AcePerl
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Ace/Browser/AceSubs.pm view on Meta::CPAN
=item $boolean = Toggle($section,[$label,$object_count,$add_plural,$add_count])
=item ($link,$bool) = Toggle($section,$label,$object_count,$add_plural,$add_count)
The Toggle() subroutine makes it easy to create HTML sections that
open and close when the user selects a toggle icon (a yellow
triangle).
Toggle() can be used to manage multiple collapsible HTML sections, but
each section must have a unique name. The required first argument is
the section name. Optional arguments are:
$label The text of the generated link, for example "sequence"
$object_count The number of objects that opening the section will reveal
$add_plural If true, the label will be pluralized when
appropriate
$add_count If true, the label will have the object count added
Ace/Browser/SearchSubs.pm view on Meta::CPAN
a({-name=>'search'},''),
table({-border=>0,-width=>'100%'},
TR({-valign=>'MIDDLE'},
td({-class=>'searchbody'},@body))),
end_form;
}
=item AceResultsTable($objects,$count,$offset,$title)
This subroutine formats the results of a search into a pageable list
and prints out the resulting HTML. The following arguments are required:
$objects An array reference containing the objects to place in the
table.
$count The total number of objects.
$offset The offset into the array, as returned by AceSearchOffset()
$title A title for the table.
Ace/Sequence.pm view on Meta::CPAN
=item -name
As an alternative to using an I<Ace::Object> with the B<-source>
argument, you may specify a source sequence using B<-name> and B<-db>.
The I<Ace::Sequence> module will use the provided database accessor to
fetch a Sequence object with the specified name. new() will return
undef is no Sequence by this name is known.
=item -db
This argument is required if the source sequence is specified by name
rather than by object reference.
=back
If new() is successful, it will create an I<Ace::Sequence> object and
return it. Otherwise it will return undef and return a descriptive
message in Ace->error(). Certain programming errors, such as a
failure to provide required arguments, cause a fatal error.
=head2 Reference Sequences and the Coordinate System
When retrieving information from an I<Ace::Sequence>, the coordinate
system is based on the sequence segment selected at object creation
time. That is, the "+1" strand is the natural direction of the
I<Ace::Sequence> object, and base pair 1 is its first base pair. This
behavior can be overridden by providing a reference sequence to the
new() method, in which case the orientation and position of the
reference sequence establishes the coordinate system for the object.
Ace/Sequence/Multi.pm view on Meta::CPAN
=item -name
As an alternative to using an I<Ace::Object> with the B<-source>
argument, you may specify a source sequence using B<-name> and B<-db>.
The I<Ace::Sequence> module will use the provided database accessor to
fetch a Sequence object with the specified name. new() will return
undef is no Sequence by this name is known.
=item -db
This argument is required if the source sequence is specified by name
rather than by object reference. It must be a previously opened
handle to the reference database.
=item -secondary
This argument points to one or more previously-opened annotation
databases. You may use a scalar if there is only one annotation
database. Otherwise, use an array reference. You may add and delete
annotation databases after the object is created by using the
add_secondary() and delete_secondary() methods.
=back
If new() is successful, it will create an I<Ace::Sequence::Multi>
object and return it. Otherwise it will return undef and return a
descriptive message in Ace->error(). Certain programming errors, such
as a failure to provide required arguments, cause a fatal error.
=head1 OBJECT METHODS
Most methods are inherited from I<Ace::Sequence>. The following
additional methods are supported:
=over 4
=item secondary()
README.ACEBROWSER view on Meta::CPAN
newdisplay => {
url => "/cgi-bin/ace/newscript",
label => 'New Display',
icon => '/ico/layout.gif',
},
The hash key, in this case "newdisplay", is a symbolic name for the
display. It can correspond to the acual name of the CGI script, or
not. The hash value is itself an anonymous hash containing the
required keys "url" and "label", and the optional key "icon". "url"
gives the path to the script that will display, and "label" gives a
human readable label for the link that Acebrowser puts in the type
selector. The "icon" key, if present, will display the indicated icon
in the type selector.
3. Bind this display to the class (or classes) for which this display
is valid, by adding an entry to the %CLASSES array. For example:
NewObject => ['newdisplay'],
acelib/helpsubs.c view on Meta::CPAN
UTIL_FUNC_DEF char *helpSubjectGetFilename (char *subject)
/* this function attempts to find the file name corresponding
to a particular help-subject.
It will attempt to find a matching file according to
the current settings of helpDir and HELP_FILE_EXTENSION.
the subject '?' will just return ? again. This is a special
code within the help system to tell the help display
function that the user required some kind of help.
Usually the helpOnRegister'd function would display a
dynamically created index of the help-directory.
this function can be even cleverer by doing keyword searches
on <TITLE> and <H1> strings in files that might be relevant
of no obvious match is found.
