AcePerl
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1.40 Internal version, never released
1.39 1. Workaround for problem with dropped date fields
1.38 1. list() is now deprecated. Use fetch() instead
2. grep() method added
3. -total parameter added to fetch() grep() and find()
4. ace.pl added to exampe directory
5. new patch file adds a few essential bug fixes to ace 4_5e.
6. asGIF() method is now documented
7. updated patchfile to include "phoenix effect" aceserver bug
1.37 1. Added timestamp and comment handling.
2. Added -filled and -chunksize arguments to fetch_many().
3. Quashed a bug in list(-filled).
4. More regression tests.
1.36 6/6/98 Substantial API changes:
1. row() now returns everything to the right of the current object INCLUSIVE
of the object. Calling row() in a scalar context returns the size of the
array, not the first member of the array.
acelib/call.c view on Meta::CPAN
static Stack command = 0 ;
/*#ifdef ACEDB*/ /* until we resolve this bit, we have to include wscripts bit even ifndef ACEDB */
char *cp ;
static Stack s = 0 ; /* don't use messprintf() - often used to make args */
s = stackReCreate (s, 32) ;
if (!dir)
{
catText (s, "wscripts/") ;
catText (s, script) ;
if ((cp = filName (stackText (s, 0), 0, "x")))
script = cp ; /* mieg else fall back on direct unix call */
}
/*#endif*/
command = stackReCreate (command, 128) ;
if (dir)
{ catText (command, "cd ") ;
catText (command, dir) ;
catText (command, "; ") ;
}
catText (command, script) ;
acelib/wh/mystdlib.h view on Meta::CPAN
/* _MAX_PATH is 260 in WIN32 but each path component can be max. 256 in size */
#undef DIR_BUFFER_SIZE
#define DIR_BUFFER_SIZE FIL_BUFFER_SIZE
#define MAXPATHLEN _MAX_PATH
#define popen _popen
#define pclose _pclose
/* rename to actual WIN32 built-in functions
* (rbrusk): this little code generated a "trigraph" error message
* when built in unix with the gcc compiler; however, I don't understand
* why gcc even sees this code, which is #if defined(WIN32)..#endif protected.
* Changing these to macros is problematic in lex4subs.c et al, which expects
* the names as function names (without parentheses. So, I change them back..
* If the trigraph error message returns, look for another explanation,
* like MSDOS carriage returns, or something? */
#define strcasecmp _stricmp
#define strncasecmp _strnicmp
#endif /* WIN32 */
#else /* not POSIX etc. e.g. SUNOS */
acelib/wh/regular.h view on Meta::CPAN
/*******************************************************************/
/************* randsubs.c random number generator ******************/
UTIL_FUNC_DCL double randfloat (void) ;
UTIL_FUNC_DCL double randgauss (void) ;
UTIL_FUNC_DCL int randint (void) ;
UTIL_FUNC_DCL void randsave (int *arr) ;
UTIL_FUNC_DCL void randrestore (int *arr) ;
/* Unix debugging. */
/* put "break invokeDebugger" in your favourite debugger init file */
/* this function is empty, it is defined in messubs.c used in
messerror, messcrash and when ever you need it.
*/
UTIL_FUNC_DCL void invokeDebugger(void) ;
/*******************************************************************/
acelib/wmake/ALPHA_4_DEF view on Meta::CPAN
# $Id: ALPHA_4_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = ALPHA
COMPILER = cc -g -std1 -ieee_with_inexact -DACEDB4
LINKER = cc -g
acelib/wmake/ALPHA_4_NEW_DEF view on Meta::CPAN
# $Id: ALPHA_4_NEW_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = ALPHA
COMPILER = cc -g -std1 -DACEDB4 -DNEW_MODELS
LINKER = cc
acelib/wmake/ALPHA_4_OPT_DEF view on Meta::CPAN
# $Id: ALPHA_4_OPT_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = ALPHA
COMPILER = cc -O -Olimit 3000 -std1 -DACEDB4 -ieee_with_inexact
# rd 970131 - I am told that -O does the most optimisation possible
acelib/wmake/ALPHA_CHRONO_4_DEF view on Meta::CPAN
# $Id: ALPHA_CHRONO_4_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = ALPHA
COMPILER = cc -g -std1 -DACEDB4 -DCHRONO
LINKER = cc
acelib/wmake/ALPHA_G3_DEF view on Meta::CPAN
# $Id: ALPHA_G3_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $ #
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = ALPHA
COMPILER = gcc -g -DACEDB3
LINKER = gcc -g
acelib/wmake/DEC_OSF_DEF view on Meta::CPAN
# $Id: DEC_OSF_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = ALPHA
COMPILER = cc -O -Olimit 3000 -std1 -DACEDB4 -ieee_with_inexact
# rd 970131 - I am told that -O does the most optimisation possible
acelib/wmake/HPUX_DEF view on Meta::CPAN
# $Id: HPUX_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = HP
COMPILER = gcc -g -DNO_LEFT_CASTING -DACEDB4 -I/usr/include/X11R5 -I/usr/local/include/MIT/X11R5/include
LINKER = gcc -g -L/usr/lib/X11R5
acelib/wmake/HP_4_GCC_DEF view on Meta::CPAN
# $Id: HP_4_GCC_DEF,v 1.1 2002/11/14 20:00:06 lstein Exp $
#################################################################
############### acedb: R.Durbin and J.Thierry-Mieg ##############
########### wmake/DEC_ALPHA_DEF March-18-1993 ##########
#################################################################
#################################################################
########## Machine dependant compiler modification ##############
####### for the DEC-Alpha 3000 model 500 running Unix ###########
#################################################################
########### This file is included by wmake/truemake #############
###### Edit this file to adapt the ACeDB to a new machine ######
##### following the explanations given in wmake/truemake #####
#################################################################
NAME = HP
COMPILER = gcc -g -DNO_LEFT_CASTING -DACEDB4 -I/usr/include/X11R5 -I/usr/local/include/MIT/X11R5/include
LINKER = gcc -g -L/usr/lib/X11R5
docs/GFF_Spec.html view on Meta::CPAN
<P>
In particular, establishing GFF would allow people to develop features
and have them tested without having to maintain a complete
gene-finding system. Equally, it would help those developing and
applying integrated gene-finding programs to test new feature
detectors developed by others, or even by themselves.
<P>
We want the GFF format to be easy to parse and process by a variety of
programs in different languages. e.g. it would be useful if Unix
tools like grep, sort and simple perl and awk scripts could easily
extract information out of the file. For these reasons, for the
primary format, we propose a record-based structure, where each
feature is described on a single line, and line order is not relevant.
<P>
We do not intend GFF format to be used for complete data management of
the analysis and annotation of genomic sequence. Systems such as
Acedb, Genotator etc. that have much richer data representation
semantics have been designed for that purpose. The disadvantages in
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