S3method("pattern",ff)
S3method("pattern<-",ff)
S3method("pattern<-",ffdf)
S3method("filename",ffdf)
S3method("filename",ff_pointer)
S3method("filename",default)
S3method("filename<-",ff)
S3method(is.readonly, ff)
S3method(is.open, ff_pointer)
S3method(is.open, ff)
S3method(pagesize, ff)
S3method(maxlength, ff)
S3method(maxlength, default)
S3method(symmetric,ff)
S3method(symmetric,default)
S3method(symmetric,dist)
S3method(fixdiag,ff)
S3method(fixdiag,dist)
S3method(fixdiag,default)
S3method(is.sorted, default)
S3method("is.sorted<-", default)
S3method(na.count, ff)
S3method("na.count<-", ff)
S3method(na.count, default)
S3method("na.count<-", default)
S3method(length, ff)
S3method("length<-", ff)
S3method(levels, ff)
S3method("levels<-", ff)
S3method(is.factor, ff)
S3method(is.ordered, ff)
S3method("ramclass",ff)
S3method("ramclass",default)
S3method("ramattribs",ff)
S3method("ramattribs",default)
S3method(names,ff)
S3method("names<-",ff)
S3method(names,ff_array)
S3method("names<-",ff_array)
S3method(dim,ff)
S3method("dim<-",ff)
S3method(dimnames,ff_array)
S3method("dimnames<-",ff_array)
S3method(dimorder,ff_array)
S3method(dimorder,default)
S3method("dimorder<-",ff_array)
S3method(vw,ff)
S3method("vw<-",ff_vector)
S3method("vw<-",ff_array)
S3method(vw,default)
#S3method(virtual,default)
S3method(virtual,ff)
S3method("virtual<-",ff)
#S3method(print,virtual)
#S3method(physical,default)
S3method(physical,ff)
S3method("physical<-",ff)
#S3method(print,physical)
S3method(print,ff)
S3method(print,ff_vector)
S3method(print,ff_matrix)
S3method(str,ff)
S3method(update,ff)
S3method(clone,ff)
S3method(finalizer, ff)
S3method("finalizer<-", ff)
S3method(finalize, ff_pointer)
S3method(finalize, ff)
S3method(finalize, ffdf)
S3method(open, ff)
S3method(close, ff_pointer)
S3method(close, ff)
S3method(deleteIfOpen, ff_pointer)
S3method(deleteIfOpen, ff)
#S3method(deleteIfOpen, default)
S3method(delete, ff_pointer)
S3method(delete, ff)
S3method(delete,default)
S3method("[[",ff)
S3method("[[<-",ff)
S3method("swap",ff)
S3method("swap",ff_array)
S3method("swap",default)
S3method("[",ff)
S3method("[",ff_array)
S3method("[<-",ff)
S3method("[<-",ff_array)
S3method("add",ff)
S3method("add",default)
S3method(chunk, ff_vector)
# -- ffapply.R - applying expressions (not functions) to large ff (or ram) objects (R.ff foundation) --
# -- ffreturn.R - basic infrastructure for checking/creating FF_RETURN values (R.ff foundation) --
# -- getpagesize.R - utility for getting default pagesize --
# -- regtest.R --  # xx TODO just draft fragments yet


# -- hi.R - class for Hybrid Index Preprocessing (HIP) --
S3method(print, hi)
S3method(str, hi)
S3method(as.hi, NULL)
S3method(as.hi, "(")
S3method(as.hi, hi)
S3method(as.hi, ri)
S3method(as.hi, name)
S3method(as.hi, call)
S3method(as.hi, matrix)
S3method(as.hi, integer)
S3method(as.hi, logical)
S3method(as.hi, which)
S3method(as.hi, double)
S3method(as.hi, character)
S3method(as.matrix, hi)
S3method(as.which, hi)
S3method(as.integer, hi)
S3method(as.logical, hi)
S3method(as.character, hi)
S3method(length, hi)
S3method(maxindex, hi)
S3method(poslength, hi)

# -- ffbit.R - functions related to package bit --
S3method(as.hi,ri)
S3method(as.hi,bit)
S3method(as.bit,hi)
S3method(as.bitwhich,hi)
S3method(as.hi,bitwhich)
S3method(as.ff,bit)
S3method(as.bit,ff)

