AcePerl
view release on metacpan or search on metacpan
Ace/Object.pm view on Meta::CPAN
# simple clone
sub clone {
my $self = shift;
return bless {%$self},ref $self;
}
# selective clone
sub _clone {
my $self = shift;
my $pack = ref($self);
my @public_keys = grep {substr($_,0,1) ne '.'} keys %$self;
my %newobj;
@newobj{@public_keys} = @{$self}{@public_keys};
# Turn into a toplevel object
$newobj{'.root'}++;
return bless \%newobj,$pack;
}
sub _fill {
my $self = shift;
return if $self->filled;
return unless $self->db && $self->isObject;
DISCLAIMER.txt view on Meta::CPAN
OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER
WARRANTY, EXPRESS OR IMPLIED. CSHL MAKES NO REPRESENTATION OR
WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR
OTHER PROPRIETARY RIGHT.
By downloading this SOFTWARE, your Institution hereby indemnifies CSHL
against any loss, claim, damage or liability, of whatsoever kind or
nature, which may arise from your Institution's respective use,
handling or storage of the SOFTWARE.
If publications result from research using this SOFTWARE, we ask that
CSHL be acknowledged and/or credit be given to CSHL scientists, as
scientifically appropriate.
See the ChangeLog for important notices, including recent user
interfaces changes. Please see DISCLAIMER.txt for disclaimers of
warranty.
INSTALLATION:
In addition to this package, you will need Perl 5.00503 or higher
(5.6.0 or higher recommended), and the Digest::MD5 module. Both are
available on CPAN (http://www.cpan.org).
If you are using AcePerl to communicate with WormBase, a public server
is running on host aceserver.cshl.org, port 2005. You can open a
connection to this server like this:
$db = Ace->connect('sace://aceserver.cshl.org:2005');
Otherwise, if you wish to communicate with your own ACEDB database,
you must use ACEDB version 4.8a or higher, available from this
location:
ftp://ncbi.nlm.nih.gov/repository/acedb/
acelib/Makefile view on Meta::CPAN
libaceperl.a : $(FREE_OBJS) aceclientlib.o rpcace_clnt.o rpcace_xdr.o
ar $(AR_OPTIONS) $@ $?
if ( $(RANLIB_NEEDED) ) then ranlib $@; fi
libfree.a : $(FREE_OBJS)
ar $(AR_OPTIONS) libfree.a $?
if ( $(RANLIB_NEEDED) ) then ranlib libfree.a; fi
#########################################
#### public C interface: libace #########
#########################################
#
# aceversion.c is recompiled & rearchived every time one of the
# other libace objects is recompiled. Hence aceversion.c enables
# us to record the link date of the library along with the ACEDB
# version.
# (this is not quite true at the moment because of the graphic/
# non-graphic split in libace, but this will go away)
#
acelib/wh/bump_.h view on Meta::CPAN
* HISTORY:
* Last edited: Dec 17 16:20 1998 (fw)
* Created: Thu Dec 17 16:17:32 1998 (fw)
*-------------------------------------------------------------------
*/
#ifndef DEF_BUMP__H
#define DEF_BUMP__H
#include "bump.h" /* include public header */
/* allow verification of a BUMP pointer */
extern magic_t BUMP_MAGIC;
/* completion of public opaque type as declared in bump.h */
struct BumpStruct {
magic_t *magic ; /* == &BUMP_MAGIC */
int n ; /* max x, i.e. number of columns */
float *bottom ; /* array of largest y in each column */
int minSpace ; /* longest loop in y */
float sloppy ;
float maxDy ; /* If !doIt && maxDy !=0, Do not add further down */
int max ; /* largest x used (maxX <= n) */
int xAscii, xGapAscii ;
acelib/wh/dict.h view on Meta::CPAN
/* File: dict.h
* Author: Richard Durbin (rd@sanger.ac.uk)
* Copyright (C) J Thierry-Mieg and R Durbin, 1995
*-------------------------------------------------------------------
* This file is part of the ACEDB genome database package, written by
* Richard Durbin (MRC LMB, UK) rd@mrc-lmb.cam.ac.uk, and
* Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.cnrs-mop.fr
*
* Description: public header for cut-out lex package in dict.c
* Exported functions:
* HISTORY:
* Last edited: Dec 4 14:50 1998 (fw)
* Created: Tue Jan 17 17:34:44 1995 (rd)
*-------------------------------------------------------------------
