From d1d6724c7a22a6955f0a1213686f56e254b68546 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 6 Sep 2015 17:31:21 +0100 Subject: [PATCH] JAL-1368 JAL-1863 JAL-1304 reformatting and revision of wording, clarify RNA secondary structure example --- help/html/features/annotationsFormat.html | 47 ++++++++++++++++------------- 1 file changed, 26 insertions(+), 21 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index ce29e82..60c9e23 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -59,10 +59,9 @@ ignored. The sections below describe the structure of an annotation file.
  • ROWPROPERTIES control the display of individual annotation rows
  • SEQUENCE_GROUP to define groups of sequences for further annotation
  • PROPERTIES to set visualisation properties for sequence groups
    • -
  • SEQUENCE_REF and GROUP_REF for attaching annotation to sequences and groups
    • +
  • SEQUENCE_REF and GROUP_REF for specifying target sequences and groups for annotation, reference sequence and column visibilty commands.
  • VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS - for defining a reference sequence on the alignment and hiding regions - based on gaps in a reference sequence
    • + for assigning the reference sequence on the alignment and hiding columns.

    At the end of this document, you can also find notes on Please note: URL links embedded in HTML descriptions are not yet supported.

    -

    The final Values - field contains a series of "|" separated value fields. Each - value field is itself a comma separated list of fields of a particular - type defined by the annotation row's GRAPH_TYPE. The allowed values of - GRAPH_TYPE and corresponding interpretation of each Value are shown below: +

    + The final Values field contains a series of "|" + separated value fields. Each value field is itself a comma separated + list of fields of a particular type defined by the annotation row's GRAPH_TYPE. + The allowed values of GRAPH_TYPE and corresponding + interpretation of each Value are shown below:

    Any or all value fields may be left empty, as well as the BAR_GRAPH's -text character field, and either or both of the text-label and secondary -structure symbol fields of the NO_GRAPH type annotation rows.

    + text character field, and either or both of the text-label and + secondary structure symbol fields of the NO_GRAPH type annotation rows. +

    Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.

    -- 1.7.10.2