diff options
Diffstat (limited to 'biology/emboss/files/patch-ajindex.h')
| -rw-r--r-- | biology/emboss/files/patch-ajindex.h | 170 |
1 files changed, 170 insertions, 0 deletions
diff --git a/biology/emboss/files/patch-ajindex.h b/biology/emboss/files/patch-ajindex.h new file mode 100644 index 0000000..bcd3faa --- /dev/null +++ b/biology/emboss/files/patch-ajindex.h @@ -0,0 +1,170 @@ +--- ajax/ajindex.h.orig Mon Jan 23 12:17:10 2006 ++++ ajax/ajindex.h Thu Dec 22 13:12:32 2005 +@@ -67,6 +67,23 @@ + } AjOBtNode; + #define AjPBtNode AjOBtNode* + ++ ++ ++ ++typedef struct AjSBtMem ++{ ++ struct AjSBtMem *next; ++ struct AjSBtMem *prev; ++ AjPStr *karray; ++ ajlong *parray; ++ ajlong *overflows; ++ AjBool used; ++} AjOBtMem; ++#define AjPBtMem AjOBtMem* ++ ++ ++ ++ + /* @data AjPBtId *************************************************** + ** + ** Btree ID +@@ -137,6 +154,54 @@ + + + ++/* @data AjPBtNumId *************************************************** ++** ++** Btree ID ++** ++** @attr id [AjPStr] Unique ID ++** @attr dbno [ajint] Database file number ++** @attr dups [ajint] Duplicates ++** @attr offset [ajlong] Offset within database file (ftello) ++** @attr refoffset [ajlong] Offset within reference database file (ftello) ++******************************************************************************/ ++ ++typedef struct AjSBtNumId ++{ ++ ajint dbno; ++ ajlong offset; ++ ajlong refoffset; ++} AjOBtNumId; ++#define AjPBtNumId AjOBtNumId* ++ ++ ++ ++ ++/* @data AjPNumBucket *************************************************** ++** ++** Offset bucket structure on disc ++** ++** Key, filenumber, ftell ID, subkey page (char*, ajint, ajlong, ajlong) ++** ++** @attr NodeType [ajint] Node type ++** @attr Nentries [ajint] Number of entries ++** @attr Overflow [ajlong] Offset to overflow block ++** @attr offset [ajlong*] file offsets ++** @attr refoffset [ajlong*] ref file offsets ++** @attr offset [ajint*] database numbers ++******************************************************************************/ ++ ++typedef struct AjSNumBucket ++{ ++ ajint NodeType; ++ ajint Nentries; ++ ajlong Overflow; ++ AjPBtNumId *NumId; ++} AjONumBucket; ++#define AjPNumBucket AjONumBucket* ++ ++ ++ ++ + /* Database file name structure + ** + ** ajint order Order of B+tree +@@ -387,6 +452,10 @@ + ** @attr snperbucket [ajint] Undocumented + ** @attr secrootblock [ajlong] secondary tree root block + ** @attr kwlimit [ajint] Max length of secondary key ++** @attr bmem [AjPBtMem] primary memory allocation MRU bottom ++** @attr bsmem [AjPBtMem] secondary memory allocation MRU bottom ++** @attr tmem [AjPBtMem] primary memory allocation MRU top ++** @attr tsmem [AjPBtMem] secondary memory allocation MRU top + ******************************************************************************/ + + typedef struct AjSBtCache +@@ -409,6 +478,12 @@ + ajint snperbucket; + ajlong secrootblock; + ajint kwlimit; ++ ++ AjPBtMem bmem; ++ AjPBtMem tmem; ++ AjPBtMem bsmem; ++ AjPBtMem tsmem; ++ + } AjOBtcache; + #define AjPBtcache AjOBtcache* + +@@ -511,6 +586,32 @@ + + + ++/* @data AjPBtHybrid *************************************************** ++** ++** Btree ID ++** ++** @attr key1 [AjPStr] Unique ID ++** @attr dbno [ajint] Database file number ++** @attr dups [ajint] Duplicates ++** @attr offset [ajlong] Offset within database file (ftello)** @attr refoffset [ajlong] Offset within reference database file (ftello) ++** @attr refoffset [ajlong] Offset within reference database file (ftello) ++** @attr treeblock [ajlong] Secondary tree root page ++******************************************************************************/ ++ ++typedef struct AjSBtHybrid ++{ ++ AjPStr key1; ++ ajint dbno; ++ ajint dups; ++ ajlong offset; ++ ajlong refoffset; ++ ajlong treeblock; ++} AjOBtHybrid; ++#define AjPBtHybrid AjOBtHybrid* ++ ++ ++ ++ + AjPBtcache ajBtreeCacheNewC(const char *file, const char *ext, + const char *idir, const char *mode, + ajint pagesize, ajint order, ajint fill, +@@ -553,7 +654,8 @@ + AjBool ajBtreeReplaceId(AjPBtcache cache, const AjPBtId rid); + + ajint ajBtreeReadEntries(const char *filename, const char *indexdir, +- AjPStr **seqfiles, AjPStr **reffiles); ++ const char *directory, ++ AjPStr **seqfiles, AjPStr **reffiles); + void ajBtreeInsertDupId(AjPBtcache cache, AjPBtId id); + AjPList ajBtreeDupFromKey(AjPBtcache cache, const char *key); + +@@ -580,6 +682,21 @@ + void ajBtreeInsertKeyword(AjPBtcache cache, const AjPBtPri pri); + + void ajBtreeLockTest(AjPBtcache cache); ++ ++ ++ ++AjPBtpage ajBtreeHybFindInsert(AjPBtcache cache, const char *key); ++AjPBtpage ajBtreeNumFindInsert(AjPBtcache cache, const ajlong key); ++ ++void ajBtreeInsertNum(AjPBtcache cache, AjPBtNumId num, AjPBtpage page); ++void ajBtreeHybInsertId(AjPBtcache cache, AjPBtHybrid hyb); ++AjPBtHybrid ajBtreeHybNew(void); ++void ajBtreeHybDel(AjPBtHybrid *thys); ++void ajBtreeFreePriArray(AjPBtcache cache); ++void ajBtreeFreeSecArray(AjPBtcache cache); ++void ajBtreeHybLeafList(AjPBtcache cache, ajlong rootblock, ++ AjPStr idname, AjPList list); ++ + + #endif + |
