#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"

#include "ppport.h"

#include "emboss_perl.h"
#include "bio_emboss_config.h"

MODULE = Bio::Emboss_file		PACKAGE = Bio::Emboss		

PROTOTYPES: ENABLE

 # code from ajfile.c: automatically generated

AjPOutfile
ajOutfileNew (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPDir
ajDirNew (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPDir
ajDirNewS (name, ext)
       const AjPStr name
       const AjPStr ext
    OUTPUT:
       RETVAL

AjPDir
ajDirNewSS (name, prefix, ext)
       const AjPStr name
       const AjPStr prefix
       const AjPStr ext
    OUTPUT:
       RETVAL

AjPDir
ajDiroutNew (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPDir
ajDiroutNewS (name, ext)
       const AjPStr name
       const AjPStr ext
    OUTPUT:
       RETVAL

AjPDir
ajDiroutNewSS (name, prefix, ext)
       const AjPStr name
       const AjPStr prefix
       const AjPStr ext
    OUTPUT:
       RETVAL

AjPStr
ajDirName (thys)
       const AjPDir thys
    OUTPUT:
       RETVAL

AjPStr
ajDirExt (thys)
       const AjPDir thys
    OUTPUT:
       RETVAL

AjPFile
ajFileNew ()
    OUTPUT:
       RETVAL

AjPFile
ajFileNewInPipe (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewIn (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewInC (name)
       const char* name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewInList (list)
       AjPList list
    OUTPUT:
       RETVAL

AjPFile
ajFileNewApp (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewOut (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewOutC (name)
       const char* name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewOutD (dir, name)
       const AjPStr dir
       const AjPStr name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewOutDir (dir, name)
       const AjPDir dir
       const AjPStr name
    OUTPUT:
       RETVAL

AjBool
ajFileSetDir (pname, dir)
       AjPStr& pname
       const AjPStr dir
    OUTPUT:
       RETVAL
       pname

AjBool
ajFileHasDir (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPFile
ajFileNewF (file)
       FILE* file
    OUTPUT:
       RETVAL

void
ajOutfileClose (pthis)
       AjPOutfile& pthis
    OUTPUT:
       pthis

void
ajOutfileDel (pthis)
       AjPOutfile& pthis
    OUTPUT:
       pthis

void
ajDirDel (pthis)
       AjPDir& pthis
    OUTPUT:
       pthis

void
ajDiroutDel (pthis)
       AjPDir& pthis
    OUTPUT:
       pthis

void
ajFileClose (pthis)
       AjPFile& pthis
    OUTPUT:
       pthis

void
ajFileOutClose (pthis)
       AjPFile& pthis
    OUTPUT:
       pthis

void
ajFileDataNew (tfile, fnew)
       const AjPStr tfile
       AjPFile& fnew
    OUTPUT:
       fnew

void
ajFileDataNewC (s, f)
       const char* s
       AjPFile& f
    OUTPUT:
       f

void
ajFileDataDirNew (tfile, dir, fnew)
       const AjPStr tfile
       const AjPStr dir
       AjPFile& fnew
    OUTPUT:
       fnew

void
ajFileDataDirNewC (s, d, f)
       const char* s
       const char* d
       AjPFile& f
    OUTPUT:
       f

ajint
ajFileSeek (thys, offset, wherefrom)
       AjPFile thys
       ajlong offset
       ajint wherefrom
    OUTPUT:
       RETVAL

size_t
ajFileRead (ptr, element_size, count, thys)
       char& ptr
       size_t element_size
       size_t count
       AjPFile thys
    OUTPUT:
       RETVAL
       ptr

ajuint
ajFileReadUint (thys, Bigendian)
       AjPFile thys
       AjBool Bigendian
    OUTPUT:
       RETVAL

size_t
ajFileWrite (thys, ptr, element_size, count)
       AjPFile thys
       const char* ptr
       size_t element_size
       size_t count
    OUTPUT:
       RETVAL

AjBool
ajFileNext (thys)
       AjPFile thys
    OUTPUT:
       RETVAL

FILE*
ajFileReopen (thys, name)
       AjPFile thys
       const AjPStr name
    OUTPUT:
       RETVAL

