/* File: array.h * Author: Richar Durbin (rd@sanger.ac.uk) * Copyright (C) J Thierry-Mieg and R Durbin, 1998 * ------------------------------------------------------------------- * Acedb is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt * ------------------------------------------------------------------- * This file is part of the ACEDB genome database package, written by * Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk, and * Jean Thierry-Mieg (CRBM du CNRS, France) mieg@crbm.cnrs-mop.fr * * Description: header for arraysub.c * NOT to be included by the user, included by regular.h * Exported functions: * the Array type and associated functions * the Stack type and associated functions * the Associator functions * HISTORY: * Last edited: August 27 1:30 2000 (lstein) * Created: Fri Dec 4 11:01:35 1998 (fw) *------------------------------------------------------------------- */ #ifndef DEF_ARRAY_H #define DEF_ARRAY_H unsigned int stackused (void) ; /************* Array package ********/ /* #define ARRAY_CHECK either here or in a single file to check the bounds on arr() and arrp() calls if defined here can remove from specific C files by defining ARRAY_NO_CHECK (because some of our finest code relies on abuse of arr!) YUCK!!!!!!! */ /* #define ARRAY_CHECK */ typedef struct ArrayStruct { char* base ; /* char* since need to do pointer arithmetic in bytes */ int dim ; /* length of alloc'ed space */ int size ; int max ; /* largest element accessed via array() */ int id ; /* unique identifier */ int magic ; } *Array ; /* NB we need the full definition for arr() for macros to work do not use it in user programs - it is private. */ #define ARRAY_MAGIC 8918274 #define STACK_MAGIC 8918275 #define ASS_MAGIC 8918276 Array uArrayCreate_dbg (int n, int size, STORE_HANDLE handle, const char *hfname,int hlineno) ; void arrayExtend_dbg (Array a, int n, const char *hfname,int hlineno) ; Array arrayCopy_dbg(Array a, STORE_HANDLE handle, const char *hfname,int hlineno) ; Array uArrayReCreate_dbg (Array a, int n, int size, const char *hfname,int hlineno) ; void uArrayDestroy_dbg (Array a, const char *hfname, int hlineno); char *uArray_dbg (Array a, int index, const char *hfname, int hlineno); char *uArrCheck_dbg (Array a, int index, const char *hfname, int hlineno) ; char *uArrayCheck_dbg (Array a, int index, const char *hfname, int hlineno) ; #define arrayCreate(n,type) uArrayCreate_dbg(n,sizeof(type), 0, __FILE__, __LINE__) #define arrayHandleCreate(n,type,handle) uArrayCreate_dbg(n, sizeof(type), handle, __FILE__, __LINE__) #define arrayReCreate(a,n,type) uArrayReCreate_dbg(a,n,sizeof(type), __FILE__, __LINE__) #define arrayExtend(a, n) arrayExtend_dbg(a, n, __FILE__, __LINE__) #define arrayHandleCopy(a, h) arrayCopy_dbg(a, h, __FILE__, __LINE__) #define arrayCopy(a) arrayCopy_dbg(a, 0, __FILE__, __LINE__) #define arrayDestroy(x) ((x) ? uArrayDestroy_dbg(x, __FILE__, __LINE__), x=0, TRUE : FALSE) #if (defined(ARRAY_CHECK) && !defined(ARRAY_NO_CHECK)) #define arrp(ar,i,type) ((type*)uArrCheck_dbg(ar,i, __FILE__, __LINE__)) #define arr(ar,i,type) (*(type*)uArrCheck_dbg(ar,i, __FILE__, __LINE__)) #define arrayp(ar,i,type) ((type*)uArrayCheck_dbg(ar,i, __FILE__, __LINE__)) #define array(ar,i,type) (*(type*)uArrayCheck_dbg(ar,i, __FILE__, __LINE__)) #else #define arr(ar,i,type) ((*(type*)((ar)->base + (i)*(ar)->size))) #define arrp(ar,i,type) (((type*)((ar)->base + (i)*(ar)->size))) #define arrayp(ar,i,type) ((type*)uArray_dbg(ar,i, __FILE__, __LINE__)) #define array(ar,i,type) (*(type*)uArray_dbg(ar,i, __FILE__, __LINE__)) #endif /* ARRAY_CHECK */ /* only use arr() when there is no danger of needing expansion */ Array arrayTruncatedCopy_dbg (Array a, int x1, int x2, const char *hfname, int hlineno) ; #define arrayTruncatedCopy(a,x1,x2) arrayTruncatedCopy_dbg(a,x1,x2,__FILE__, __LINE__) void arrayStatus (int *nmadep,int* nusedp, int *memAllocp, int *memUsedp) ; int arrayReportMark (void) ; /* returns current array number */ void arrayReport (int j) ; /* write stderr about all arrays since j */ #define arrayMax(ar) ((ar)->max) #define arrayForceFeed(ar,j) (uArray_dbg(ar,j,__FILE__,__LINE__), (ar)->max = (j)) #define arrayExists(ar) ((ar) && (ar)->magic == ARRAY_MAGIC ? (ar)->id : 0 ) /* JTM's package to hold sorted arrays of ANY TYPE */ typedef int array_order (void*, void*); /* call back function prototype for sorting arrays */ BOOL arrayInsert(Array a, void * s, array_order *order); BOOL arrayRemove(Array a, void * s, array_order *order); void arraySort(Array a, array_order *order) ; void arraySortPos (Array a, int pos, array_order *order); void arrayCompress(Array a) ; BOOL arrayFind(Array a, void *s, int *ip, array_order *order); BOOL arrayIsEntry_dbg(Array a, int i, void *s, const char *hfname, int hlineno); #define arrayIsEntry(a,i,s) arrayIsEntry_dbg(a,i,s,__FILE__, __LINE__) /************** Stack package **************/ typedef struct StackStruct /* assumes objects <= 16 bytes long */ { Array a ; int magic ; char* ptr ; /* current end pointer */ char* pos ; /* potential internal pointer */ char* safe ; /* need to extend beyond here */ BOOL textOnly; /* If this is set, don't align the stack. This (1) save space (esp on ALPHA) and (2) provides stacks which can be stored and got safely between architectures. Once you've set this, using stackTextOnly() only pushText, popText, etc, no other types. */ } *Stack ; /* as with ArrayStruct, the user should NEVER access StackStruct members directly - only through the subroutines/macros */ Stack stackHandleCreate_dbg (int n, STORE_HANDLE handle, const char *hfname, int hlineno) ; #define stackHandleCreate(n, handle) stackHandleCreate_dbg(n, handle, __FILE__, __LINE__) #define stackCreate(n) stackHandleCreate_dbg(n, 0, __FILE__, __LINE__) Stack stackReCreate_dbg (Stack s, int n, const char *hfname, int hlineno); #define stackReCreate(s, n) stackReCreate_dbg(s, n, __FILE__, __LINE__) Stack stackCopy_dbg (Stack, STORE_HANDLE handle, const char *hfname, int hlineno); #define stackCopy(s,handle) stackCopy_dbg(s,handle,__FILE__, __LINE__) void stackTextOnly(Stack s); void uStackDestroy (Stack s); #define stackDestroy(x) ((x) ? uStackDestroy(x), (x)=0, TRUE : FALSE) void stackExtend_dbg (Stack s, int n, const char *hfname, int hlineno) ; #define stackExtend(s,n) stackExtend_dbg(s,n,__FILE__, __LINE__) void stackClear (Stack s) ; #define stackEmpty(stk) ((stk)->ptr <= (stk)->a->base) #define stackExists(stk) ((stk) && (stk)->magic == STACK_MAGIC ? arrayExists((stk)->a) : 0) /* Stack alignment: we use two strategies: the smallest type we push is a short, so if the required alignment is to 2 byte boundaries, we push each type to its size, and alignments are kept. Otherwise, we push each type to STACK_ALIGNMENT, this ensures alignment but can waste space. On machines with 32 bits ints and pointers, we make satck alignment 4 bytes, and do the consequent unaligned access to doubles by steam. Characters and strings are aligned separately to STACK_ALIGNMENT. */ #if (STACK_ALIGNMENT<=2) #define push(stk,x,type) ((stk)->ptr < (stk)->safe ? \ ( *(type *)((stk)->ptr) = (x) , (stk)->ptr += sizeof(type)) : \ (stackExtend (stk,16), \ *(type *)((stk)->ptr) = (x) , (stk)->ptr += sizeof(type)) ) #define pop(stk,type) ( ((stk)->ptr -= sizeof(type)) >= (stk)->a->base ? \ *((type*)((stk)->ptr)) : \ (messcrash ("User stack underflow"), *((type*)0)) ) #define rot(stk,type,pos) ( if ( (stk)->ptr - (pos * sizeof(type) ) >= (stk)->a->base) { \ *(type *)((stk)->ptr) = *(type *) (stk)->ptr - (pos * sizeof(type)); \ memmove((stk)->ptr - (pos * sizeof(type)),(stk)->ptr,sizeof(type)); \ } else { \ (messcrash ("User stack underflow"), *((type*)0)) \ } ) #define stackNext(stk,type) (*((type*)( (stk)->pos += sizeof(type) ) - 1 ) ) #else #define push(stk,x,type) ((stk)->ptr < (stk)->safe ? \ ( *(type *)((stk)->ptr) = (x) , (stk)->ptr += STACK_ALIGNMENT) : \ (stackExtend (stk,16), \ *(type *)((stk)->ptr) = (x) , (stk)->ptr += STACK_ALIGNMENT) ) #define pop(stk,type) ( ((stk)->ptr -= STACK_ALIGNMENT) >= (stk)->a->base ? \ *((type*)((stk)->ptr)) : \ (messcrash ("User stack underflow"), *((type*)0)) ) #define rot(stk,type,pos) ( (stk)->ptr - ((pos+1) * STACK_ALIGNMENT ) >= (stk)->a->base ? \ ( memcpy((stk)->ptr,(stk)->ptr - ((pos+1) * STACK_ALIGNMENT),STACK_ALIGNMENT), \ memmove((stk)->ptr - ((pos+1) * STACK_ALIGNMENT), \ (stk)->ptr - (pos * STACK_ALIGNMENT) , \ (pos+1) * STACK_ALIGNMENT) ) : \ ( messcrash ("User stack underflow"), *((type*)0)) ) #define stackNext(stk,type) (*((type*)( ((stk)->pos += STACK_ALIGNMENT ) - \ STACK_ALIGNMENT )) ) #endif #if STACK_DOUBLE_ALIGNMENT > STACK_ALIGNMENT void uStackDoublePush(Stack stk, double x); double uStackDoublePop(Stack stk); double uStackDoubleNext(Stack stk); #define pushDouble(stk,x) uStackDoublePush(stk, x) #define popDouble(stk) uStackDoublePop(stk) #define stackDoubleNext(stk) uStackDoubleNext(stk) #else #define pushDouble(stk,x) push(stk, x, double) #define popDouble(stk) pop(stk, double) #define stackDoubleNext(stk) stackNext(stk, double) #endif void pushText (Stack s, char *text) ; char* popText (Stack s) ; /* returns last text and moves pointer before it */ void catText (Stack s, char *text) ; /* like strcat */ void stackTokeniseTextOn(Stack s, char *text, char *delimiters) ; /* tokeniser */ int stackMark (Stack s) ; /* returns a mark of current ptr */ int stackPos (Stack s) ; /* returns a mark of current pos, useful with stackNextText */ void stackCursor (Stack s, int mark) ; /* sets ->pos to mark */ #define stackAtEnd(stk) ((stk)->pos >= (stk)->ptr) char* stackNextText (Stack s) ; char *stackText_dbg (Stack s, int mark, const char *hfname, int hlineno); #define stackText(s,mark) stackText_dbg(s,mark,__FILE__, __LINE__) #define stackTextForceFeed(stk,j) (arrayForceFeed((stk)->a,j) ,\ (stk)->ptr = (stk)->pos = (stk)->a->base + (j) ,\ (stk)->safe = (stk)->a->base + (stk)->a->dim - 16 ) void catBinary (Stack s, char* data, int size) ; /********** Line breaking package **********/ int uLinesText (char *text, int width) ; char *uNextLine (char *text) ; char *uPopLine (char *text) ; char **uBrokenLines (char *text, int width) ; /* array of lines */ char *uBrokenText (char *text, int width) ; /* \n's intercalated */ /********** Associator package *************/ typedef struct AssStruct { int magic ; /* Ass_MAGIC */ int id ; /* unique identifier */ int n ; /* number of items stored */ int m ; /* power of 2 = size of arrays - 1 */ int i ; /* Utility state */ void **in,**out ; unsigned int mask ; /* m-1 */ } *Associator ; #define assExists(a) ((a) && (a)->magic == ASS_MAGIC ? (a)->id : 0 ) Associator assHandleCreate_dbg (STORE_HANDLE handle, const char *hfname, int hlineno) ; Associator assBigCreate_dbg (int size, const char *hfname, int hlineno) ; Associator assReCreate_dbg (Associator a, const char *hfname, int hlineno) ; #define assCreate() assHandleCreate_dbg(0, __FILE__, __LINE__) #define assHandleCreate(h) assHandleCreate_dbg(h, __FILE__, __LINE__) #define assBigCreate(s) assBigCreate_dbg(s, __FILE__, __LINE__) #define assReCreate(a) assReCreate_dbg(a, __FILE__, __LINE__) void uAssDestroy (Associator a) ; #define assDestroy(x) ((x) ? uAssDestroy(x), x = 0, TRUE : FALSE) BOOL uAssFind (Associator a, void* xin, void* *pout) ; BOOL uAssFindNext(Associator a, void* xin, void * *pout); #define assFind(ax,xin,pout) uAssFind((ax),(xin),(void**)(pout)) /* if found, updates *pout and returns TRUE, else returns FALSE */ #define assFindNext(ax,xin,pout) uAssFindNext((ax),(xin),(void**)(pout)) BOOL assInsert (Associator a, void* xin, void* xout) ; /* if already there returns FALSE, else inserts and returns TRUE */ void assMultipleInsert(Associator a, void* xin, void* xout); /* allow multiple Insertions */ BOOL assRemove (Associator a, void* xin) ; /* if found, removes entry and returns TRUE, else returns FALSE */ BOOL assPairRemove (Associator a, void* xin, void* xout) ; /* remove only if both fit */ void assDump (Associator a) ; /* for debug - uses fprintf to stderr */ void assClear (Associator a) ; BOOL uAssNext (Associator a, void* *pin, void* *pout) ; #define assNext(ax,pin,pout) uAssNext((ax),(void**)(pin),(void**)pout) /* convert an integer to a void * without generating a compiler warning */ #define assVoid(i) ((void *)(((char *)0) + (i))) #define assInt(v) ((int)(((char *)v) - ((char *)0))) #endif /* !DEF_ARRAY_H */ /**************************** End of File ******************************/