# -- util.R - some utitlities --

# -- vmode.R - metadata and functions for virtual storage modes --
S3method(vmode,default)
S3method(vmode,ff)
S3method("vmode<-",default)
S3method("vmode<-",ff)
S3method(as.vmode,default)
S3method(as.vmode,ff)
S3method(as.boolean,default)
S3method(as.quad,default)
S3method(as.nibble,default)
S3method(as.byte,default)
S3method(as.ubyte,default)
S3method(as.short,default)
S3method(as.ushort,default)

# -- vt.R - cloned and virtual matrix transpose --
S3method(vt, default)
S3method(vt, ff)
S3method(t, ff)


# -- fffactor.R - utilities for factors ---
S3method(recodeLevels, factor)
S3method(recodeLevels, ff)
S3method(sortLevels, factor)
S3method(sortLevels, ff)
S3method(sortLevels, ffdf)


# -- ffdf.R - dataframe class on top of ff --
S3method(chunk, ffdf)
S3method(clone, ffdf)
S3method(update, ffdf)
S3method("$", ffdf)
S3method("$<-", ffdf)
S3method("[[", ffdf)
S3method("[[<-", ffdf)
S3method("[", ffdf)
S3method("[<-", ffdf)
S3method(as.ffdf, ff_matrix)
S3method(as.ffdf, ff_vector)
S3method(as.ffdf, data.frame)
S3method(as.data.frame, ffdf)
S3method(length, ffdf)
S3method("length<-", ffdf)
S3method(vmode, ffdf)
S3method("vmode<-", ffdf)
S3method(vw, ffdf)
S3method("vw<-", ffdf)
S3method(dim, ffdf)
S3method("dim<-", ffdf)
S3method(dimorder, ffdf)
S3method("dimorder<-", ffdf)
S3method(names, ffdf)
S3method("names<-", ffdf)
S3method(row.names, ffdf)
S3method("row.names<-", ffdf)
S3method(dimnames, ffdf)
S3method("dimnames<-", ffdf)
S3method(physical, ffdf)
S3method("physical<-", ffdf)
S3method(virtual, ffdf)
S3method("virtual<-", ffdf)
S3method(is.open, ffdf)
S3method(open, ffdf)
S3method(close, ffdf)
S3method(delete, ffdf)
S3method(print, ffdf)
S3method(str, ffdf)


# -- x_ff_symm.R - ff extension (dual licensing, no GPL): symmetric  ff matrices with free and fixed diagonal --
#S3method(diag, default)
#S3method("diag<-", default)
#S3method("fixdiag<-",ff_symm)
#S3method("dim<-",ff_symm)
#S3method(dimnames,ff_symm)
#S3method("dimnames<-",ff_symm)
#S3method("na.count<-", ff_symm)
#S3method(print,ff_symm)
#S3method(swap,ff_symm)
#S3method("[",ff_symm)
#S3method("[<-",ff_symm)
#S3method(swapdiag,ff_symm)
#S3method(diag,ff_symm)
#S3method("diag<-",ff_symm)
#S3method(swapset,ff_symm)
#S3method(subset,ff_symm)
#S3method("subset<-",ff_symm)

# -- x_symm.R    - ff extension (dual licensing, no GPL): symmetric ram matrices with free and fixed diagonal --
#S3method(dim,symm)
#S3method("dim<-",symm)
#S3method(dimnames,symm)
#S3method("dimnames<-",symm)
#S3method(symmetric,symm)
#S3method(fixdiag,symm)
#S3method("fixdiag<-",symm)
#S3method(diag,symm)
#S3method("diag<-",symm)
#S3method(as.matrix,symm)
#S3method(as.symm,matrix)
#S3method("na.count<-", symm)
#S3method(print,symm)
#S3method("[",symm)
#S3method("[<-",symm)
#S3method(subset,symm)
#S3method("subset<-",symm)

# -- ordermerge.R  --
S3method("mergeorder", default)
S3method("mergesort", default)
S3method("shellorder", default)
S3method("shellsort", default)
S3method("keyorder", default)
S3method("keysort", default)
S3method("radixorder", default)
S3method("radixsort", default)
S3method("ramorder", default)
S3method("ramsort", default)
# wish of CRAN maintainers: export another time here (now maintained and exported in bit)
#S3method(clone, default)