GBrowse

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The code will be invoked during preparation of the page and must
return a string value to use as the header.  See COMPUTED OPTIONS
for details.

Example:

    footer = <hr>
	<table width="100%">
	<TR>
	<TD align="LEFT" class="databody">
	For the source code for this browser, see the <a href="http://www.gmod.org">
	Generic Model Organism Database Project.</a>  For other questions, send
	mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
	</TD>
	</TR>
	</table>

=item * examples

You can provide GBrowse with some canned examples of "interesting
regions" for the user to click on.  The examples option, if
present, provides a space-delimited list of interesting regions.
For example:

       examples = II  NPY1 NAB2 Orf:YGL123W

=item * automatic classes

When the user types in a search string that is not qualified by a
class (as in EST:yk1234.5), GBrowse will automatically search for
a matching feature of class "Sequence".  You can have it search
for the name in other classes as well by defining the "automatic
classes" option.

Example:

	automatic classes = Symbol Gene Clone

When the user types in "hb3", the browser will search first for a
Sequence feature of class hb3, followed in turn by matching
features in Symbol, Gene and Clone.  The search stops when the
first match is found.  Otherwise, the browser will proceed to a
full text search of all the comment fields.

=item * search attributes (Bio::DB::SeqFeature::Store adaptor only)

When the browser has searched the name and alias of features without
success, it will do a whole database keyword search by calling the
database's search_notes() method. By default this will search the text
of all attributes, including such things as protein sequence. The
Bio::DB::SeqFeature::Store database is a bit smarter about searching,
and will only, by default, search attributes named "Note". You can
expand the search by giving a list of attribute names to the "search
attributes" option.

=item * remote sources

This option allows you to add remote annotation sources to the menu of such
sources at the bottom of the main window.  The format is:

      remote sources = "Menu Label 1" http://url1.host.com/etc/etc
		       "Menu Label 2" http://url2.host.com/etc/etc

=item * instructions, search_instructions, navigation_instructions

You may override the default instructions (as defined in the language-specific
configuration files in conf/lang) by setting these options.  For example:

         instructions = "Type in the name of a contig or clone."

=item * no search

If you don't want the "Landmark or Region" textbox to appear, set this
to true. The user will still be able to search the database by
appending q=<search term> to the URL.

          no search = 1

=item * no autosearch

If this option is set to a true value, then the user's previous search
will not be automatically re-executed the next time he visits
gbrowse. Instead, the previous search will be pasted into the
"Landmark or Region" box and the user will have to press "Search" to
reexecute it.

=item * instructions section
=item * search section
=item * overview section
=item * region section
=item * details section
=item * tracks section
=item * display_settings section
=item * upload_tracks section

These options control which sections are displayed and whether they
are initially open or collapsed. Their values are one of:

 open     Show the section initially open
 closed   Show the section initially collapsed
 off      Do not show the section at all

For example "instructions section = closed" will initially show the
instructions section in collapsed form when the user visits gbrowse
for the first time. "upload_tracks section = off" will disable the
uploads section entirely.

Note that turning off the details section will effectively disable
gbrowse, but you might want to do this if you want to show the
overview section only. Turning off the search section will also
disable the navigation buttons. If you want to disable searching
selectively, you should use the "no search" option instead.

=item * html1, html2, html3, html4, html5, html6

These options allow you to insert HTML into the GBrowse page at
strategic places.  Eventually this will be replaced with an HTML
template system, but for now, this is the best we have.

 <table>
 <tr><th>Option</th><th>Where it goes</th></tr>
 <tr><td>header</td><td>between the top and the instructions</td></tr>



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