*/
{
static char filename_array[MAXPATHLEN] = "";
char *filename = &filename_array[0];
acelib/timesubs.c view on Meta::CPAN
* mieg, mars 94: timeParse/timeShow
this pair of functions is to be used in conjunction
with the _DateType fundamental type which can
now be used in the same way as _Int _Float in models.wrm
* HISTORY:
* Last edited: Nov 27 13:19 1998 (fw)
* * Jul 9 17:23 1998 (fw): added timeComparison() function for < , = and > operators
* * Jul 8 15:49 1998 (fw): added timeDiff functions for mins,hours,months,years
as required by the new AQL date-functions
* * Jan 29 22:31 1995 (rd): allow "today" like "now", for day only
* * Nov 13 19:04 1994 (rd): allow date abbreviations, and rename
consistently, and removed timeStamp, dateStamp
* * Jun 21 17:12 1992 (mieg): changed : to _ in time stamped
: was preventing the file chooser from reading in a dump file
* * Jan 20 10:46 1992 (mieg): Fixed timeStamp, dateStamp
and removed everything else with an ifdef
* Created: a long time ago
*-------------------------------------------------------------------
*/
acelib/wh/array.h view on Meta::CPAN
void stackTextOnly(Stack s);
void uStackDestroy (Stack s);
#define stackDestroy(x) ((x) ? uStackDestroy(x), (x)=0, TRUE : FALSE)
void stackExtend (Stack s, int n) ;
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.
*/
acelib/wh/mystdlib.h view on Meta::CPAN
MALLOC_ALIGNMENT
Alignment of most restrictive data type, the system malloc will
return addresses aligned to this, and we do the same in messalloc.
STACK_ALIGNMENT
Alignment of data objects on a Stack; this should really be
the same as MALLOC_ALIGNMENT, but for most 32 bit pointer machines
we align stacks to 4 bytes to save memory.
STACK_DOUBLE_ALIGNMENT
Alignment of doubles required on stack, if this is greater than
STACK_ALIGNMENT, we read and write doubles on a stack by steam.
Put specific exceptions first, the defaults below should cope
with most cases. Oh, one more thing, STACK_ALIGNMENT and
STACK_DOUBLE ALIGNMENT are used on pre-processor constant
expressions so no sizeofs, sorry.
*/
acelib/wh/mytime.h view on Meta::CPAN
* Richard Durbin (MRC LMB, UK) rd@sanger.ac.uk, and
* Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.cnrs-mop.fr
*
* $Id: mytime.h,v 1.1 2002/11/14 20:00:06 lstein Exp $
* Description:
* Exported functions:
* HISTORY:
* Last edited: Dec 4 14:58 1998 (fw)
* * Jul 9 17:20 1998 (fw): added timeComparison function
* * Jul 8 15:48 1998 (fw): added timeDiff functions for mins,hours,months,years
* as required by the new AQL date-functions
* Created: Thu Jan 25 21:30:55 1996 (rd)
*-------------------------------------------------------------------
*/
#ifndef DEFINE_MYTIME_h
#define DEFINE_MYTIME_h
/* march 94: these functions can be used in conjunction
with the _DateType fundamental type which can
now be used in the same way as _Int _Float in models.wrm
acelib/wh/version.h view on Meta::CPAN
/* These tools assume that various numbers/strings are defined, e.g. */
/* */
/* #define SOME_TITLE "UT library" (definitive name for library) */
/* #define SOME_DESC "brief description" (purpose of library - one liner)*/
/* #define SOME_VERSION 1 (major version) */
/* #define SOME_RELEASE 0 (minor version) */
/* #define SOME_UPDATE 1 (latest fix number) */
/* */
/* 1) Use UT_MAKESTRING to make strings out of #define'd numbers. */
/* (required because of the way ANSI preprocessor handles strings) */
/* e.g. UT_MAKESTRING(6) produces "6" */
/* */
#define UT_PUTSTRING(x) #x
#define UT_MAKESTRING(x) UT_PUTSTRING(x)
/* 2) Make a single version number out of the version, release and update */
/* numbers. */
/* NOTE that there will be no more than 100 (i.e. 0 - 99) revisions per */
/* version, or updates per revision, otherwise version will be wrong. */
/* */
docs/ACE_SERVER_TRAPS.HOWTO view on Meta::CPAN
creates permissions problems that we haven't solved yet. We are using
individual user names instead.
One thing that no documentation mentions is that we had to move
gifaceserver.LINUX to /usr/local/bin/gifaceserver. Obvious, but still
makes you wonder while you do it.
Inetd.conf
Our individual inetd.conf files were completely commented out, and the
daemon stopped because of our dispersed locations. Append the required
line to the file, and enter:
Killall -HUP inetd
server.log
The server really wants a server.log file, writable by the user to
whom the gifaceserver is assigned in the inetd.conf file. We created
one by opening the gifaceserver on a fake port number (12345):
docs/ACE_SERVER_TRAPS.HOWTO.html view on Meta::CPAN
<p>Take your permissions seriously. Richard Durbin's Installation Guide is out of date, but gives good advice in this department.</p>
<p><h3>Gifaceserver<br>Warning: this isn't yet working completely</h3></p>
<p><h4>Problem</h4></p>
<p>Most documentation dealing with this software simply tells you to get it going. The software comes with no documentation whatsoever. No README at all. There is a manual that comes in /acedocs called aceserver.html. Its installation instruction...
