AcePerl

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Ace/Object.pm  view on Meta::CPAN

=head2 rollback() method

    $object->rollback;

Discard all adds, deletions and replacements, returning the object to
the state it was in prior to the last commit().

rollback() works by deleting the object from Perl memory and fetching
the object anew from AceDB.  If someone has changed the object in the
database while you were working with it, you will see this version,
ot the one you originally fetched.

If you are creating an entirely new object, you I<must> add at least
one tag in order to enter the object into the database.

=head2 kill() method

    $result_code = $object->kill;

This will remove the object from the database immediately and
completely.  It does not wait for a commit(), and does not respond to

Ace/Sequence.pm  view on Meta::CPAN

tag.  The C<SMap> tag provides genomic location information for
arbitrary object -- not just those descended from the Sequence class.
This allows ACeDB to perform genome map operations on objects that are
not directly related to sequences, such as genetic loci that have been
interpolated onto the physical map.  When an C<SMap>-containing object
is passed to the I<Ace::Sequence> new() method, the module will again
choose the smallest ACeDB Sequence object that contains both
end-points of the desired region.

If an I<Ace::Sequence> object is used to create a new I<Ace::Sequence>
object, then the original object's source is inherited.

=head1 Object Methods

Once an I<Ace::Sequence> object is created, you can query it using the
following methods:

=head2 asString()

  $name = $seq->asString;

Ace/Sequence/Feature.pm  view on Meta::CPAN

source.

=item abs_start()

  $start = $feature->abs_start;

This method returns the start of the feature relative to the sequence
segment indicated by seqname().  As in the I<Ace::Sequence> method,
you will more usually use the inherited start() method to obtain the
start of the feature relative to its source sequence (the
I<Ace::Sequence> from which it was originally derived).

=item abs_end()

  $start = $feature->abs_end;

This method returns the end of the feature relative to the sequence
segment indicated by seqname().  As in the I<Ace::Sequence> method,
you will more usually use the inherited end() method to obtain the end
of the feature relative to the I<Ace::Sequence> from which it was
derived.

Ace/Sequence/Multi.pm  view on Meta::CPAN

    # print the target's start and end positions
    print $target->start,'-',$target->end, "\n";

=head1 DESCRIPTION

I<Ace::Sequence::Multi> transparently combines information stored
about a sequence in a reference database with features tables from any 
number of annotation databases.  The resulting object can be used just 
like an Ace::Sequence object, except that the features remember their
database of origin and go back to that database for information.

This class will only work properly if the reference database and all
annotation databases share the same cosmid map.

=head1  OBJECT CREATION

You will use the new() method to create new Ace::Sequence::Multi
objects.  The arguments are identical to the those in the
Ace::Sequence parent class, with the addition of an option
B<-secondary> argument, which points to one or more secondary databases 

acelib/arraysub.c  view on Meta::CPAN

      accordingly the persistent array package asubs.c.
   */

#include "regular.h"
/*#include <limits.h>*/

extern BOOL finalCleanup ;	/* in messubs.c */

/******** tells how much system stack used *********/

char *stackorigin ;

unsigned int stackused (void)
{ char x ;
  if (!stackorigin)          /* ideally should set in main() */
    stackorigin = &x ;
  return stackorigin - &x ;        /* MSDOS stack grows down */
}

/************ Array : class to implement variable length arrays ************/

static int totalAllocatedMemory = 0 ;
static int totalNumberCreated = 0 ;
static int totalNumberActive = 0 ;
static Array reportArray = 0 ;
static void uArrayFinalise (void *cp) ;

acelib/messubs.c  view on Meta::CPAN

 *              application to register its name for use in crash messages.
 * * Sep  3 11:32 1998 (edgrif): Rationalise strings used as prefixes for
 *              messages. Add support for new messcrash macro to replace
 *              messcrash routine, this includes file/line info. for
 *              debugging (see regular.h for macro def.) and a new
 *              uMessCrash routine.
 * * Aug 25 14:51 1998 (edgrif): Made BUFSIZE enum (shows up in debugger).
 *              Rationalise the use of va_xx calls into a single macro/
 *              function and improve error checking on vsprintf.
 *              messdump was writing into messbuf half way up, I've stopped
 *              this and made two buffers of half the original size, one for
 *              messages and one for messdump.
 * * Aug 21 13:43 1998 (rd): major changes to make clean from NON_GRAPHICS
 *              and ACEDB.  Callbacks can be registered for essentially
 *              all functions.  mess*() versions continue to centralise
 *              handling of ... via stdarg.
 * * Aug 20 17:10 1998 (rd): moved memory handling to memsubs.c
 * * Jul  9 11:54 1998 (edgrif): 
 *              Fixed problem with SunOS not having strerror function, system
 *              is too old to have standard C libraries, have reverted to
 *              referencing sys_errlist for SunOS only.

acelib/randsubs.c  view on Meta::CPAN

 *-------------------------------------------------------------------
 */

 /* $Id: randsubs.c,v 1.1 2002/11/14 20:00:06 lstein Exp $ */

#ifdef ALPHA
int random(void);		/* in libc.a */
#endif /* ALPHA */

static int xrand = 18721 ;
static int yrand = 37264 ;    /* original value 67571 */
static int zrand = 28737 ;

/*******************************/

double randfloat (void)

 {double x ;

  xrand = 171*xrand % 30269;
  yrand = 172*yrand % 30307;

docs/GFF_Spec.html  view on Meta::CPAN

 <li> Integrated gene parsing. Several GFF files from different
researchers can be combined to provide the features used by an
integrated genefinder.  As mentioned above, this has the advantage
that different combinations of sensors and dynamic programming methods
for assembling sensor scores into consistent gene parses can be easily
explored.<P>

 <li> Reporting final predictions. GFF format can also be used to
communicate finished gene predictions. One simply reports final
predicted exons and other predicted gene features, either with their
original scores. or with some sort of posterior scores, rather than,
or in addition to, reporting all candidate gene features with their
scores.  To show that a set of the components belong to a single
prediction, a "group" field can be added to all the accepted sites.
This is useful for comparing the outputs of several integrated
genefinders among themselves, and to "confirmed" GFF files.  A
particular advantage of having the same format for both raw sensor
feature score files and final gene parse files is that one can easily
explore the possibility of combining the final gene parses from
several different genefinders, using another round of dynamic
programming, into a single integrated predicted parse.<P>

docs/NEW_DB.HOWTO  view on Meta::CPAN

	1) create a database directory containing the following
	subdirectories:

		wspec/		schema and other files
		database/	binary files
		wgf/		DNA analysis files [optional]
		whelp/		help files [optional]
		wscript/	helper scripts [optional]

	It's perfectly all right to ignore the optional directories.
	They are only relevant for the original C. elegans database.

	2) start acedb and allow it to initialize the binary
	files.
	
	3) load one or more .ace files.

Before you begin, you must have a models.wrm file and one or more .ace
files containing the flat-file representation of the data.  For an
example, see the moviedb example database, which is located at
usr/local/apache/htdocs/AcePerl/archive/moviedb.tar.Z.