AjBool
ajFileReadLine (thys, pdest)
       AjPFile thys
       AjPStr& pdest
    OUTPUT:
       RETVAL
       pdest

AjBool
ajFileGetsTrimL (thys, pdest, fpos)
       AjPFile thys
       AjPStr& pdest
       ajlong& fpos
    OUTPUT:
       RETVAL
       pdest
       fpos

AjBool
ajFileGetsTrim (thys, pdest)
       AjPFile thys
       AjPStr& pdest
    OUTPUT:
       RETVAL
       pdest

AjBool
ajFileGets (thys, pdest)
       AjPFile thys
       AjPStr& pdest
    OUTPUT:
       RETVAL
       pdest

AjBool
ajFileGetsL (thys, pdest, fpos)
       AjPFile thys
       AjPStr& pdest
       ajlong& fpos
    OUTPUT:
       RETVAL
       pdest
       fpos

void
ajFileUnbuffer (thys)
       AjPFile thys

AjBool
ajFileReadAppend (thys, pbuff)
       AjPFile thys
       AjPStr& pbuff
    OUTPUT:
       RETVAL
       pbuff

void
ajFileOutHeader (thys)
       AjPFile thys

AjBool
ajFileNameShorten (fname)
       AjPStr& fname
    OUTPUT:
       RETVAL
       fname

AjBool
ajFileNameTrim (fname)
       AjPStr& fname
    OUTPUT:
       RETVAL
       fname

void
ajFileDataNewWrite (tfile, fnew)
       const AjPStr tfile
       AjPFile& fnew
    OUTPUT:
       fnew

AjBool
ajFileDir (dir)
       AjPStr& dir
    OUTPUT:
       RETVAL
       dir

AjBool
ajFileDirPath (dir)
       AjPStr& dir
    OUTPUT:
       RETVAL
       dir

AjBool
ajFileGetwd (dir)
       AjPStr& dir
    OUTPUT:
       RETVAL
       dir

AjBool
ajFileDirUp (dir)
       AjPStr& dir
    OUTPUT:
       RETVAL
       dir

void
ajFileDirFix (dir)
       AjPStr& dir
    OUTPUT:
       dir

void
ajFileExit ()

void
ajFileTrace (thys)
       const AjPFile thys

AjPFile
ajOutfileFile (thys)
       const AjPOutfile thys
    OUTPUT:
       RETVAL

FILE*
ajOutfileFp (thys)
       const AjPOutfile thys
    OUTPUT:
       RETVAL

AjPStr
ajOutfileFormat (thys)
       const AjPOutfile thys
    OUTPUT:
       RETVAL

ajint
ajFileBuffSize ()
    OUTPUT:
       RETVAL

const char*
ajFileName (thys)
       const AjPFile thys
    OUTPUT:
       RETVAL

const AjPStr
ajFileNameS (thys)
       const AjPFile thys
    OUTPUT:
       RETVAL

AjBool
ajFileGetApp (thys)
       const AjPFile thys
    OUTPUT:
       RETVAL

AjPStr
ajFileGetName (thys)
       const AjPFile thys
    OUTPUT:
       RETVAL

AjBool
ajFileStat (fname, mode)
       const AjPStr fname
       ajint mode
    OUTPUT:
       RETVAL

ajlong
ajFileLength (fname)
       const AjPStr fname
    OUTPUT:
       RETVAL

ajlong
ajFileTell (thys)
       const AjPFile thys
    OUTPUT:
       RETVAL

AjBool
ajFileStdout (file)
       const AjPFile file
    OUTPUT:
       RETVAL

AjBool
ajFileStderr (file)
       const AjPFile file
    OUTPUT:
       RETVAL

AjBool
ajFileStdin (file)
       const AjPFile file
    OUTPUT:
       RETVAL

FILE*
ajFileFp (thys)
       const AjPFile thys
    OUTPUT:
       RETVAL

AjBool
ajFileEof (thys)
       const AjPFile thys
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewIn (name)
       const AjPStr name
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNew ()
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewFile (file)
       AjPFile file
    OUTPUT:
       RETVAL