*/
/* @(#)dict.h 1.4 9/16/97 */
#ifndef DICT_H
#define DICT_H
acelib/wh/help.h view on Meta::CPAN
* Last edited: Oct 23 12:19 1998 (fw)
* Created: Thu Oct 8 14:01:07 1998 (fw)
*-------------------------------------------------------------------
*/
#ifndef _HELP_H
#define _HELP_H
#include "regular.h" /* basic header for util-lib */
/************** public routines of the help-package *******************/
UTIL_FUNC_DCL BOOL helpOn (char *subject);
/* displays help on the given subject. Dispatches to registered
display function. defaults to helpPrint (text-help) */
UTIL_FUNC_DCL QueryRoutine helpOnRegister (QueryRoutine func);
/* register any func to display help-page, the functions
are >> BOOL func (char *filename) <<, where the filename
is a *full* pathname to an HTML document that is to be shown */
acelib/wh/keyset.h view on Meta::CPAN
/* File: keyset.h
* Author: R Durbin (rd@sanger.ac.uk)
* Copyright (C) J Thierry-Mieg and R Durbin, 1998
*-------------------------------------------------------------------
* 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: public header for keyset operations.
* This file is part of acedb.h and NOT to be included
* by other source files.
* The KEYSET operations are built upon the Array ops
* provided by the utilities library libfree.a
* Exported functions:
* HISTORY:
* Last edited: Dec 11 09:44 1998 (fw)
* Created: Fri Dec 11 09:42:41 1998 (fw)
*-------------------------------------------------------------------
*/
acelib/wh/menu.h view on Meta::CPAN
#ifndef DEF_MENU_H
#define DEF_MENU_H
#include "regular.h"
/************* types *****************/
#ifndef MENU_DEFINED
#define MENU_DEFINED
typedef void *MENU, *MENUITEM ; /* public handles */
typedef void (*MENUFUNCTION)(MENUITEM) ;
#endif
typedef struct menuspec
{ MENUFUNCTION f ; /* NB can be 0 if using menuSetCall() below */
char *text ;
} MENUSPEC ;
/********** MENUITEM flags ***********/
docs/GFF_Spec.html view on Meta::CPAN
Fields are:
<seqname> <source> <feature> <start> <end> <score> <strand> <frame> [group]>[comments] <P>
<dl>
<dt><seqname>
<dd>The name of the sequence. Having an explicit sequence name
allows a feature file to be prepared for a data set of multiple
sequences. Normally the seqname will be the identifier of the
sequence in an accompanying fasta format file. An alternative is that
'seqname' is the identifier for a sequence in a public database, such
as an EMBL/Genbank/DDBJ accession number. Which is the case, and
which file or database to use, should be explained in accompanying
information.<P>
<dt><source>
<dd> The source of this feature. This field will normally be used to
indicate the program making the prediction, or if it comes from public
database annotation, or is experimentally verified, etc.<P>
<dt><feature>
<dd> The feature type name. We hope to suggest a standard set of
features, to facilitate import/export, comparison etc.. Of course,
people are free to define new ones as needed. For example, Genie
splice detectors account for a region of DNA, and multiple detectors
may be available for the same site, as shown above.<P>
<A name="standard_feature_table">
(<b>Version 2 change</b>: <u>Standard Table of Features</u> -
we would like to enforce a standard nomenclature for
common GFF features. This does not forbid the use of other features,
rather, just that if the feature is obviously described in the standard
list, that the standard label should be used. For this standard table
we propose to fall back on the international public standards for genomic
database feature annotation, specifically, the
<a href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/feature_key_ref.html">
DDBJ/EMBL/GenBank feature table</a>).<P>
<dt><start>, <end>
<dd> Integers. <start> must be less than or equal to
<end>. Sequence numbering starts at 1, so these numbers
should be between 1 and the length of the relevant sequence,
inclusive. (<b>Version 2 change</b>: version 2 condones values of
<start> and <end> that extend outside the
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