# Namespace for ff (currently exporting (almost) everything in order to facilitate debugging)
# (c) 2007 Jens Oehlsch輍el
# Licence: GPL2
# Created: 2007-08-24
# Last changed: 2007-11-30

useDynLib(ff)

importFrom(utils, memory.limit, packageDescription)
import(bit)


export(

# == this is a complete list of R functions and metadata of this package sorted by filenames, non-exported functions are commented away ==



# -- generics.R - all new generics --
 as.hi
#,physical
#,"physical<-"
#,virtual
#,"virtual<-"
,maxindex
,poslength
,maxlength
#,maxwidth
,pattern
,"pattern<-"
,filename
,"filename<-"
, pagesize
,is.open
,is.readonly
,vmode
,as.vmode
,"vmode<-"
,finalizer
,"finalizer<-"
,finalize
,delete
,deleteIfOpen
,clone
,as.ff
,as.ram
,dimorder
,"dimorder<-"
,vw
,"vw<-"
,is.factor
,is.factor.default
,is.ordered
,is.ordered.default
,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
,print.matprint
,vecprint
,print.vecprint

# -- as.ff.R - coercion from ram to ff and vice versa (cache-in/cache-out of complete ff objects) --
,as.ram.default
,as.ram.ff
,as.ff.default
,as.ff.ff

# -- bigsample.R - sampling from big objects --
,bigsample.default
,bigsample.ff



# -- 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
,vmode.ff
,as.vmode.ff	# just catch invalid use
,"vmode<-.ff" 	# just catch invalid use
,is.open.ff_pointer
,is.open.ff
,pagesize.ff
#,ffdir
,pattern.ff
,"pattern<-.ff"
,"pattern<-.ffdf"
,filename.ff_pointer
,filename.ffdf
,filename.default
,"filename<-.ff"
,is.readonly.ff
,maxlength.ff
,maxlength.default
,symmetric.ff
,symmetric.dist
,symmetric.default
,fixdiag.ff
,fixdiag.dist
,fixdiag.default
,is.sorted.default
,"is.sorted<-.default"
,na.count.ff
,"na.count<-.ff"
,na.count.default
,"na.count<-.default"
#,physical.default
#,"physical<-.default"
,physical.ff
,"physical<-.ff"
#,print.physical
#,virtual.default
#,"virtual<-.default"
,virtual.ff
,"virtual<-.ff"
#,print.virtual
,ramclass.ff
,ramclass.default
,ramattribs.ff
,ramattribs.default
,length.ff
,"length<-.ff"
,levels.ff
,"levels<-.ff"
,is.factor.ff
,is.ordered.ff
,names.ff
,"names<-.ff"
,names.ff_array
,"names<-.ff_array"
,dim.ff
,"dim<-.ff"
,dimorder.ff_array
,"dimorder<-.ff_array"
,dimorder.default
,vw.ff
,"vw<-.ff_vector"
,"vw<-.ff_array"
,vw.default
,dimnames.ff_array
,"dimnames<-.ff_array"
,print.ff  
,print.ff_vector
,print.ff_matrix
,str.ff  
# xx todo print.ff_array via arrprint and print.arrprint
,ff
,update.ff
,clone.ff
,clone.default
,finalizer.ff
,"finalizer<-.ff"
,finalize.ff_pointer
,finalize.ff
,finalize.ffdf
,open.ff
,close.ff_pointer
,close.ff
,deleteIfOpen.ff_pointer
,deleteIfOpen.ff
#,deleteIfOpen.default
,delete.ff_pointer
,delete.ff
,delete.default
,getset.ff	# ,add=TRUE
,get.ff
,set.ff		# ,add=TRUE
,"[[.ff"
,"[[<-.ff"	# ,add=TRUE
,readwrite.ff	# ,add=TRUE
,read.ff
,write.ff	# ,add=TRUE
,swap.ff	# ,add=TRUE
,"[.ff"
,"[<-.ff"	# ,add=TRUE
,swap.ff_array	# ,add=TRUE
,"[.ff_array"
,"[<-.ff_array"	# ,add=TRUE
,add.ff
,add.default
,swap.default
,chunk.ff_vector


# -- 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
,print.hi
,str.hi
,hiparse  #must not be exported
,as.hi.hi
,as.hi.ri
,as.hi.name
,as.hi.call #must not be exported
,as.hi.integer
,as.hi.which
,as.hi.matrix
,as.hi.logical
,as.hi.character
,as.hi.double
,subscript2integer
,as.which.hi
,as.integer.hi
,as.matrix.hi
,as.logical.hi
,as.character.hi
,maxindex.hi
,maxindex.default
,poslength.hi
,poslength.default
,unsort
,unsort.hi
,unsort.ahi


# -- ffbit.R - functions related to package bit --
,maxindex.bitwhich
,maxindex.bit
,poslength.bitwhich
,poslength.bit
,as.hi.ri
,as.hi.bit
,as.bit.hi
,as.bitwhich.hi
,as.hi.bitwhich
,as.ff.bit
,as.bit.ff
,chunk.bit

# -- 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
,as.boolean.default
,quad
,as.quad
,as.quad.default
,nibble
,as.nibble
,as.nibble.default
,byte
,as.byte
,as.byte.default
,ubyte
,as.ubyte
,as.ubyte.default
,short
,as.short
,as.short.default
,ushort
,as.ushort
,as.ushort.default
,vector.vmode
,vmode.default
,"vmode<-.default"
,as.vmode.default
,ram2ramcode
,ram2ffcode
,maxffmode
#,charmode   # experimental, not used
,regtest.vmode

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


# --- fffactor.R - utilities for factors ---
,appendLevels
,recodeLevels.factor
,recodeLevels.ff
,sortLevels.factor
,sortLevels.ff
,sortLevels.ffdf


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


# -- ordermerge.R  --
, mergeorder.default
, mergesort.default
, shellorder.default
, shellsort.default
, keyorder.default
, keysort.default
, radixorder.default
, radixsort.default
, ramorder.default
, ramsort.default
, 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(clone,default)
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, hi)
S3method(as.hi, ri)
S3method(as.hi, name)
S3method(as.hi, call)
S3method(as.hi, matrix)
S3method(as.hi, integer)
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(maxindex, default)
S3method(poslength, hi)
S3method(poslength, default)

# -- ffbit.R - functions related to package bit --
S3method(maxindex,bitwhich)
S3method(maxindex,bit)
S3method(poslength,bitwhich)
S3method(poslength,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)
S3method(chunk, bit)

# -- 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)