From f6125c8d22fa28c5b38506e7c9926dcaa10a9629 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 12 Nov 2008 10:55:12 +0000 Subject: [PATCH] rewording and clarification --- help/html/features/featuresFormat.html | 23 ++++++++++++++++++----- help/html/features/preferences.html | 5 ++++- 2 files changed, 22 insertions(+), 6 deletions(-) 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/features/preferences.html b/help/html/features/preferences.html index c173212..36646d6 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -86,9 +86,12 @@ vbersion of the font to sequence labels.

  • Each top level parenthesis will yield a URL containing the text matched within that parenthesis.
  • Regions matching sub-parentheseses within a top-level parenthesis will be concatenated to form the text inserted into the URL for the top-level parenthesis.
    • - Please Note: the regular expressions supported by Jalview are those provided by the Stevesoft javaregex package. + Please Note: +
    • The regular expressions supported by Jalview are those provided by the Stevesoft javaregex package. +
    • Some characters must be escaped when specifying them as a match within a regular expression.

    Many Thanks to Bernd Brand of the Free University of Amsterdam for testing this new regular-expression expansion feature!     +

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