Biowiki > TWiki > InterSeqPlugin

Topics

* TWiki

Welcome
Register

TWiki Webs
- Blog
- Fall07
- Fall08
- Fly
- GBrowse
- Main
- Research
- Sandbox
- TWiki
- Teaching
- Trash
- Zabo Art

Create personal sidebar

Links

Interseq Plugin

The InterSeqPlugin links ExternalSite:Name/Start-End text to subsequences on external genome browsers based on aliases defined in the InterSeqs topic. This plugin is based on the Interwiki Plugin.

Syntax Rules

Enter ExternalSite:Name/Start-End to create a link that points to subsequence Start to End of Name on the ExternalSite sequence browser server.
All ExternalSite aliases are defined in the InterSeqs topic.
Add and edit aliases in InterSeqs.

InterSeqPlugin Settings

Plugin settings are stored as Preferences variables. To reference a plugin setting write %<plugin>_<setting>%, for example, %SEQCOORDPLUGIN_SHORTDESCRIPTION%

One-line description, shown in the TextFormattingRules topic:
- Set SHORTDESCRIPTION = Link ExternalSite:Name/Start-End text to subsequences on external genome browsers based on aliases defined in the InterSeqs topic

Link rules topic name: (default is InterSeqs)
- Set RULESTOPIC =

Suppress tooltip help for links: (0 or 1, default is 0)
- Set SUPPRESSTOOLTIP = 0

Debug plugin: (See output in data/debug.txt)
- Set DEBUG = 0

Plugin Installation Instructions

Download the ZIP file from the TWiki:Plugins web (see below)

Unzip InterSeqPlugin.zip in your TWiki installation directory. Content:

File:	Description:
`data/TWiki/InterSeqPlugin.txt`	Plugin topic
`data/TWiki/InterSeqs.txt`	Link rules topic for inter-site links
`lib/TWiki/Plugins/InterSeqPlugin.pm`	Plugin Perl module

Tests: Worm:I/1000-3000, Fly:2L/30000-40000

Plugin Info

Plugin Author:	Biowiki:Main.IanHolmes, TWiki:Main.AndreaSterbini, TWiki:Main.PeterThoeny
Plugin Version:	25 Aug 2004, 1.005
Change History:
06 Mar 2005:	Modified Interwiki Plugin to Inter Seq Plugin (Ian Holmes)
25 Aug 2004:	Updated Inter Wikis link rules (no code change)
09 Mar 2004:	Internal changes: Use only official TWiki::Func Plugin API; for increased speed, moved Interwiki link handling from outsidePREHandler to startRenderingHandler
16 Feb 2004:	Support `[[Site:Page][label]]` Interwiki links (PTh); use TWiki::Func interface for I18N regular expressions (Walter Mundt)
18 Jan 2003:	Allow number sign `#` in Page name (PTh)
31 Aug 2002:	Allow percent sign `%` in page name (PTh)
27 Jul 2001:	Allow numbers `0-9` in site name
26 Jul 2001:	Fixed alternating missed link bug due to greedy $postfixPattern (fix by Richard Donkin)
14 Jul 2001:	Changed to plug & play
16 Jun 2001:	Made tooltips optional; prevent `Module::Sub` type of link
12 Jun 2001:	Added optional tool tips (IE only); added the link rules topic name variable; added flexible link patterns; optional `$page` in URL
10 Jun 2001:	Changed rules topic to table-based syntax
20 Feb 2001:	Initial version
CPAN Dependencies:	none
Other Dependencies:	none
Perl Version:	5.0
Plugin Home:	http://biowiki.org/twiki/bin/view/TWiki/InterSeqPlugin (TWiki:Plugins/InterSeqPlugin)
Feedback:	http://biowiki.org/twiki/bin/view/TWiki/InterSeqPluginDev (TWiki:Plugins/InterSeqPluginDev)

Related Topics: InterSeqs, TWikiPreferences, TWikiPlugins

-- Biowiki:Main.IanHolmes - 20 Oct 2000
-- TWiki:Main.AndreaSterbini - 20 Oct 2000
-- TWiki:Main.MikeMannix - 01 Oct 2001
-- TWiki:Main.PeterThoeny - 25 Aug 2004

Actions: