From: jprocter Date: Tue, 4 Nov 2008 11:48:39 +0000 (+0000) Subject: links for non-positional features X-Git-Tag: Release_2_5~431 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fd6fc6bbcf3cf91b6f218729cc014997782053b1;p=jalview.git links for non-positional features --- diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index b11e96b..6b86d22 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -30,11 +30,7 @@ allowed.

Feature label	Feature Colour
A feature type has a text label, and a colour (specified as a red,green,blue 24 bit triplet either in hexadecimal (eg. 00ff00) or as comma separated -numbers (ranging from 0 to 255)). The text label may contain simple HTML -document body tags if enclosed by "<html></html>" -and will be rendered as formatted tooltips in the Jalview Application -(the Jalview applet is not capable of rendering HTML tooltips, so all -formatting tags will be removed.

+numbers (ranging from 0 to 255)).

The remaining lines in the file are the sequence annotation definitions, where the now defined features are attached to regions on particular sequences, optionally with some descriptive text (displayed @@ -50,6 +46,23 @@ sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the sequenceId field will be used in preference to the sequenceIndex field.

+

The description may contain simple HTML +document body tags if enclosed by "<html></html>" and +these will be rendered as formatted tooltips in the Jalview Application +(the Jalview applet is not capable of rendering HTML tooltips, so all +formatting tags will be removed).
+Attaching Links to Sequence Features +
Any anchor tags in an html formatted description line will be translated +into URL links. A link symbol will be displayed adjacent to any feature which +includes links, and these are made available from the +links submenu of the +popup menu which is obtained by right-clicking when a link symbol is +displayed in the tooltip.
+Non-positional features
+Specify the start and end for a feature to be 0 in order to attach it to the whole sequence. +Non-positional features are shown in a tooltip when the mouse hovers over the seuqence ID panel, and any embedded links can be accessed from the popup menu. +

+

Feature annotations can be collected into named groups by prefixing definitions with lines of the form:

startgroup	groupname
.. and subsequently post-fixing the group with:
endgroup	groupname
Feature diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index a836c9f..9cf5358 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -84,11 +84,14 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

All sequences in the current selection group will be hidden, apart from (Sequence Id). Any edits performed on the visible representative sequence will be propagated to the hidden sequences. -
  • Link
    +
  • Link
    This menu item lists all links which have been set up in the     Preferences Connections tab.
    Since Jalview 2.4, links will also be made for database cross references (where the database name exactly matches the link name set up in Preferences). +
    Since Jalview 2.4.1, links are also shown for non-positional sequence features attached to + the sequence, and any regular-expression based URL links that + matched the description line.