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

#include "ppport.h"

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

MODULE = Bio::Emboss_index		PACKAGE = Bio::Emboss		

PROTOTYPES: ENABLE

 # code from ajindex.c: automatically generated

AjPBtcache
ajBtreeCacheNewC (file, ext, idir, mode, pagesize, order, fill, level, cachesize)
       const char * file
       const char * ext
       const char * idir
       const char * mode
       ajint pagesize
       ajint order
       ajint fill
       ajint level
       ajint cachesize
    OUTPUT:
       RETVAL

void
ajBtreeCacheDel (thys)
       AjPBtcache& thys
    OUTPUT:
       thys

AjPBtpage
ajBtreeCacheRead (cache, pageno)
       AjPBtcache cache
       ajlong pageno
    OUTPUT:
       RETVAL
       cache

void
ajBtreeCacheSync (cache, rootpage)
       AjPBtcache cache
       ajlong rootpage

AjPBtpage
ajBtreeCacheWrite (cache, pageno)
       AjPBtcache cache
       ajlong pageno
    OUTPUT:
       RETVAL
       cache

void
ajBtreeCreateRootNode (cache, rootpage)
       AjPBtcache cache
       ajlong rootpage
    OUTPUT:
       cache

AjPBtpage
ajBtreeFindInsert (cache, key)
       AjPBtcache cache
       const char* key
    OUTPUT:
       RETVAL

AjPBtId
ajBtreeIdNew ()
    OUTPUT:
       RETVAL

void
ajBtreeIdDel (thys)
       AjPBtId& thys
    OUTPUT:
       thys

void
ajBtreeInsertId (cache, id)
       AjPBtcache cache
       const AjPBtId id

AjPBtId
ajBtreeIdFromKey (cache, key)
       AjPBtcache cache
       const char * key
    OUTPUT:
       RETVAL

void
ajBtreeWriteParams (cache, fn, ext, idir)
       const AjPBtcache cache
       const char * fn
       const char * ext
       const char * idir

void
ajBtreeReadParams (fn, ext, idir, order, nperbucket, pagesize, level, cachesize, sorder, snperbucket, count, kwlimit)
       const char * fn
       const char * ext
       const char * idir
       ajint& order
       ajint& nperbucket
       ajint& pagesize
       ajint& level
       ajint& cachesize
       ajint& sorder
       ajint& snperbucket
       ajlong& count
       ajint& kwlimit
    OUTPUT:
       order
       nperbucket
       pagesize
       level
       cachesize
       sorder
       snperbucket
       count
       kwlimit

AjBool
ajBtreeDeleteId (cache, id)
       AjPBtcache cache
       const AjPBtId id
    OUTPUT:
       RETVAL

AjPBtWild
ajBtreeWildNew (cache, wild)
       AjPBtcache cache
       const AjPStr wild
    OUTPUT:
       RETVAL

void
ajBtreeWildDel (thys)
       AjPBtWild& thys
    OUTPUT:
       thys

AjPBtKeyWild
ajBtreeKeyWildNew (cache, wild)
       AjPBtcache cache
       const AjPStr wild
    OUTPUT:
       RETVAL

void
ajBtreeKeyWildDel (thys)
       AjPBtKeyWild& thys
    OUTPUT:
       thys

AjPBtpage
ajBtreeFindInsertW (cache, key)
       AjPBtcache cache
       const char* key
    OUTPUT:
       RETVAL

AjPBtId
ajBtreeIdFromKeyW (cache, wild)
       AjPBtcache cache
       AjPBtWild wild
    OUTPUT:
       RETVAL

void
ajBtreeListFromKeyW (cache, key, idlist)
       AjPBtcache cache
       const char * key
       AjPList idlist