AjBool
ajFileBuffSetFile (pthys, file, samefile)
       AjPFileBuff& pthys
       AjPFile file
       AjBool samefile
    OUTPUT:
       RETVAL
       pthys

AjPFileBuff
ajFileBuffNewS (data)
       const AjPStr data
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewF (fp)
       FILE* fp
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewDW (dir, wildfile)
       const AjPStr dir
       const AjPStr wildfile
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewDWE (dir, wildfile, exclude)
       const AjPStr dir
       const AjPStr wildfile
       const AjPStr exclude
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewDC (dir, filename)
       const AjPStr dir
       const char* filename
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewDF (dir, filename)
       const AjPStr dir
       const AjPStr filename
    OUTPUT:
       RETVAL

AjPFile
ajFileNewDW (dir, wildfile)
       const AjPStr dir
       const AjPStr wildfile
    OUTPUT:
       RETVAL

AjPFile
ajFileNewDWE (dir, wildfile, exclude)
       const AjPStr dir
       const AjPStr wildfile
       const AjPStr exclude
    OUTPUT:
       RETVAL

AjPFile
ajFileNewDF (dir, filename)
       const AjPStr dir
       const AjPStr filename
    OUTPUT:
       RETVAL

AjPFile
ajFileNewDirF (dir, filename)
       const AjPDir dir
       const AjPStr filename
    OUTPUT:
       RETVAL

AjPFile
ajFileNewDC (dir, filename)
       const AjPStr dir
       const char* filename
    OUTPUT:
       RETVAL

AjPFileBuff
ajFileBuffNewInList (list)
       AjPList list
    OUTPUT:
       RETVAL

void
ajFileBuffDel (pthis)
       AjPFileBuff& pthis
    OUTPUT:
       pthis

AjBool
ajFileBuffGet (thys, pdest)
       AjPFileBuff thys
       AjPStr& pdest
    OUTPUT:
       RETVAL
       pdest

AjBool
ajFileBuffGetStore (thys, pdest, store, astr)
       AjPFileBuff thys
       AjPStr& pdest
       AjBool store
       AjPStr& astr
    OUTPUT:
       RETVAL
       pdest
       astr

AjBool
ajFileBuffGetStoreL (thys, pdest, fpos, store, astr)
       AjPFileBuff thys
       AjPStr& pdest
       ajlong& fpos
       AjBool store
       AjPStr& astr
    OUTPUT:
       RETVAL
       pdest
       fpos
       astr

AjBool
ajFileBuffGetL (thys, pdest, fpos)
       AjPFileBuff thys
       AjPStr& pdest
       ajlong& fpos
    OUTPUT:
       RETVAL
       pdest
       fpos

void
ajFileBuffStripHtml (thys)
       AjPFileBuff thys

void
ajFileBuffLoadC (thys, line)
       AjPFileBuff thys
       const char* line

void
ajFileBuffLoadS (thys, line)
       AjPFileBuff thys
       const AjPStr line

AjBool
ajFileBuffEof (thys)
       const AjPFileBuff thys
    OUTPUT:
       RETVAL

AjBool
ajFileBuffEnd (thys)
       const AjPFileBuff thys
    OUTPUT:
       RETVAL

void
ajFileBuffReset (thys)
       AjPFileBuff thys

void
ajFileBuffResetStore (thys, store, astr)
       AjPFileBuff thys
       AjBool store
       AjPStr& astr
    OUTPUT:
       astr

void
ajFileBuffResetPos (thys)
       AjPFileBuff thys

void
ajFileBuffFix (thys)
       AjPFileBuff thys

void
ajFileBuffFreeClear (thys)
       AjPFileBuff thys

void
ajFileBuffClear (thys, lines)
       AjPFileBuff thys
       ajint lines

void
ajFileBuffClearStore (thys, lines, rdline, store, astr)
       AjPFileBuff thys
       ajint lines
       const AjPStr rdline
       AjBool store
       AjPStr& astr
    OUTPUT:
       astr