<p><h4>Solution</h4></p>
<p>The best installation information is in the <strong>README</strong> file for <em>AcePerl-1.54</em>. A few more hints are listed here.</p>
<p>The <em>AcePerl</em> <strong>README</strong> file implies creating a user called <em>acedb</em>. This creates permissions problems that we haven't solved yet. We are using individual user names instead.</p>
<p>One thing that <strong>no</strong> documentation mentions is that we had to move <em>gifaceserver.LINUX</em> to <em>/usr/local/bin/gifaceserver</em>. Obvious, but still makes you wonder while you do it.</p>
<p><h4>Inetd.conf</h4></p>
<p>Our individual <em>inetd.conf</em> files were completely commented out, and the daemon stopped because of our dispersed locations. Append the required line to the file, and enter:</p>
<p><em>Killall -HUP inetd</em></p>
<p><h4>server.log</h4></p>
<p>The server really wants a <em>server.log</em> file, writable by the user to whom the <em>gifaceserver</em> is assigned in the <em>inetd.conf</em> file. We created one by opening the <em>gifaceserver</em> on a fake port number (12345):</p>
<p><em> /usr/local/bin/gifaceserver /home/httpd/database/contacts 12345 1200:1200:10</em></p>
<p><h2>Models</h2></p>
<p><h3>Documentation</h3></p>
The <strong>best</strong> documentation for models is in <em>/acedocs/exploring/*.</em> The table of contents is in <em>/acedocs/exploring/toc_models.html</em>. Unfortunately, like all the ACEDB documentation, it uses absolute pathnames. We have c...
<p>The moviedb database is the best simple example of a database.</p>
<p><h3>Editors</h3></p>
<p>ACEDB is picky about its ascii. <em>vi</em> works great. Can't vouch for <em>emacs</em> ;-). <strong>Don't</strong> use anything nasty like a word processor.</p>
docs/GFF_Spec.html view on Meta::CPAN
objects in a .ace file, flattened onto one line by semicolon
separators. Tags must be standard identifiers
([A-Za-z][A-Za-z0-9_]*). Free text values must be quoted with double
quotes. <em>Note: all non-printing characters in such free text value strings
(e.g. newlines, tabs, control characters, etc)
must be explicitly represented by their C (UNIX) style backslash-escaped
representation (e.g. newlines as '\n', tabs as '\t').</em>
As in ACEDB, multiple values can follow a specific tag. The
aim is to establish consistent use of particular tags, corresponding
to an underlying implied ACEDB model if you want to think that way
(but acedb is not required). Examples of these would be:
<font size="3"><pre>
seq1 BLASTX similarity 101 235 87.1 + 0 Target "HBA_HUMAN" 11 55 ; E_value 0.0003
dJ102G20 GD_mRNA coding_exon 7105 7201 . - 2 Sequence "dJ102G20.C1.1"
</pre></font>
</dl>
All strings (i.e. values of the <seqname>,
<source> or <feature> fields) should be under 256
characters long, and should not include whitespace. The whole line
docs/GFF_Spec.html view on Meta::CPAN
<P>
Back to <A HREF="#TOC">Table of Contents</A>
<P>
<HR>
<A NAME="comments"><h3> Comments </h3>
Comments are allowed, starting with "#" as in Perl, awk etc.
Everything following # until the end of the line is ignored.
Effectively this can be used in two ways. Either it must be at the
beginning of the line (after any whitespace), to make the whole line a
comment, or the comment could come after all the required fields on
the line.
<P>
We also permit extra information to be given on the line following the
group field without a '#' character (<b>Version 2 change</b>: this extra
information <B>must</B> be delimited by the '#' comment delimiter <B>OR</B>
by another tab field delimiter character, following
any and all [group] field tag-value pairs).
<P>
This allows extra method-specific information to be transferred with the line. However,
we discourage overuse of this feature: better to find a way to do it
docs/GFF_Spec.html view on Meta::CPAN
In the example given above the feature "splice5" indicates that there
is a candidate 5' splice site between positions 172 and 173. The
"sp5-20" feature is a prediction based on a window of 20 bp for the
same splice site. To use either of these, you must know the position
within the feature of the predicted splice site. This only needs to
be given once, possibly in comments at the head of the file, or in a
separate document. <P>
Another example is the scoring scheme; we ourselves would like the
score to be a log-odds likelihood score in bits to a defined null
model, but that is not required, because different methods take
different approaches.
Avoiding a prespecified feature set also leaves open the possibility
for GFF to be used for new feature types, such as CpG islands,
hypersensitive sites, promoter/enhancer elements, etc.
<P>
Back to <A HREF="#TOC">Table of Contents</A>
<P>
<HR>
<A NAME="GFF_use"><h2> Ways to use GFF </h2>
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