AjBool
ajBtreeReplaceId (cache, rid)
       AjPBtcache cache
       const AjPBtId rid
    OUTPUT:
       RETVAL

ajint
ajBtreeReadEntries (filename, indexdir, directory, seqfiles, reffiles)
       const char* filename
       const char* indexdir
       const char* directory
       AjPStr*& seqfiles
       AjPStr*& reffiles
    OUTPUT:
       RETVAL
       seqfiles
       reffiles

void
ajBtreeInsertDupId (cache, id)
       AjPBtcache cache
       AjPBtId id

AjPList
ajBtreeDupFromKey (cache, key)
       AjPBtcache cache
       const char * key
    OUTPUT:
       RETVAL

AjPBtPri
ajBtreePriNew ()
    OUTPUT:
       RETVAL

void
ajBtreePriDel (thys)
       AjPBtPri& thys
    OUTPUT:
       thys

void
ajBtreeInsertKeyword (cache, pri)
       AjPBtcache cache
       const AjPBtPri pri

AjPBtPri
ajBtreePriFromKeyword (cache, key)
       AjPBtcache cache
       const char * key
    OUTPUT:
       RETVAL

AjPBtcache
ajBtreeSecCacheNewC (file, ext, idir, mode, pagesize, order, fill, level, cachesize, sorder, slevel, sfill, count, kwlimit)
       const char * file
       const char * ext
       const char * idir
       const char * mode
       ajint pagesize
       ajint order
       ajint fill
       ajint level
       ajint cachesize
       ajint sorder
       ajint slevel
       ajint sfill
       ajlong count
       ajint kwlimit
    OUTPUT:
       RETVAL

void
ajBtreeInsertSecId (cache, id)
       AjPBtcache cache
       const AjPStr id

AjBool
ajBtreeSecFromId (cache, key)
       AjPBtcache cache
       const char * key
    OUTPUT:
       RETVAL

AjPBtpage
ajBtreeSecFindInsert (cache, key)
       AjPBtcache cache
       const char* key
    OUTPUT:
       RETVAL

void
ajBtreeLockTest (cache)
       AjPBtcache cache

AjPList
ajBtreeSecLeafList (cache, rootblock)
       AjPBtcache cache
       ajlong rootblock
    OUTPUT:
       RETVAL

AjBool
ajBtreeVerifyId (cache, rootblock, id)
       AjPBtcache cache
       ajlong rootblock
       const char * id
    OUTPUT:
       RETVAL

AjPBtId
ajBtreeIdFromKeywordW (cache, wild, idcache)
       AjPBtcache cache
       AjPBtKeyWild wild
       AjPBtcache idcache
    OUTPUT:
       RETVAL

void
ajBtreeListFromKeywordW (cache, key, idcache, btidlist)
       AjPBtcache cache
       const char * key
       AjPBtcache idcache
       AjPList btidlist

AjPBtHybrid
ajBtreeHybNew ()
    OUTPUT:
       RETVAL

void
ajBtreeHybDel (thys)
       AjPBtHybrid& thys
    OUTPUT:
       thys

AjPBtpage
ajBtreeHybFindInsert (cache, key)
       AjPBtcache cache
       const char* key
    OUTPUT:
       RETVAL

void
ajBtreeHybInsertId (cache, hyb)
       AjPBtcache cache
       const AjPBtHybrid hyb

AjPBtpage
ajBtreeNumFindInsert (cache, key)
       AjPBtcache cache
       const ajlong key
    OUTPUT:
       RETVAL

void
ajBtreeInsertNum (cache, num, page)
       AjPBtcache cache
       const AjPBtNumId num
       AjPBtpage page
    OUTPUT:
       page

void
ajBtreeFreePriArray (cache)
       AjPBtcache cache

void
ajBtreeFreeSecArray (cache)
       AjPBtcache cache

void
ajBtreeHybLeafList (cache, rootblock, idname, list)
       AjPBtcache cache
       ajlong rootblock
       const AjPStr idname
       AjPList list

void
ajBtreeDumpHybKeys (cache, dmin, dmax, outf)
       AjPBtcache cache
       ajint dmin
       ajint dmax
       AjPFile outf