AjBool
ajFileBuffNobuff (thys)
       AjPFileBuff thys
    OUTPUT:
       RETVAL

AjBool
ajFileBuffBuff (thys)
       AjPFileBuff thys
    OUTPUT:
       RETVAL

AjBool
ajFileBuffEmpty (thys)
       const AjPFileBuff thys
    OUTPUT:
       RETVAL

void
ajFileBuffTrace (thys)
       const AjPFileBuff thys

void
ajFileBuffTraceFull (thys, nlines, nfree)
       const AjPFileBuff thys
       size_t nlines
       size_t nfree

void
ajFileBuffPrint (thys, title)
       const AjPFileBuff thys
       const char* title

AjBool
ajFileBuffIsBuffered (thys)
       const AjPFileBuff thys
    OUTPUT:
       RETVAL

FILE*
ajFileBuffFp (thys)
       const AjPFileBuff thys
    OUTPUT:
       RETVAL

AjPFile
ajFileBuffFile (thys)
       const AjPFileBuff thys
    OUTPUT:
       RETVAL

void
ajFileBuffLoad (thys)
       AjPFileBuff thys

AjBool
ajFileNameDir (filename, dir, name)
       AjPStr& filename
       const AjPDir dir
       const AjPStr name
    OUTPUT:
       RETVAL
       filename

AjBool
ajFileNameDirSet (filename, dir)
       AjPStr& filename
       const AjPStr dir
    OUTPUT:
       RETVAL
       filename

AjBool
ajFileNameDirSetC (filename, dir)
       AjPStr& filename
       const char* dir
    OUTPUT:
       RETVAL
       filename

AjBool
ajFileNameExt (filename, extension)
       AjPStr& filename
       const AjPStr extension
    OUTPUT:
       RETVAL
       filename

AjBool
ajFileNameExtC (filename, extension)
       AjPStr& filename
       const char* extension
    OUTPUT:
       RETVAL
       filename

ajint
ajFileScan (path, filename, result, show, dolist, list, rlist, recurs, outf)
       const AjPStr path
       const AjPStr filename
       AjPList & result
       AjBool show
       AjBool dolist
       AjPList & list
       AjPList rlist
       AjBool recurs
       AjPFile outf
    OUTPUT:
       RETVAL
       result
       list

AjBool
ajFileTestSkip (fullname, exc, inc, keep, ignoredirectory)
       const AjPStr fullname
       const AjPStr exc
       const AjPStr inc
       AjBool keep
       AjBool ignoredirectory
    OUTPUT:
       RETVAL

AjBool
ajFileDirTrim (name)
       AjPStr& name
    OUTPUT:
       RETVAL
       name

AjBool
ajFileExtnTrim (name)
       AjPStr& name
    OUTPUT:
       RETVAL
       name

AjBool
ajFileDirExtnTrim (name)
       AjPStr& name
    OUTPUT:
       RETVAL
       name

const char*
ajFileTempName (dir)
       const char* dir
    OUTPUT:
       RETVAL

ajint
ajFileWriteByte (thys, ch)
       AjPFile thys
       char ch
    OUTPUT:
       RETVAL

ajint
ajFileWriteChar (thys, str, len)
       AjPFile thys
       const char* str
       ajint len
    OUTPUT:
       RETVAL

ajint
ajFileWriteInt2 (thys, i)
       AjPFile thys
       short i
    OUTPUT:
       RETVAL

ajint
ajFileWriteInt4 (thys, i)
       AjPFile thys
       ajint i
    OUTPUT:
       RETVAL

ajint
ajFileWriteInt8 (thys, l)
       AjPFile thys
       ajlong l
    OUTPUT:
       RETVAL

ajint
ajFileWriteStr (thys, str, len)
       AjPFile thys
       const AjPStr str
       ajuint len
    OUTPUT:
       RETVAL

AjBool
ajFileBuffStripHtmlPre (thys)
       AjPFileBuff thys
    OUTPUT:
       RETVAL

AjPList
ajFileFileList (files)
       const AjPStr files
    OUTPUT:
       RETVAL

AjBool
ajFileBuffGetTrim (thys, pdest)
       AjPFileBuff thys
       AjPStr& pdest
    OUTPUT:
       RETVAL
       pdest

AjBool
ajFileNameValid (fname)
       const AjPStr fname
    OUTPUT:
       RETVAL